http://2013.igem.org/wiki/index.php?title=Special:Contributions/PSchneider&feed=atom&limit=50&target=PSchneider&year=&month=2013.igem.org - User contributions [en]2024-03-29T01:58:44ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/Team:TU-Munich/Modeling/OverviewTeam:TU-Munich/Modeling/Overview2013-10-29T03:47:30Z<p>PSchneider: /* Modeling Overview */</p>
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== Modeling Overview ==<br />
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In our modeling efforts, we tried to cover a very wide range of different methods, reaching from simple and ordinary differential equations, over partial differential equations, to stochastic differential equations as well as bioinformatical methods. To gain the largest possible output, we stayed in close contact with our wetlab team, answered their design questions and fitted parameters which could then be used for implementation aspects.<br />
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===Protein Predictions===<br />
For the immobilization of effectors on the cell membrane, we needed to design a transmembrane domain. Using several bioinformatical methods we identified the transmembrane region of the SERK receptor which we later used as starting point for our constructs. [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions Read More]<br />
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===Enzyme Kinetics===<br />
For an effective implementation of our filter system it is essential to analyze the enzymatic activity of our effectors. Using experimental data we fitted the respective kinetic parameters and carried out rigorous uncertainty analysis to assess the reliability of the fitted parameters. [https://2013.igem.org/Team:TU-Munich/Modeling/Enzyme Read More]<br />
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===Kill Switch===<br />
During the planning stage of our project, we had several different ideas on how to efficiently implement a kill-switch in our moss. In this section of the wiki we documented our mathematical train of thought that eventually led us to our final design.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Kill_Switch Read More]<br />
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===Filter Model===<br />
The filter model is designed to simulate different remediation scenarios. It should be used to calculate the necessary amount of PhyscoFilters, referring to the environmental parameters.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Filter Read More]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/OverviewTeam:TU-Munich/Results/Overview2013-10-29T03:43:10Z<p>PSchneider: /* Results Overview */</p>
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== Results Overview ==<br />
Having spent our summer in the lab, we are proud to present our accomplishments. Up to the European regional jamboree in Lyon, we have created 72 BioBricks and devices, transformed and selected 20 different transgenic GM-mosses and characterized our effectors as recombinant proteins produced in ''E. coli'' and in our moss ''Physcomitrella patens'', a chassis newly introduced into iGEM. We took further steps to put our phytoremediation project into practice by developing concepts for the implementation of our PhyscoFilter in the environment and by analyzing the economic potential of this innovative technology in our Entrepreneurship section. Additional to our wetlab work, we contributed a very powerful software tool for the annotation of BioBricks from the Parts Registry and created tutorials to pass this summer´s experiences and skills on to the subsequent iGEM generations. <br />
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<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/d/dc/TUM13_results-1.jpg" /></html><br />
===BioBricks===<br />
We created 72 BioBricks, including BioBricks advancing the use of ''Physcomitrella patens'' as a chassis, BioBricks enhancing phytoremediation applications and BioBricks for the light triggered kill-switch mechanism.<br><br />
[https://2013.igem.org/Team:TU-Munich/Results/BioBricks Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_results-2.jpg" /></html><br />
===Effector studies===<br />
We selected six different effector proteins, produced them in ''Escherichia coli'' and characterized them, concerning stability and activity.<br><br />
[https://2013.igem.org/Team:TU-Munich/Results/Recombinant Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/ee/TUM13_results-3.jpg" /></html><br />
===Moss Methods===<br />
We performed some general experi- ments to optimize ''Physcomitrella patens'' concerning tolerance of toxins, growth optimization and the use of different cultivation surfaces. Furthermore, we created 20 different strains of transformed moss during our visit to Prof. Reski's lab in Freiburg. [https://2013.igem.org/Team:TU-Munich/Results/Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e0/TUM13_Receptor_small.png" /></html><br />
===Localization===<br />
In order to ensure the best functionality for our effectors, we designed and used several localization methods as well as different verification techniques to see if our localizations were successful. <br />
<br>[https://2013.igem.org/Team:TU-Munich/Results/Localization Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/2/2a/TUM13_results-4.jpg" /></html><br />
===PhyscoFilter===<br />
After the selection and regeneration of the transgenic moss plants, we performed experiments with them and characterized their properties as PhyscoFilter. <br>[https://2013.igem.org/Team:TU-Munich/Results/GM-Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/6/63/TUM13_project-6.jpg" /></html><br />
===Kill Switch===<br />
In order to prevent uncontrolled growth of transgenic moss in the environment, we developed a Kill-Switch which is triggered by sunlight. The GM-Moss can only be grown where red-light is filtered out of the electromagnetic spectrum. <br>[https://2013.igem.org/Team:TU-Munich/Results/KillSwitch Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/6/6d/TUM13_project-8.jpg" /></html><br />
===Implementation===<br />
The creation of new environmental solutions doesn't stop at the development of GM moss. We tried to find out how a large-scale biofilter could be implemented.<br>[https://2013.igem.org/Team:TU-Munich/Results/Implementation Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/b/bc/TUM13_results-5.jpg" /></html><br />
===AutoAnnotator===<br />
Protein coding BioBricks constitute large parts of the Parts Registry. We created a software tool for in-silico characterization of various para- meters summed up in a standardized table. To improve the parts registry, <nowiki>RFC 96</nowiki> proposes a range of characteristics determined by the AutoAnnotator.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Software Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e6/TUM13_results-7.jpg" /></html><br />
===Entrepreneurship===<br />
To translate science into applied technology, available to the public, economic and business factors play increasingly important roles. We took the first steps into this direction by examining criteria for implementation and possibilities of business models in biotechnology.<br> [https://2013.igem.org/Team:TU-Munich/Results/Economics Read more]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/OverviewTeam:TU-Munich/Results/Overview2013-10-29T03:41:37Z<p>PSchneider: /* Results Overview */</p>
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== Results Overview ==<br />
Having spent our summer in the lab, we are proud to present our accomplishments. Up to the European regional jamboree in Lyon, we have created 72 BioBricks and devices, transformed and selected 20 different transgenic GM-mosses and characterized our effectors as recombinant proteins produced in ''E. coli'' and in our moss ''Physcomitrella patens'', a chassis newly introduced into iGEM. We took further steps to put our phytoremediation project into practice by developing concepts for the implementation of our PhyscoFilter in the environment and by analyzing the economic potential of this innovative technology in our Entrepreneurship section. Additional to our wetlab work, we contributed a very powerful software tool for the annotation of BioBricks from the Parts Registry and created tutorials to pass this summer´s experiences and skills on to the subsequent iGEM generations. <br />
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<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/d/dc/TUM13_results-1.jpg" /></html><br />
===BioBricks===<br />
We created 72 BioBricks, including BioBricks advancing the use of ''Physcomitrella patens'' as a chassis, BioBricks enhancing phytoremediation applications and BioBricks for the light triggered kill-switch mechanism.<br><br />
[https://2013.igem.org/Team:TU-Munich/Results/BioBricks Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_results-2.jpg" /></html><br />
===Effector studies===<br />
We selected six different effector proteins, produced them in ''Escherichia coli'' and characterized them, concerning stability and activity.<br><br />
[https://2013.igem.org/Team:TU-Munich/Results/Recombinant Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/ee/TUM13_results-3.jpg" /></html><br />
===Moss Methods===<br />
We performed some general experiments to optimize ''Physcomitrella patens'' concerning tolerance of toxins, growth optimization and the use of different cultivation surfaces. Furthermore, we created 20 different strains of transformed moss during our visit to Prof. Reski's lab in Freiburg. [https://2013.igem.org/Team:TU-Munich/Results/Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e0/TUM13_Receptor_small.png" /></html><br />
===Localization===<br />
In order to ensure the best functionality for our effectors, we designed and used several localization methods as well as different verification techniques to see if our localizations were successful. <br />
<br>[https://2013.igem.org/Team:TU-Munich/Results/Localization Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/2/2a/TUM13_results-4.jpg" /></html><br />
===PhyscoFilter===<br />
After the selection and regeneration of the transgenic moss plants, we performed experiments with them and characterized their properties as PhyscoFilter. <br>[https://2013.igem.org/Team:TU-Munich/Results/GM-Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/6/63/TUM13_project-6.jpg" /></html><br />
===Kill Switch===<br />
In order to prevent uncontrolled growth of transgenic moss in the environment, we developed a Kill-Switch which is triggered by sunlight. The GM-Moss can only be grown where red-light is filtered out of the electromagnetic spectrum. <br>[https://2013.igem.org/Team:TU-Munich/Results/KillSwitch Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/6/6d/TUM13_project-8.jpg" /></html><br />
===Implementation===<br />
The creation of new environmental solutions doesn't stop at the development of GM moss. We tried to find out how a large-scale biofilter could be implemented.<br>[https://2013.igem.org/Team:TU-Munich/Results/Implementation Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/b/bc/TUM13_results-5.jpg" /></html><br />
===AutoAnnotator===<br />
Protein coding BioBricks constitute large parts of the Parts Registry. We created a software tool for in-silico characterization of various para- meters summed up in a standardized table. To improve the parts registry, <nowiki>RFC 96</nowiki> proposes a range of characteristics determined by the AutoAnnotator.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Software Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e6/TUM13_results-7.jpg" /></html><br />
===Entrepreneurship===<br />
To translate science into applied technology, available to the public, economic and business factors play increasingly important roles. We took the first steps into this direction by examining criteria for implementation and possibilities of business models in biotechnology.<br> [https://2013.igem.org/Team:TU-Munich/Results/Economics Read more]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/OverviewTeam:TU-Munich/Results/Overview2013-10-29T03:38:34Z<p>PSchneider: /* Results Overview */</p>
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== Results Overview ==<br />
Having spent our summer in the lab, we are proud to present our accomplishments. Up to the European regional jamboree in Lyon, we have created 72 BioBricks and devices, transformed and selected 20 different transgenic GM-mosses and characterized our effectors as recombinant proteins produced in ''E. coli'' and in our moss ''Physcomitrella patens'', a chassis newly introduced into iGEM. We took further steps to put our phytoremediation project into practice by developing concepts for the implementation of our PhyscoFilter in the environment and by analyzing the economic potential of this innovative technology in our Entrepreneurship section. Additional to our wetlab work, we contributed a very powerful software tool for the annotation of BioBricks from the Parts Registry and created tutorials to pass this summer´s experiences and skills on to the subsequent iGEM generations. <br />
<br />
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<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/d/dc/TUM13_results-1.jpg" /></html><br />
===BioBricks===<br />
We created 72 BioBricks, including BioBricks advancing the use of ''Physcomitrella patens'' as a chassis, BioBricks enhancing phytoremediation applications and BioBricks for the light triggered kill-switch mechanism.<br />
[https://2013.igem.org/Team:TU-Munich/Results/BioBricks Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_results-2.jpg" /></html><br />
===Effector studies===<br />
We selected six different effector proteins, produced them in ''Escherichia coli'' and characterized them, concerning stability and activity.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Recombinant Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/ee/TUM13_results-3.jpg" /></html><br />
===Moss Methods===<br />
We performed some general experiments to optimize ''Physcomitrella patens'' concerning tolerance of toxins, growth optimization and the use of different cultivation surfaces. Furthermore, we created 20 different strains of transformed moss during our visit to Prof. Reski's lab in Freiburg. [https://2013.igem.org/Team:TU-Munich/Results/Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e0/TUM13_Receptor_small.png" /></html><br />
===Localization===<br />
In order to ensure the best functionality for our effectors, we designed and used several localization methods as well as different verification techniques to see if our localizations were successful. <br />
[https://2013.igem.org/Team:TU-Munich/Results/Localization Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/2/2a/TUM13_results-4.jpg" /></html><br />
===PhyscoFilter===<br />
After the selection and regeneration of the transgenic moss plants, we performed experiments with them and characterized their properties as PhyscoFilter. [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/6/63/TUM13_project-6.jpg" /></html><br />
===Kill Switch===<br />
In order to prevent uncontrolled growth of transgenic moss in the environment, we developed a Kill-Switch which is triggered by sunlight. The GM-Moss can only be grown where red-light is filtered out of the electromagnetic spectrum. [https://2013.igem.org/Team:TU-Munich/Results/KillSwitch Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/6/6d/TUM13_project-8.jpg" /></html><br />
===Implementation===<br />
The creation of new environmental solutions doesn't stop at the development of GM moss. We tried to find out how a large-scale biofilter could be implemented.<br>[https://2013.igem.org/Team:TU-Munich/Results/Implementation Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/b/bc/TUM13_results-5.jpg" /></html><br />
===AutoAnnotator===<br />
Protein coding BioBricks constitute large parts of the Parts Registry. We created a software tool for in-silico characterization of various para- meters summed up in a standardized table. To improve the parts registry, <nowiki>RFC 96</nowiki> proposes a range of characteristics determined by the AutoAnnotator.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Software Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e6/TUM13_results-7.jpg" /></html><br />
===Entrepreneurship===<br />
To translate science into applied technology available to the public, economic and business factors play increasingly important roles. We took the first steps into this direction by examining criteria for implementation and possibilities of business models in biotechnology. ([https://2013.igem.org/Team:TU-Munich/Results/Economics Read more])<br />
</div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/OverviewTeam:TU-Munich/Results/Overview2013-10-29T03:38:03Z<p>PSchneider: /* Results Overview */</p>
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== Results Overview ==<br />
Having spent our summer in the lab, we are proud to present our accomplishments. Up to the European regional jamboree in Lyon, we have created 72 BioBricks and devices, transformed and selected 20 different transgenic GM-mosses and characterized our effectors as recombinant proteins produced in ''E. coli'' and in our moss ''Physcomitrella patens'', a chassis newly introduced into iGEM. We took further steps to put our phytoremediation project into practice by developing concepts for the implementation of our PhyscoFilter in the environment and by analyzing the economic potential of this innovative technology in our Entrepreneurship section. Additional to our wetlab work, we contributed a very powerful software tool for the annotation of BioBricks from the Parts Registry and created tutorials to pass this summer´s experiences and skills on to the subsequent iGEM generations. <br />
<br />
<html><br />
<a class="tour previous" href="https://2013.igem.org/Team:TU-Munich/Project/Overview">Previous</a><br />
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</html><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/d/dc/TUM13_results-1.jpg" /></html><br />
===BioBricks===<br />
We created 72 BioBricks, including BioBricks advancing the use of ''Physcomitrella patens'' as a chassis, BioBricks enhancing phyto-remediation applications and BioBricks for the light triggered kill-switch mechanism.<br />
([https://2013.igem.org/Team:TU-Munich/Results/BioBricks Read more])<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_results-2.jpg" /></html><br />
===Effector studies===<br />
We selected six different effector proteins, produced them in ''Escherichia coli'' and characterized them, concerning stability and activity.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Recombinant Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/e/ee/TUM13_results-3.jpg" /></html><br />
===Moss Methods===<br />
We performed some general experiments to optimize ''Physcomitrella patens'' concerning tolerance of toxins, growth optimization and the use of different cultivation surfaces. Furthermore, we created 20 different strains of transformed moss during our visit to Prof. Reski's lab in Freiburg. [https://2013.igem.org/Team:TU-Munich/Results/Moss Read more]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/e/e0/TUM13_Receptor_small.png" /></html><br />
===Localization===<br />
In order to ensure the best functionality for our effectors, we designed and used several localization methods as well as different verification techniques to see if our localizations were successful. <br />
[https://2013.igem.org/Team:TU-Munich/Results/Localization Read more]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/2/2a/TUM13_results-4.jpg" /></html><br />
===PhyscoFilter===<br />
After the selection and regeneration of the transgenic moss plants, we performed experiments with them and characterized their properties as PhyscoFilter. [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss Read more]<br />
</div><br />
<br />
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===Kill Switch===<br />
In order to prevent uncontrolled growth of transgenic moss in the environment, we developed a Kill-Switch which is triggered by sunlight. The GM-Moss can only be grown where red-light is filtered out of the electromagnetic spectrum. [https://2013.igem.org/Team:TU-Munich/Results/KillSwitch Read more]<br />
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===Implementation===<br />
The creation of new environmental solutions doesn't stop at the development of GM moss. We tried to find out how a large-scale biofilter could be implemented.<br>[https://2013.igem.org/Team:TU-Munich/Results/Implementation Read more]<br />
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===AutoAnnotator===<br />
Protein coding BioBricks constitute large parts of the Parts Registry. We created a software tool for in-silico characterization of various para- meters summed up in a standardized table. To improve the parts registry, <nowiki>RFC 96</nowiki> proposes a range of characteristics determined by the AutoAnnotator.<br />
[https://2013.igem.org/Team:TU-Munich/Results/Software Read more]<br />
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===Entrepreneurship===<br />
To translate science into applied technology available to the public, economic and business factors play increasingly important roles. We took the first steps into this direction by examining criteria for implementation and possibilities of business models in biotechnology. ([https://2013.igem.org/Team:TU-Munich/Results/Economics Read more])<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Project/OverviewTeam:TU-Munich/Project/Overview2013-10-29T03:27:47Z<p>PSchneider: /* Project Overview */</p>
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== Project Overview ==<br />
In the 2013 competition, the TU Munich iGEM team has developed a transgenic moss filter which is capable of reducing the contamination of aquatic ecosystems with xenobiotics. The topic of remediation using transgenic organisms is present in every year of iGEM and we want to take this idea to the next level. For this reason we decided to use a photoautotrophic chassis, the moss ''Physcomitrella patens''. The following section gives an overview of the theoretical background.<br />
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===Phytoremediation===<br />
Phytoremediation describes the treatment of environmental problems through the use of plants. Here we identified problematic substances and described basic principles.<br>[https://2013.igem.org/Team:TU-Munich/Project/Phytoremediation Read more]<br />
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===''Physcomitrella''===<br />
Next, we introduced ''Physcomitrella patens'' as a new chassis into iGEM. We described advantages, options and our expression strategy.<br>[https://2013.igem.org/Team:TU-Munich/Project/Physcomitrella Read more]<br />
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===Localization===<br />
As the mechanisms of the effectors responsible for Phytoremediation are very different, it is necessary to have a protein expression system which is able to accomplish cytosolic, secreted and receptor bound localization of proteins.<br>[https://2013.igem.org/Team:TU-Munich/Project/Localisation Read more]<br />
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===BioDegradation===<br />
BioDegradation describes the application of enzymatic catalysis for the degradation of problematic xenobiotics using the enzymes erythromycin esterase, catechol dioxygenase and laccase.<br>[https://2013.igem.org/Team:TU-Munich/Project/Biodegradation Read more]<br />
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===BioAccumulation===<br />
For BioAccumulation we employed different binding proteins which immobilize pollutants on the moss cells. In this context we targeted the substances fluorescein, DDT and microcystin.<br />
<br>[https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation Read more]<br />
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===Kill-Switch===<br />
In order to prevent uncontrolled growth of transgenic moss in the environment, we developed a Kill-Switch which is triggered by sunlight. The GM-Moss can only be grown where red-light is filtered out of the electromagnetic spectrum. [https://2013.igem.org/Team:TU-Munich/Project/Killswitch Read more]<br />
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===Safety===<br />
Our safety page describes our evaluation concerning safety issues, especially a safety evaluation of our BioBricks and ''Physcomitrella patens''.<br>[https://2013.igem.org/Team:TU-Munich/Project/Safety Read more]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Project/PhyscomitrellaTeam:TU-Munich/Project/Physcomitrella2013-10-29T02:55:59Z<p>PSchneider: /* Moss methods - working with Physcomitrella */</p>
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==''Physcomitrella'' - A new chassis for iGEM==<br />
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===General description===<br />
<br />
The moss ''Physcomitrella patens'' belongs to the land plant division Bryophyta, which are one of the earliest representatives of the land plants (Embryophyta) having evolved from green algae about 470 million years ago during the early Paleozoic. Hence mosses have a much simpler anatomy than higher land plants such as trees and flowering plants, which in particular means that they have not yet developed a vascular system, i.e an internal transport system for water and nutrients. Since they also lack a complex waterproofing system to prevent absorbed water from evaporating they need a moist environment to grow. Their main habitats are therefore shady and damp places such as woods and edges of streams but they are also found to be resistant to periods of drought and therefore can be found widely spread around the world, from the tropics to tundra regions, from coastal sand dunes up to high mountains.<br />
<br />
The general organization of plant tissue into roots, stem and leaves is found in a much more basic version in mosses. They show a differentiated stem with simple leaves, usually only a single layer of cells thick and lacking veins, that are used to absorb water and nutrients. Instead of roots they have similar threadlike rhizoids [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]]. These have a primary function as mechanical attachment rather than extraction of soil nutrients. Due to not having a vascular system bryophytes are doomed to stay small throughout their life-cycle typically stretching about 1-10 cm.<br />
<br />
However different mosses and vascular plants are because of the early diverge of the evolutionary lineages, they share fundamental genetic and physiological processes. Hence a good approach to studying the complexity of higher land plants is to look at the bryophytes with their much simpler phenotype. Here researchers chose ''Physcomitrella patens'' as a model organism with a genome size of about 450 Mb along 27 chromosomes that is highly similar to other land plants in both exon-intron-structure and codon usage. [[http://www.plantphysiol.org/content/127/4/1430 Schaefer and Zryd, 2001]]<br />
<br />
===Life cycle===<br />
<br />
[[File:TUM13 Physco-lifecycle.png|thumb|right|350px|'''Figure 1:''' ''Physcomitrella'' life cycle]]<br />
Generally land plants show an alternation of generations, the haploid (1n) gametophyte produces sperm and eggs which fuse and transform into the diploid (2n) sporophyte. This then forms haploid spores which become new gametophytes. Besides having no vascular system, bryophytes also differ from higher land plants in the fact that the gametophyte is the dominant phase of their life cycle, whereas in vascular plants the principal generation is the sporophyte.<br />
<br />
The life cycle of ''P. patens'' [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] only takes about 3 months and starts with the spore developing into a filamentous structure, the juvenile, transitory stage of the gametophyte, called protonema, which is composed of two types of cells. The chloronema cells with large and numerous chloroplasts mostly perform photosynthesis and thus supply the photoautotrophic plant with energy while the task of the caulonema cells is fast growth. The adult stage of the gametophyte, called gametophore ("gamete-bearer") has a more complex structure bearing leafs, stem and rhizoids. The transition from juvenile to adult gametophyte is started by initial cells in the protonema filament that differentiate into buds. The budding is therefore a single-cell-event, greatly stimulated by the plant hormone cytokinin, which promotes cell division.<br />
<br />
The sex organs of the moss develop from the tip of the gametophore. ''P. patens'' is monoicous, meaning that male and female organs are produced in one plant. When liquid water is surrounding the tip, flagellate sperm cells can swim from the male sex organ to the female organ and fertilize the egg within. A zygote then develops into the sporophyte, which in turn produces thousands of haploid spores by meiosis. Sporophytes are typically physically attached to and dependent on supply from the dominating gametophyte.<br />
<br />
==Advantages of ''Physcomitrella'' as a model organism==<br />
<br />
===General advantages===<br />
<br />
[[File:TUM13 Bioreactor Cultivation.jpg|thumb|right|350px|'''Figure 2:''' Cultivation of moss in a Bioreactor]]<br />
<br />
*''P. patens'' stands out among the whole plant kingdom as the sole exception where gene targeting is feasible as an easy and fast routine procedure, even with an efficiency similar to ''S. cerevisiae'', due to highly efficient homologous recombination. [[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]] For that reason it is very easy to create knockout mosses by precise mutagenesis following the approach of reverse genetics in order to study the function of genes. Performing functional genomics in higher organisms is very important to understand biological functions of proteins in a multicellular context, e.g. in the context of cell-cell-contacts.<br />
*As mosses mainly are in a haploid stage during their life cycle they are very straight-forward objects for genetics because complex backcrosses to determine changes in the genotype are not necessary<br />
*Moss development starts with a filamentous tissue, the protonema, which is growing by apical cell division and, therefore is perfectly suitable for cell-lineage analysis since development of the plant can be pinpointed to the differentiation of a single cell. [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Also the simple life cycle makes ''P. patens'' a very useful item for developmental biology<br />
*''P. patens'' is increasingly used in biotechnology as a study object with implications for crop improvement or human health. Moss bioreactors (see Figure 2) can be used as an alternative to animal cell cultures (e.g. CHO cells) for the easy, inexpensive and safe production of complex biopharmaceuticals [[http://www.sciencedirect.com/science/article/pii/S0958166907000948 Reski and Decker, 2007]] . For example it is a successful tool to produce asialo-EPO, a specific variant of Erythropoetin, which can perform its protective role by inhibiting apoptosis but has lost the potential doping activity. This safe drug is hard to produce in animal cell culture but easy to produce in the moss without impacting its growth or general performance [[http://www.ncbi.nlm.nih.gov/pubmed/22621344 Decker et al., 2012]].<br />
<br />
===Expertbox: Prof. Reski===<br />
[[File:TUM13_expert_Reski.png|thumb|450px|left| '''Figure 3:''' Expert interview with Professor Reski. ]]<br />
When we chose Phytoremediation as our project for this year´s competition, it soon became clear that ''Physcomitrella patens'' is a great chassis that could bring iGEM closer to the real world applications we were looking for. Therefore we contacted Prof. Dr. Reski, who is a recognized expert on ''Physcomitrella patens'' and its biotechnological applications.<br />
<br />
Prof. Dr. Reski liked our idea of introducing his ''Physco'' to iGEM from the very beginning and offered his help wherever we would need it. Members of our team traveled to his lab in Freiburg (350 km) five times in total [https://2013.igem.org/Team:TU-Munich/Results/Moss#3._Transformation_of_Physcomitrella_patens] to fetch plasmids known to be functional in ''Physcomitrealla patens'' or for discussions with him or his co-workers. We could win him over as an advisor for our team, which shows how iGEM brings together universities and scientific groups from many different places.<br />
<br />
===Advantages as a new chassis for iGEM===<br />
*As a plant, ''P. patens'' offers interesting opportunities for application as it is self sustaining, renewable and a natural part of our environment. Therefore it is much easier to implement it into real world scenarios than bacteria or yeast. And although there is the disadvantage of having to wait about 4-6 weeks after transformation until experiments can be done, this is still very short considering the high complexity of the organism. Working with ''P. patens'' can easily be done in the timeframe of the competition by preparing the DNA constructs in bacteria. <br />
*''P. patens'' is a well studied model organism which means that besides having its full genome sequenced in 2006 there are well equipped [http://www.cosmoss.org databases]. Furthermore, there exists an [http://www.moss-stock-center.org International Moss Stock Center (IMSC)] in which many ecotypes, mutants and transgenic strains of ''P. patens'' are stored and accessible to the scientific community. So there is enough knowledge and material to work on for synthetic biologists. <br />
*At the same time the moss offers access to very exciting new physiological processes since it is a much more complex multicellular eukaryotic organism than the chassis already established in iGEM.<br />
*''P. patens'' is an easy plant to work with and requires neither expensive maintenance facilities nor large laboratory space. Most of the basic tools for high precision mutagenesis have been tested on this plant, were found to work and are easily available (see Moss methods below).<br />
<br />
==Moss methods - working with ''Physcomitrella''==<br />
<br />
The techniques used for the cultivation and manipulation of Physcomitrella patens are based on the knowledge of the chair for Plantbiotechnology of Prof. Dr. Reski at Freiburg University, which are available at [http://www.plant-biotech.net Plant-Biotech.net]. <br />
<br />
[[File:TUM13 Bench.png|thumb|right|350px|'''Figure 4:''' Working with cultivated moss on our laboratory bench]]<br />
*<b>Cell culture</b>: ''Physcomitrella patens'' plants can be cultivated either on solidified medium or in liquid medium. Liquid cultures can be kept in Erlenmeyer flasks under constant rotation and light exposure or in bioreactors for large scale production. By regularly (ideally weekly) disrupting the plants mechanically with a mixer (e.g. Ultra-Turrax) a homogenized culture can be achieved.<br />
*<b>Storage</b>: Long-term storage of ''Physcomitrella'' strains can be achieved by cryo-preservation. This procedure ensures a maximum survival rate of the plant by preconditioning and controlled freezing. [[http://www.plant-biotech.net/paper/PlantBiol_2004_Schulte_pageproof.pdf Schulte and Reski, 2004]]<br />
*<b>Targeted knockout</b>: ''P. patens'' is unique among plants in its high efficiency of gene targeting by homologous recombination. To knockout a specific gene a disruption construct has to be generated. This consists of the gene to be silenced with a selection cassette (usually the nptII gene) inserted into its center by suitable restriction sites. The moss is then transformed with this DNA construct which is integrated into the genome by homologous recombination. [[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]]<br />
[[File:TUM13 Transformation.png|thumb|right|350px|'''Figure 5:''' Transformation procedure]]<br />
*<b>Transformation</b>: Transformation of ''P. patens'' requires protoplasts of the plant, which can be obtained by cell wall digesting enzymes. The protoplasts can either be transformed by particle bombardment or via polyethylene glycol (PEG), which is the easiest and most commonly used method. The DNA constructs should be linearized for optimal transformation and contain a selection marker for subsequent screening. After transformation, the protoplasts are cultivated in the dark for 12-16 h followed by 9 days under normal growth conditions during which they regenerate their cell wall. Afterwards they are plated on solidified medium in normal petri dishes and first experiments can be executed. [[http://link.springer.com/article/10.1007/BF00260654 Schaefer et al., 1991]]<br />
*<b>Analysis of transformants</b>: First, the transformed protoplasts are plated on solidified medium containing the antibiotic G418 (Geneticin), to which successfully transformed plants are resistant due to the selection marker nptII which encodes the enzyme neomycin phosphotransferase. Secondly, the transformants are analyzed by a PCR screen using primers derived the selection marker cassette´s sequences [[http://www.plant-biotech.net/paper/PlantMolecularBiologyReporter_2002_Schween.pdf Schween et al., 2002]].<br />
<br />
[[File:TUM13_timeline.png|thumb|center|910px| '''Figure 6:''' Comparing work flow for ''E. coli'', ''S. cerevisiae'' and ''P. patens'']]<br />
<br />
In '''conclusion''', it naturally takes a bit more time to work with a plant in comparison to bacteria or yeast (see figure 6), but the advantages definitely outweigh the time factor and if teams start early enough, it is perfectly possible to work with ''P. patens'' as a chassis in an iGEM project!<br />
<br />
This is a brief summary of the most important techniques in working with ''P. patens''. For a full description of these methods please see [https://2013.igem.org/Team:TU-Munich/Notebook/Methods#Physcomitrella_Methods our methods page].<br />
<br />
==BioBricks for protein expression in ''Physcomitrella''==<br />
<br />
[[File:TUM13_plant biobricks.png|thumb|right|300px| '''Figure 7:''' Our transformation vector ]]<br />
To transform the moss, we created an all-purpose backbone into which all our constructs could be integrated easily. Therefore we modified the common iGEM pSB1C3 plasmid with the following plant-specific components:<br />
<br />
* '''pAct5 (Actin 5 promoter from ''Physcomitrella patens''):''' for strong protein expression.<br />
<br />
* '''miniMCS:''' This miniature multiple cloning site contains restriction sites for the enzymes MfeI and SbfI which allows you to insert BioBrick between two other Biobricks (in our case: pAct5 and t35S_npt-cassette) as a result of the compability of MfeI with EcoRI and SbfI with PstI.<br />
<br />
* '''t35S (35S terminator):''' This terminator originates from the 35S transcript of the cauliflower mosaic virus.<br />
<br />
* '''nptII-cassette:''' This selection cassette contains the neomycon phosphotransferase II gene, encoding the enzyme aminoglycoside-3'-phosphotransferase (NPTII), which inactivates a range of aminoglycoside antibiotics such as Kanamycin, Neomycin and Geneticin (G418) by phosphorylation. The latter antibiotic is used as selective agent for transformed ''P. patens'' plants, inhibiting the growth of untransformed plants very effectively. The neomycon phosphotransferase II gene is under control of the NOS promoter and terminator.<br />
<br />
==References:==<br />
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<!-- Ab hier richtige Referenzen einfügen --><br />
[[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Reski, R. (1998). Development, Genetics and Molecular Biology of Mosses. ''Bot. Acta'', 111:1-15.<br /><br />
<br />
[[http://www.plantphysiol.org/content/127/4/1430 Schaefer and Zryd, 2001]] Schaefer, D.G. and Zrÿd, J. (2001). The Moss ''Physcomitrella patens'', Now and Then. ''Plant Physiology'', 127(4):1430-1438.<br /><br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]] Hohe, A., Egener, T., Lucht, J.M., Holtorf, H., Reinhard, C., Schween, G. and Reski, R. (2004). An improved and highly standardised transformation procedure allows efficient production of single and multiple targeted gene-knockouts in a moss, Physcomitrella patens. ''Curr Genet.'', 44(6):339-47.<br /><br />
<br />
[[http://www.sciencedirect.com/science/article/pii/S0958166907000948 Reski and Decker, 2007]] Decker, E.L. and Reski, R. (2007). Moss bioreactors producing improved biopharmaceuticals. ''Current Opinion in Biotechnology'', 18(5):393-398.<br /><br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/22621344 Reski et al., 2012]] Parsons, J., Altmann, F., Arrenberg, C. K., Koprivova, A., Beike, A. K., Stemmer, C., Gorr, G., Reski, R. and Decker, E. L. (2012). Moss-based production of asialo-erythropoietin devoid of Lewis A and other plant-typical carbohydrate determinants. ''Plant Biotechnology Journal'', 10:851–861.<br /><br />
<br />
[[http://www.plant-biotech.net/paper/PlantBiol_2004_Schulte_pageproof.pdf Schulte and Reski, 2004]] Schulte, J. and Reski, R. (2004). High throughput Cryopreservation of 140 000 Physcomitrella patens Mutants. ''Plant Biology'', 6:119-127.<br /><br />
<br />
[[http://link.springer.com/article/10.1007/BF00260654 Schaefer et al., 1991]] Schaefer, D., Zryd, J.-P., Knight, C., Cove, D. (1991). Stable transformation of the moss ''Physcomitrella patens''. ''Molecular and General Genetics'', 226:418-424.<br /><br />
<br />
[[http://www.plant-biotech.net/paper/PlantMolecularBiologyReporter_2002_Schween.pdf Schween et al., 2002]] Schween, G., Fleig, S., Reski, R. (2002). High-throughput-PCR screen of 15,000 transgenic Physcomitrella plants. ''Plant Molecular Biology Reporter'', 20:43–47.<br /><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Project/PhyscomitrellaTeam:TU-Munich/Project/Physcomitrella2013-10-29T02:54:44Z<p>PSchneider: /* Moss methods - working with Physcomitrella */</p>
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==''Physcomitrella'' - A new chassis for iGEM==<br />
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===General description===<br />
<br />
The moss ''Physcomitrella patens'' belongs to the land plant division Bryophyta, which are one of the earliest representatives of the land plants (Embryophyta) having evolved from green algae about 470 million years ago during the early Paleozoic. Hence mosses have a much simpler anatomy than higher land plants such as trees and flowering plants, which in particular means that they have not yet developed a vascular system, i.e an internal transport system for water and nutrients. Since they also lack a complex waterproofing system to prevent absorbed water from evaporating they need a moist environment to grow. Their main habitats are therefore shady and damp places such as woods and edges of streams but they are also found to be resistant to periods of drought and therefore can be found widely spread around the world, from the tropics to tundra regions, from coastal sand dunes up to high mountains.<br />
<br />
The general organization of plant tissue into roots, stem and leaves is found in a much more basic version in mosses. They show a differentiated stem with simple leaves, usually only a single layer of cells thick and lacking veins, that are used to absorb water and nutrients. Instead of roots they have similar threadlike rhizoids [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]]. These have a primary function as mechanical attachment rather than extraction of soil nutrients. Due to not having a vascular system bryophytes are doomed to stay small throughout their life-cycle typically stretching about 1-10 cm.<br />
<br />
However different mosses and vascular plants are because of the early diverge of the evolutionary lineages, they share fundamental genetic and physiological processes. Hence a good approach to studying the complexity of higher land plants is to look at the bryophytes with their much simpler phenotype. Here researchers chose ''Physcomitrella patens'' as a model organism with a genome size of about 450 Mb along 27 chromosomes that is highly similar to other land plants in both exon-intron-structure and codon usage. [[http://www.plantphysiol.org/content/127/4/1430 Schaefer and Zryd, 2001]]<br />
<br />
===Life cycle===<br />
<br />
[[File:TUM13 Physco-lifecycle.png|thumb|right|350px|'''Figure 1:''' ''Physcomitrella'' life cycle]]<br />
Generally land plants show an alternation of generations, the haploid (1n) gametophyte produces sperm and eggs which fuse and transform into the diploid (2n) sporophyte. This then forms haploid spores which become new gametophytes. Besides having no vascular system, bryophytes also differ from higher land plants in the fact that the gametophyte is the dominant phase of their life cycle, whereas in vascular plants the principal generation is the sporophyte.<br />
<br />
The life cycle of ''P. patens'' [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] only takes about 3 months and starts with the spore developing into a filamentous structure, the juvenile, transitory stage of the gametophyte, called protonema, which is composed of two types of cells. The chloronema cells with large and numerous chloroplasts mostly perform photosynthesis and thus supply the photoautotrophic plant with energy while the task of the caulonema cells is fast growth. The adult stage of the gametophyte, called gametophore ("gamete-bearer") has a more complex structure bearing leafs, stem and rhizoids. The transition from juvenile to adult gametophyte is started by initial cells in the protonema filament that differentiate into buds. The budding is therefore a single-cell-event, greatly stimulated by the plant hormone cytokinin, which promotes cell division.<br />
<br />
The sex organs of the moss develop from the tip of the gametophore. ''P. patens'' is monoicous, meaning that male and female organs are produced in one plant. When liquid water is surrounding the tip, flagellate sperm cells can swim from the male sex organ to the female organ and fertilize the egg within. A zygote then develops into the sporophyte, which in turn produces thousands of haploid spores by meiosis. Sporophytes are typically physically attached to and dependent on supply from the dominating gametophyte.<br />
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==Advantages of ''Physcomitrella'' as a model organism==<br />
<br />
===General advantages===<br />
<br />
[[File:TUM13 Bioreactor Cultivation.jpg|thumb|right|350px|'''Figure 2:''' Cultivation of moss in a Bioreactor]]<br />
<br />
*''P. patens'' stands out among the whole plant kingdom as the sole exception where gene targeting is feasible as an easy and fast routine procedure, even with an efficiency similar to ''S. cerevisiae'', due to highly efficient homologous recombination. [[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]] For that reason it is very easy to create knockout mosses by precise mutagenesis following the approach of reverse genetics in order to study the function of genes. Performing functional genomics in higher organisms is very important to understand biological functions of proteins in a multicellular context, e.g. in the context of cell-cell-contacts.<br />
*As mosses mainly are in a haploid stage during their life cycle they are very straight-forward objects for genetics because complex backcrosses to determine changes in the genotype are not necessary<br />
*Moss development starts with a filamentous tissue, the protonema, which is growing by apical cell division and, therefore is perfectly suitable for cell-lineage analysis since development of the plant can be pinpointed to the differentiation of a single cell. [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Also the simple life cycle makes ''P. patens'' a very useful item for developmental biology<br />
*''P. patens'' is increasingly used in biotechnology as a study object with implications for crop improvement or human health. Moss bioreactors (see Figure 2) can be used as an alternative to animal cell cultures (e.g. CHO cells) for the easy, inexpensive and safe production of complex biopharmaceuticals [[http://www.sciencedirect.com/science/article/pii/S0958166907000948 Reski and Decker, 2007]] . For example it is a successful tool to produce asialo-EPO, a specific variant of Erythropoetin, which can perform its protective role by inhibiting apoptosis but has lost the potential doping activity. This safe drug is hard to produce in animal cell culture but easy to produce in the moss without impacting its growth or general performance [[http://www.ncbi.nlm.nih.gov/pubmed/22621344 Decker et al., 2012]].<br />
<br />
===Expertbox: Prof. Reski===<br />
[[File:TUM13_expert_Reski.png|thumb|450px|left| '''Figure 3:''' Expert interview with Professor Reski. ]]<br />
When we chose Phytoremediation as our project for this year´s competition, it soon became clear that ''Physcomitrella patens'' is a great chassis that could bring iGEM closer to the real world applications we were looking for. Therefore we contacted Prof. Dr. Reski, who is a recognized expert on ''Physcomitrella patens'' and its biotechnological applications.<br />
<br />
Prof. Dr. Reski liked our idea of introducing his ''Physco'' to iGEM from the very beginning and offered his help wherever we would need it. Members of our team traveled to his lab in Freiburg (350 km) five times in total [https://2013.igem.org/Team:TU-Munich/Results/Moss#3._Transformation_of_Physcomitrella_patens] to fetch plasmids known to be functional in ''Physcomitrealla patens'' or for discussions with him or his co-workers. We could win him over as an advisor for our team, which shows how iGEM brings together universities and scientific groups from many different places.<br />
<br />
===Advantages as a new chassis for iGEM===<br />
*As a plant, ''P. patens'' offers interesting opportunities for application as it is self sustaining, renewable and a natural part of our environment. Therefore it is much easier to implement it into real world scenarios than bacteria or yeast. And although there is the disadvantage of having to wait about 4-6 weeks after transformation until experiments can be done, this is still very short considering the high complexity of the organism. Working with ''P. patens'' can easily be done in the timeframe of the competition by preparing the DNA constructs in bacteria. <br />
*''P. patens'' is a well studied model organism which means that besides having its full genome sequenced in 2006 there are well equipped [http://www.cosmoss.org databases]. Furthermore, there exists an [http://www.moss-stock-center.org International Moss Stock Center (IMSC)] in which many ecotypes, mutants and transgenic strains of ''P. patens'' are stored and accessible to the scientific community. So there is enough knowledge and material to work on for synthetic biologists. <br />
*At the same time the moss offers access to very exciting new physiological processes since it is a much more complex multicellular eukaryotic organism than the chassis already established in iGEM.<br />
*''P. patens'' is an easy plant to work with and requires neither expensive maintenance facilities nor large laboratory space. Most of the basic tools for high precision mutagenesis have been tested on this plant, were found to work and are easily available (see Moss methods below).<br />
<br />
==Moss methods - working with ''Physcomitrella''==<br />
<br />
The techniques used for the cultivation and manipulation of Physcomitrella patens are based on the knowledge of the chair for Plantbiotechnology of Prof. Dr. Reski at Freiburg University, which are available at [http://www.plant-biotech.net Plant-Biotech.net]. <br />
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[[File:TUM13 Bench.png|thumb|right|350px|'''Figure 4:''' Working with cultivated moss on our laboratory bench]]<br />
*<b>Cell culture</b>: ''Physcomitrella patens'' plants can be cultivated either on solidified medium or in liquid medium. Liquid cultures can be kept in Erlenmeyer flasks under constant rotation and light exposure or in bioreactors for large scale production. By regularly (ideally weekly) disrupting the plants mechanically with a mixer (e.g. Ultra-Turrax) a homogenized culture can be achieved.<br />
*<b>Storage</b>: Long-term storage of ''Physcomitrella'' strains can be achieved by cryo-preservation. This procedure ensures a maximum survival rate of the plant by preconditioning and controlled freezing. [[http://www.plant-biotech.net/paper/PlantBiol_2004_Schulte_pageproof.pdf Schulte and Reski, 2004]]<br />
*<b>Targeted knockout</b>: ''P. patens'' is unique among plants in its high efficiency of gene targeting by homologous recombination. To knockout a specific gene a disruption construct has to be generated. This consists of the gene to be silenced with a selection cassette (usually the nptII gene) inserted into its center by suitable restriction sites. The moss is then transformed with this DNA construct which is integrated into the genome by homologous recombination. [[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]]<br />
[[File:TUM13 Transformation.png|thumb|right|350px|'''Figure 5:''' Transformation procedure]]<br />
*<b>Transformation</b>: Transformation of ''P. patens'' requires protoplasts of the plant, which can be obtained by cell wall digesting enzymes. The protoplasts can either be transformed by particle bombardment or via polyethylene glycol (PEG), which is the easiest and most commonly used method. The DNA constructs should be linearized for optimal transformation and contain a selection marker for subsequent screening. After transformation, the protoplasts are cultivated in the dark for 12-16 h followed by 9 days under normal growth conditions during which they regenerate their cell wall. Afterwards they are plated on solidified medium in normal petri dishes and first experiments can be executed. [[http://link.springer.com/article/10.1007/BF00260654 Schaefer et al., 1991]]<br />
*<b>Analysis of transformants</b>: First, the transformed protoplasts are plated on solidified medium containing the antibiotic G418 (Geneticin), to which successfully transformed plants are resistant due to the selection marker nptII which encodes the enzyme neomycin phosphotransferase. Secondly, the transformants are analyzed by a PCR screen using primers derived the selection marker cassette´s sequences [[http://www.plant-biotech.net/paper/PlantMolecularBiologyReporter_2002_Schween.pdf Schween et al., 2002]].<br />
<br />
In '''conclusion''', it naturally takes a bit more time to work with a plant in comparison to bacteria or yeast (see Figure 6), but the advantages definitely outweigh the time factor and if teams start early enough, it is perfectly possible to work with ''P. patens'' as a chassis in an iGEM project!<br />
<br />
This is a brief summary of the most important techniques in working with ''P. patens''. For a full description of these methods please see [https://2013.igem.org/Team:TU-Munich/Notebook/Methods#Physcomitrella_Methods our methods page].<br />
<br />
[[File:TUM13_timeline.png|thumb|center|910px| '''Figure 6:''' Comparing work flow for ''E. coli'', ''S. cerevisiae'' and ''P. patens'']]<br />
<br />
==BioBricks for protein expression in ''Physcomitrella''==<br />
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[[File:TUM13_plant biobricks.png|thumb|right|300px| '''Figure 7:''' Our transformation vector ]]<br />
To transform the moss, we created an all-purpose backbone into which all our constructs could be integrated easily. Therefore we modified the common iGEM pSB1C3 plasmid with the following plant-specific components:<br />
<br />
* '''pAct5 (Actin 5 promoter from ''Physcomitrella patens''):''' for strong protein expression.<br />
<br />
* '''miniMCS:''' This miniature multiple cloning site contains restriction sites for the enzymes MfeI and SbfI which allows you to insert BioBrick between two other Biobricks (in our case: pAct5 and t35S_npt-cassette) as a result of the compability of MfeI with EcoRI and SbfI with PstI.<br />
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* '''t35S (35S terminator):''' This terminator originates from the 35S transcript of the cauliflower mosaic virus.<br />
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* '''nptII-cassette:''' This selection cassette contains the neomycon phosphotransferase II gene, encoding the enzyme aminoglycoside-3'-phosphotransferase (NPTII), which inactivates a range of aminoglycoside antibiotics such as Kanamycin, Neomycin and Geneticin (G418) by phosphorylation. The latter antibiotic is used as selective agent for transformed ''P. patens'' plants, inhibiting the growth of untransformed plants very effectively. The neomycon phosphotransferase II gene is under control of the NOS promoter and terminator.<br />
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==References:==<br />
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[[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Reski, R. (1998). Development, Genetics and Molecular Biology of Mosses. ''Bot. Acta'', 111:1-15.<br /><br />
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[[http://www.plantphysiol.org/content/127/4/1430 Schaefer and Zryd, 2001]] Schaefer, D.G. and Zrÿd, J. (2001). The Moss ''Physcomitrella patens'', Now and Then. ''Plant Physiology'', 127(4):1430-1438.<br /><br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/14586556 Reski et al., 2004]] Hohe, A., Egener, T., Lucht, J.M., Holtorf, H., Reinhard, C., Schween, G. and Reski, R. (2004). An improved and highly standardised transformation procedure allows efficient production of single and multiple targeted gene-knockouts in a moss, Physcomitrella patens. ''Curr Genet.'', 44(6):339-47.<br /><br />
<br />
[[http://www.sciencedirect.com/science/article/pii/S0958166907000948 Reski and Decker, 2007]] Decker, E.L. and Reski, R. (2007). Moss bioreactors producing improved biopharmaceuticals. ''Current Opinion in Biotechnology'', 18(5):393-398.<br /><br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/22621344 Reski et al., 2012]] Parsons, J., Altmann, F., Arrenberg, C. K., Koprivova, A., Beike, A. K., Stemmer, C., Gorr, G., Reski, R. and Decker, E. L. (2012). Moss-based production of asialo-erythropoietin devoid of Lewis A and other plant-typical carbohydrate determinants. ''Plant Biotechnology Journal'', 10:851–861.<br /><br />
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[[http://www.plant-biotech.net/paper/PlantBiol_2004_Schulte_pageproof.pdf Schulte and Reski, 2004]] Schulte, J. and Reski, R. (2004). High throughput Cryopreservation of 140 000 Physcomitrella patens Mutants. ''Plant Biology'', 6:119-127.<br /><br />
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[[http://link.springer.com/article/10.1007/BF00260654 Schaefer et al., 1991]] Schaefer, D., Zryd, J.-P., Knight, C., Cove, D. (1991). Stable transformation of the moss ''Physcomitrella patens''. ''Molecular and General Genetics'', 226:418-424.<br /><br />
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[[http://www.plant-biotech.net/paper/PlantMolecularBiologyReporter_2002_Schween.pdf Schween et al., 2002]] Schween, G., Fleig, S., Reski, R. (2002). High-throughput-PCR screen of 15,000 transgenic Physcomitrella plants. ''Plant Molecular Biology Reporter'', 20:43–47.<br /><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:51:56Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
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==Science Communication & Publicity==<br />
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<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
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The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
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But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
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Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
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==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
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We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
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Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
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====PhyscoFilter presentation at the German Museum====<br />
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==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
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===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
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====Our survey booth in the city of Freising====<br />
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==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
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[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
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<li><img src="https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in the <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/8a/TUM13_Press_trinational.png" alt="<b>Figure 8:</b> Article in <a href='http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/'>Trinational Institute for Plant research News</a>"/>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/c6/TUM13_Biotechnologie_de.png" alt="<b>Figure 9:</b> Article in <a href='http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462&'>www.biotechnologie.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/cb/TUM13_Innovations-report.png" alt="<b>Figure 10:</b> Article on <a href='http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html'>www.innovations-report.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/82/TUM13_Schmude.JPG" alt="<b>Figure 11:</b> At the interview with Magdalena Schmude from <a href='http://www.dradio.de/dlf/'> Deutschlandfunk radio station</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/eb/TUM13_Deutschlandfunk.png" alt="<b>Figure 12:</b> Report from <a href='http://www.dradio.de/dlf/sendungen/forschak/2283279/'>Deutschlandfunk</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
<br />
<div class="box-right" style="height: 350px;"><br />
<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
<br />
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<div style="width:450px;font-size:8px;text-align:right;float:right;"><iframe width="450" height="505" src="http://twitterforweb.com/iframe/twitterbox/iGEM_TUM.html?s=1,0,3,450,505,f4f4f4,0,c4c4c4,101010,1,1,336699" frameborder="0" scrolling="no" allowtransparency="1"></iframe>Created by: <a href="http://twitterforweb.com" target="_blank">twitter website widget</a></div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:50:04Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
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<!-- Star des Inhalts --><br />
==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
<html><br />
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<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/78/TUM13_Foto_Germanmuseum_01.png/350px-TUM13_Foto_Germanmuseum_01.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/2f/TUM13_Foto_Germanmuseum_02.png/350px-TUM13_Foto_Germanmuseum_02.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/00/TUM13_Foto_Germanmuseum_03.png/350px-TUM13_Foto_Germanmuseum_03.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/50/TUM13_Foto_Germanmuseum_04.png/350px-TUM13_Foto_Germanmuseum_04.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cd/TUM13_Foto_Germanmuseum_05.png/350px-TUM13_Foto_Germanmuseum_05.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fa/TUM13_Foto_Germanmuseum_06.png/350px-TUM13_Foto_Germanmuseum_06.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b1/TUM13_Foto_Germanmuseum_07.png/350px-TUM13_Foto_Germanmuseum_07.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_Foto_Germanmuseum_08.png/350px-TUM13_Foto_Germanmuseum_08.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/94/TUM13_Foto_Germanmuseum_09.png/350px-TUM13_Foto_Germanmuseum_09.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b7/TUM13_Foto_Germanmuseum_10.png/350px-TUM13_Foto_Germanmuseum_10.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/20/TUM13_Foto_Germanmuseum_11.png/350px-TUM13_Foto_Germanmuseum_11.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6b/TUM13_Foto_Germanmuseum_12.png/350px-TUM13_Foto_Germanmuseum_12.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/28/TUM13_Foto_Germanmuseum_13.png/350px-TUM13_Foto_Germanmuseum_13.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/47/TUM13_Foto_Germanmuseum_14.png/350px-TUM13_Foto_Germanmuseum_14.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/1f/TUM13_Foto_Germanmuseum_15.png/350px-TUM13_Foto_Germanmuseum_15.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/31/TUM13_Foto_Germanmuseum_16.png/350px-TUM13_Foto_Germanmuseum_16.png" /></li> <br />
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<br />
==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/36/TUM13_Foto_Information_Freising1.jpg/350px-TUM13_Foto_Information_Freising1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/e8/TUM13_Foto_Information_Freising2.jpg/350px-TUM13_Foto_Information_Freising2.jpg" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/a8/TUM13_Foto_Information_Freising4.jpg/350px-TUM13_Foto_Information_Freising4.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/67/TUM13_Foto_Information_Freising5.jpg/350px-TUM13_Foto_Information_Freising5.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/4c/TUM13_Foto_Information_Freising6.jpg/350px-TUM13_Foto_Information_Freising6.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/00/TUM13_Foto_Information_Freising7.jpg/350px-TUM13_Foto_Information_Freising7.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/bb/TUM13_Foto_Information_Freising8.jpg/350px-TUM13_Foto_Information_Freising8.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Foto_Information_Freising9.jpg/350px-TUM13_Foto_Information_Freising9.jpg" /></li><br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in the <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/8a/TUM13_Press_trinational.png" alt="<b>Figure 8:</b> Article in <a href='http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/'>Trinational Institute for Plant research News</a>"/>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/c6/TUM13_Biotechnologie_de.png" alt="<b>Figure 9:</b> Article in <a href='http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462&'>www.biotechnologie.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/cb/TUM13_Innovations-report.png" alt="<b>Figure 10:</b> Article on <a href='http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html'>www.innovations-report.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/82/TUM13_Schmude.JPG" alt="<b>Figure 11:</b> At the interview with Magdalena Schmude from <a href='http://www.dradio.de/dlf/'> Deutschlandfunk radio station</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/eb/TUM13_Deutschlandfunk.png" alt="<b>Figure 12:</b> Report from <a href='http://www.dradio.de/dlf/sendungen/forschak/2283279/'>Deutschlandfunk</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
<br />
<div class="box-right" style="height: 350px;"><br />
<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:48:14Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
<hr />
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<!-- Star des Inhalts --><br />
==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b1/TUM13_Foto_Germanmuseum_07.png/350px-TUM13_Foto_Germanmuseum_07.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_Foto_Germanmuseum_08.png/350px-TUM13_Foto_Germanmuseum_08.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/94/TUM13_Foto_Germanmuseum_09.png/350px-TUM13_Foto_Germanmuseum_09.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b7/TUM13_Foto_Germanmuseum_10.png/350px-TUM13_Foto_Germanmuseum_10.png" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6b/TUM13_Foto_Germanmuseum_12.png/350px-TUM13_Foto_Germanmuseum_12.png" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/31/TUM13_Foto_Germanmuseum_16.png/350px-TUM13_Foto_Germanmuseum_16.png" /></li> <br />
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<br />
==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
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<li><img src="https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in the <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/8a/TUM13_Press_trinational.png" alt="<b>Figure 8:</b> Article in <a href='http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/'>Trinational Institute for Plant research News</a>"/>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/c6/TUM13_Biotechnologie_de.png" alt="<b>Figure 9:</b>Article in <a href='http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462&'>www.biotechnologie.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/cb/TUM13_Innovations-report.png" alt="<b>Figure 10:</b>Article on <a href='http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html'>www.innovations-report.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/82/TUM13_Schmude.JPG" alt="<b>Figure 11:</b>At the interview with Magdalena Schmude from <a href='http://www.dradio.de/dlf/'> Deutschlandfunk radio station</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/eb/TUM13_Deutschlandfunk.png" alt="<b>Figure 12:</b>Report from <a href='http://www.dradio.de/dlf/sendungen/forschak/2283279/'>Deutschlandfunk</a>"/></li><br />
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[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
<br />
<div class="box-right" style="height: 350px;"><br />
<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
<br />
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<div style="width:450px;font-size:8px;text-align:right;float:right;"><iframe width="450" height="505" src="http://twitterforweb.com/iframe/twitterbox/iGEM_TUM.html?s=1,0,3,450,505,f4f4f4,0,c4c4c4,101010,1,1,336699" frameborder="0" scrolling="no" allowtransparency="1"></iframe>Created by: <a href="http://twitterforweb.com" target="_blank">twitter website widget</a></div><br />
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<div style="float: left; margin-right: 20px; background: white;" class="fb-like-box" data-href="https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629" data-width="450" data-height="600" data-colorscheme="light" data-show-faces="true" data-header="true" data-stream="true" data-show-border="true"></div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:46:58Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
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==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
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</ul><br />
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</html><br />
<br />
==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/bb/TUM13_Foto_Information_Freising8.jpg/350px-TUM13_Foto_Information_Freising8.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Foto_Information_Freising9.jpg/350px-TUM13_Foto_Information_Freising9.jpg" /></li><br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in the <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/8a/TUM13_Press_trinational.png" alt="<b>Figure 8:</b> Article in <a href='http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/'>Trinational Institute for Plant research News</a>"/>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/c6/TUM13_Biotechnologie_de.png" alt="<b>Figure 9:</b>Article in <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>www.biotechnologie.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/cb/TUM13_Innovations-report.png" alt="<b>Figure 10:</b>Article on <a href='http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html'>www.innovations-report.de</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/82/TUM13_Schmude.JPG" alt="<b>Figure 11:</b>At the interview with Magdalena Schmude from <a href='http://www.dradio.de/dlf/'> Deutschlandfunk radio station</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/eb/TUM13_Deutschlandfunk.png" alt="<b>Figure 12:</b>Report from <a href='http://www.dradio.de/dlf/sendungen/forschak/2283279/'>Deutschlandfunk</a>"/></li><br />
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[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
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<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
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<div style="width:450px;font-size:8px;text-align:right;float:right;"><iframe width="450" height="505" src="http://twitterforweb.com/iframe/twitterbox/iGEM_TUM.html?s=1,0,3,450,505,f4f4f4,0,c4c4c4,101010,1,1,336699" frameborder="0" scrolling="no" allowtransparency="1"></iframe>Created by: <a href="http://twitterforweb.com" target="_blank">twitter website widget</a></div><br />
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<div style="float: left; margin-right: 20px; background: white;" class="fb-like-box" data-href="https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629" data-width="450" data-height="600" data-colorscheme="light" data-show-faces="true" data-header="true" data-stream="true" data-show-border="true"></div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:39:05Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
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==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b1/TUM13_Foto_Germanmuseum_07.png/350px-TUM13_Foto_Germanmuseum_07.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_Foto_Germanmuseum_08.png/350px-TUM13_Foto_Germanmuseum_08.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/94/TUM13_Foto_Germanmuseum_09.png/350px-TUM13_Foto_Germanmuseum_09.png" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6b/TUM13_Foto_Germanmuseum_12.png/350px-TUM13_Foto_Germanmuseum_12.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/28/TUM13_Foto_Germanmuseum_13.png/350px-TUM13_Foto_Germanmuseum_13.png" /></li><br />
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==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in the <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/8/8a/TUM13_Press_trinational.png" alt="<b>Figure 8:</b> Article in <a href='http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/'>Trinational Institute for Plant research News</a>"/>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/c/c6/TUM13_Biotechnologie_de.png" alt="<b>Figure 9:</b>Article in <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'> TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/50/TUM13_Foto_Germanmuseum_04.png/350px-TUM13_Foto_Germanmuseum_04.png" /></li><br />
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[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
<br />
<div class="box-right" style="height: 350px;"><br />
<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
<br />
<html><br />
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<div style="width:450px;font-size:8px;text-align:right;float:right;"><iframe width="450" height="505" src="http://twitterforweb.com/iframe/twitterbox/iGEM_TUM.html?s=1,0,3,450,505,f4f4f4,0,c4c4c4,101010,1,1,336699" frameborder="0" scrolling="no" allowtransparency="1"></iframe>Created by: <a href="http://twitterforweb.com" target="_blank">twitter website widget</a></div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:32:43Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
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<!-- Star des Inhalts --><br />
==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fa/TUM13_Foto_Germanmuseum_06.png/350px-TUM13_Foto_Germanmuseum_06.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b1/TUM13_Foto_Germanmuseum_07.png/350px-TUM13_Foto_Germanmuseum_07.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_Foto_Germanmuseum_08.png/350px-TUM13_Foto_Germanmuseum_08.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/94/TUM13_Foto_Germanmuseum_09.png/350px-TUM13_Foto_Germanmuseum_09.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b7/TUM13_Foto_Germanmuseum_10.png/350px-TUM13_Foto_Germanmuseum_10.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/20/TUM13_Foto_Germanmuseum_11.png/350px-TUM13_Foto_Germanmuseum_11.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6b/TUM13_Foto_Germanmuseum_12.png/350px-TUM13_Foto_Germanmuseum_12.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/28/TUM13_Foto_Germanmuseum_13.png/350px-TUM13_Foto_Germanmuseum_13.png" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/1f/TUM13_Foto_Germanmuseum_15.png/350px-TUM13_Foto_Germanmuseum_15.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/31/TUM13_Foto_Germanmuseum_16.png/350px-TUM13_Foto_Germanmuseum_16.png" /></li> <br />
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<br />
==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/36/TUM13_Foto_Information_Freising1.jpg/350px-TUM13_Foto_Information_Freising1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/e8/TUM13_Foto_Information_Freising2.jpg/350px-TUM13_Foto_Information_Freising2.jpg" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/4c/TUM13_Foto_Information_Freising6.jpg/350px-TUM13_Foto_Information_Freising6.jpg" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/bb/TUM13_Foto_Information_Freising8.jpg/350px-TUM13_Foto_Information_Freising8.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Foto_Information_Freising9.jpg/350px-TUM13_Foto_Information_Freising9.jpg" /></li><br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><li><img src="<br />
https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="<b>Figure 7:</b> Article in <a href='http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573'>TUM WZW News</a>"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/2f/TUM13_Foto_Germanmuseum_02.png/350px-TUM13_Foto_Germanmuseum_02.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/00/TUM13_Foto_Germanmuseum_03.png/350px-TUM13_Foto_Germanmuseum_03.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/50/TUM13_Foto_Germanmuseum_04.png/350px-TUM13_Foto_Germanmuseum_04.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cd/TUM13_Foto_Germanmuseum_05.png/350px-TUM13_Foto_Germanmuseum_05.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/fa/TUM13_Foto_Germanmuseum_06.png/350px-TUM13_Foto_Germanmuseum_06.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b1/TUM13_Foto_Germanmuseum_07.png/350px-TUM13_Foto_Germanmuseum_07.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_Foto_Germanmuseum_08.png/350px-TUM13_Foto_Germanmuseum_08.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/94/TUM13_Foto_Germanmuseum_09.png/350px-TUM13_Foto_Germanmuseum_09.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b7/TUM13_Foto_Germanmuseum_10.png/350px-TUM13_Foto_Germanmuseum_10.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/20/TUM13_Foto_Germanmuseum_11.png/350px-TUM13_Foto_Germanmuseum_11.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6b/TUM13_Foto_Germanmuseum_12.png/350px-TUM13_Foto_Germanmuseum_12.png" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/2/28/TUM13_Foto_Germanmuseum_13.png/350px-TUM13_Foto_Germanmuseum_13.png" /></li><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/31/TUM13_Foto_Germanmuseum_16.png/350px-TUM13_Foto_Germanmuseum_16.png" /></li> <br />
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[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
<br />
<div class="box-right" style="height: 350px;"><br />
<html><iframe width="430" height="270" style="border:1px #FFFFFF solide;" name="myiframe" scrolling="auto" frameborder="1" align=aus marginheight="5px" marginwidth="5px" src="http://www.youtube.com/embed/iRO0-fMIW9I?feature=player_detailpage" frameborder="0" allowfullscreen><br />
</iframe></html><br />
"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
<br />
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<div style="width:450px;font-size:8px;text-align:right;float:right;"><iframe width="450" height="505" src="http://twitterforweb.com/iframe/twitterbox/iGEM_TUM.html?s=1,0,3,450,505,f4f4f4,0,c4c4c4,101010,1,1,336699" frameborder="0" scrolling="no" allowtransparency="1"></iframe>Created by: <a href="http://twitterforweb.com" target="_blank">twitter website widget</a></div><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/HumanPractice/MediaTeam:TU-Munich/HumanPractice/Media2013-10-29T02:30:28Z<p>PSchneider: /* Media coverage on iGEM 2013 project */</p>
<hr />
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<br />
<div id="wikicontent-container"><br />
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<!-- Star des Inhalts --><br />
==Science Communication & Publicity==<br />
<br />
<div class="quote"><br />
"A scientist has to be neutral in his search for the truth, but he cannot be neutral as to the use of that truth when found. If you know more than other people, you have more responsibility, rather than less."<br />
<div class="author">- Baron C.P. Snow</div><br />
</div><br />
<br />
The importance of science communication cannot be stressed enough. As students, we spend huge amounts of time at the TUM life science campus and at the lab, allowing us to dig deep into our subjects, focus on our studies and enjoy the privilege of an environment designed to support us in the pursuit of our scientific interests. <br />
<br />
But our knowledge and experiences wouldn't be of much use if we didn't communicate and share them. New technology can't find the support it needs if no one apart from a few experts understands what it is all about and many great ideas wouldn't have seen the light of day without the creative synergies that develop through interdisciplinary dialog. Communicating ideas to people with different backgrounds not only provides valuable new input and views from way outside the box: The necessity to take a step back and explain the bigger picture also brings us to look at our work and intentions from a whole new perspective, deepens our understanding and brings up aspects previously missed. <br />
<br />
Furthermore, a well informed public creates the kind of open minded environment that catalyzes bold thinking and allows great ideas to thrive. As undergrads, we're still halfway between the experts of our fields and the public. So as part of our project, we set out to mediate between those two worlds, to inspire and get inspired.<br />
<br />
==Deutsches Museum Munich==<br />
[[File:TUM13 German_Museum.jpg|thumb|right|250px| '''Figure 1:''' Our poster for the museum (german)]]<br />
<br />
We had the chance to introduce the PhyscoFilter and our iGEM team to the public at the visitors lab at the German Museum of Munich. Green biotechnology is perceived rather negatively in Germany, but the majority of expressed concerns relates to applications in agriculture and food. So additional to presenting our project and answering a lot of interested questions about synthetic biology, we asked people about their views to see if projects like the PhyscoFilter can bring a different perspective into the public debate about biotechnology.<br />
<br />
Because of the Oktoberfest, we had a large and very international audience with whom we had very interesting discussions. We had prepared a poster aimed at a larger audience in German language, but we could have needed posters in English, Italian, French, Russian, Chinese and Hebrew as well and had the chance to use all the foreign language skills we had. The feedback we received was much more positive than expected. People appreciated our idea and considered this application of green biotechnology as much more feasible due to its thorough biosafety profile.<br />
<br />
We really enjoyed this campaign because of all the valuable feedback and the large diversity of input we got. It was very inspiring to meet and talk to all those people and once again, our iGEM activities enriched our views.<br />
<br />
====PhyscoFilter presentation at the German Museum====<br />
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==Survey on the public perception of SynBio==<br />
The public perception of biotechnology in Germany is traditionally not very positive. But how much do people know about synthetic biology? Are red, white and green biotechnology perceived equally positive or negative? On the iGEM-day-Germany, we set out to inform, explain and investigate. How much impact does the pollution of water through pharmaceuticals and hormones have on people's private life as well as globally according to public opinion? Are the projects addressing these problems able to increase the acceptance of synthetic biology? And would people want to use our filter or support its use in public sewage plants?<br />
<br />
[[File:Fragebogen_iGEM_Germany_day_Translated_copy_01.png|thumb|left|430px| '''Figure 2:''' Our questionnaire page 1 (translated to English)]] [[File:Fragebogen_iGEM_Germany_day_Translated_copy_02.png|thumb|right|430px| '''Figure 3:''' Our questionnaire page 2 (translated to English)]] <br />
<br />
===Results:===<br />
<br />
[[File:Auswertung_Umfrage_translated_01.png|thumb|left|430px| '''Figure 4:''' Results page 1 (translated to English)]][[File:Auswertung_Umfrage_translated_02.png|thumb|right|430px| '''Figure 5:''' Results page 2 (translated to English)]]<br />
<br />
Green biotechnology is seen as far more controversial than industrial biotechnology, while medical applications are widely accepted. Most people feel personally concerned by water pollution and also perceive this problem as highly relevant in a global context. If synthetic biology can offer solutions for problems like these, people would be more likely to approve genetic engineering. Nearly two thirds would use a moss filter in their homes and 84% would agree with its use e.g. for hospital wastewater. We were happy to learn from the evaluation that our project is widely perceived as positive and that people found our survey and the conversations helpful to learn more about synthetic biology.<br />
<br />
====Our survey booth in the city of Freising====<br />
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<br />
==13th Munich Science Days==<br />
November 16th to 19th we will be presenting our project at the [http://www.muenchner-wissenschaftstage.de/2013/front_content.php 13th Munich Science Days]. This popular public science fair offers workshops for school classes, public discussions, about 30 presentations and four theme nights, next to a large exhibition, tours and programs for kids.<br />
<br />
==Speech about iGEM at the GoBiochem Team TU Munich==<br />
<br />
[[File:TUM13 GoBiochem.jpg|thumb|right|250px| '''Figure 6:''' Speech at the GoBiochem Team TU Munich]]<br />
<br />
To inform scientifically interested pupils about the iGEM competition, Leonie and Johanna gave a lecture on our project to students participating in the [http://www.ch.tum.de/gobiochem/ GoBiochem] program. This program is an initiative from several biochemistry and molecular biotechnology students of the TU Munich who give pupils, aged between 15 and 18, the opportunity to get an insight into the biochemistry degree both into theoretical and practical aspects. They listen to talks about biological and chemical topics, perform a two-week introductive laboratory course and visit different TUM institutes to get an insight into real science. <br />
Therefore the presentation about synthetic biology and the iGEM competition in particular was given to an ideal target audience to inspire a new generation.<br />
<br />
==Media coverage on iGEM 2013 project==<br />
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https://static.igem.org/mediawiki/2013/a/a7/TUM13_Pressrelease.png" alt="'''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News]"/></li><br />
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[[File:TUM13 Pressrelease.png|thumb|left|430px| '''Figure 7:''' Article in [http://www.wzw.tum.de/index.php?id=185&no_cache=1&tx_ttnews%5Btt_news%5D=573 TUM WZW News] (german)]]<br />
<br />
[[File:TUM13 Press_trinational.png|thumb|right|430px| '''Figure 8:''' Article in the [http://www.tip-itp.eu/2013/09/igem-team-tu-munich-visiting-labs-of-the-tip-in-freiburg/ Trinational Institute for Plant research News] ]]<br />
<br />
[[File:TUM13_Biotechnologie_de.png|thumb|left|430px| '''Figure 9:''' Article on [http://www.biotechnologie.de/BIO/Navigation/DE/root,did=166602.html?listBlId=74462& www.biotechnologie.de] (german)]]<br />
<br />
[[File:TUM13_Innovations-report.png|thumb|right|430px| '''Figure 10:''' Article on [http://www.innovations-report.de/html/berichte/biowissenschaften_chemie/moos_sauberes_wasser_abwasserreinigung_physcofilter_220378.html www.innovations-report.de] (german)]]<br />
<br />
[[File:TUM13 Schmude.JPG|thumb|left|430px| '''Figure 11:''' At the interview with Magdalena Schmude from [http://www.dradio.de/dlf/ Deutschlandfunk radio station] ]]<br />
<br />
[[File:TUM13_Deutschlandfunk.png|thumb|right|430px| '''Figure 12:''' Report from [http://www.dradio.de/dlf/sendungen/forschak/2283279/ Deutschlandfunk](german) ]]<br />
<br />
==Media coverage on iGEM 2012 project after the Jamboree==<br />
<br />
<div class="box-left" style="height: 350px;"><br />
[[File:TUM13 Beer_advocat.jpg|thumb|right|200px| '''Figure 13:''' "Munich Scientists Tinker with Yeast"]]<br />
This [http://aleszu.com/2013/01/munich-scientists-tinker-with-yeast/ article] by Aleszu Bajak covered our 2012 project in [http://beeradvocate.com/community/threads/beeradvocate-magazine-72-pierogies-baileys-range-lawsons-vivant-buenos-aires-class-of-2012.59179/ BeerAdvocate magazine, #72]<br />
</div><br />
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"A gateway to a lot of Synthetic Biology" - The part about our last years iGEM project is from minute 14.20 on. An interesting video from the beginning to the end by the way.<br />
</div><br />
<br />
==Representation on Social Media Networks==<br />
To be easily aproachable for people´s questions about iGEM, our project and our team and to stay in touch, we used our accounts on [https://www.facebook.com/pages/iGEM-TU-M%C3%BCnchen/149746078408629 Facebook] and [https://twitter.com/iGEM_TUM Twitter].<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-MunichTeam:TU-Munich2013-10-29T02:20:05Z<p>PSchneider: </p>
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<br />
== PhyscoFilter &ndash; Clean different. ==<br />
The contamination of aquatic ecosystems with a multitude of anthropogenic pollutants has been a problem since the industrial revolution. Antibiotics, hormones and various noxious substances threaten environmental health and are not effectively removed by conventional waste water treatment. We propose to employ transgenic plants which produce effectors for enzymatic degradation ([https://2013.igem.org/Team:TU-Munich/Project/Biodegradation BioDegradation]) or specific binding ([https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation]) of pollutants. The autotrophic, sedentary, aquatic nature of the moss [https://2013.igem.org/Team:TU-Munich/Project/Physcomitrella ''Physcomitrella patens''] makes it an optimal chassis for a self-renewing, low-maintenance and cheap water filter. A light-triggered [https://2013.igem.org/Team:TU-Munich/Project/Killswitch kill switch] prevents unintended environmental spreading by limiting viability to places where the spectrum of sunlight is appropriately filtered. Furthermore, we have developed a device to [https://2013.igem.org/Team:TU-Munich/Results/Implementation implement our filter] in an aquatic environment, investigated the application of this new technology and examined its [https://2013.igem.org/Team:TU-Munich/Results/Economics economic feasibility]. Based on our results, the PhyscoFilter may become a game-changing approach to improve global water quality in an affordable and sustainable fashion.<br />
<br />
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<br />
== Achievements ==<br />
<br />
At the European Jamboree our team achieved the following:<br />
<div class="achievements"><br />
*We won a gold medal.<br />
*We advanced to the World Championship Jamboree.<br />
*We won the Best Wiki prize.<br />
*We were the first runner up in the undergrad section.<br />
</div><br />
<br />
== Sponsors ==<br />
<html><br />
<a class="sponsor" href="http://www.tum.de/"><img src="https://static.igem.org/mediawiki/2013/9/97/Logo_TU-Muenchen_01.png" width="190px"></a><br />
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<a class="sponsor" href="http://www.daad.de/de/index.html"><img src="https://static.igem.org/mediawiki/2013/f/f7/TUM13_DAAD.jpg" width="120px"></a><br />
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<a class="sponsor" href="http://www.eurofins.de/"><img src="https://static.igem.org/mediawiki/2013/b/bc/TUM_Eurofins.png" width="200px"></a><br />
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<a class="sponsor" href="http://www.qiagen.com/"><img src="https://static.igem.org/mediawiki/2013/6/60/TUM13_Sponsor_Qiagen.png" width="100px"></a> <br />
<a class="sponsor" href="http://www.iba-lifesciences.com/"><img src="https://static.igem.org/mediawiki/2013/9/9c/Iba_logo_claim_r_farbe.jpg" width="180px"></a> <br />
<a class="sponsor" href="http://eu.idtdna.com/site/"><img src="https://static.igem.org/mediawiki/2013/1/13/Bonn_sponsor_idt.jpg" width="180px"></a> <br />
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<a class="sponsor" style="float: none; margin: 10px auto;" href="http://www.roche.com/"><img src="https://static.igem.org/mediawiki/2013/d/d2/TUM13_Roche.jpg" height="80px"></a><br />
<br />
<center style="margin-top: 10px;"><a href="http://www2.clustrmaps.com/user/c81109e0d" id="clustrMapsLink"><img src="http://www2.clustrmaps.com/stats/maps-no_clusters/2013.igem.org-Team-TU-Munich-thumb.jpg" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com';" width="150" /></a></center><br />
</html><br />
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<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-MunichTeam:TU-Munich2013-10-29T02:14:15Z<p>PSchneider: </p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><html><ul class="bxslider"> <!-- das muss so hässlich sein, damit kein absatz eingefügt wird --><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/3f/TUM13_Foto_Germanmuseum_12.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a9/TUM13_labor.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/4/4c/TUM13_WP_20130927_19_03_23_Pro_edit_sliced.jpg" /></li><br />
</ul><br />
<div style="height: 50px; margin: 14px 0px 5px;"><br />
<div style="float: left; text-align: right; width: 140px; height: 40px; margin: 5px 0px;"><br />
<span id="counter" style="color: #502204; font: normal 24px/40px sketch_rockwell,Arial,sans-serif;">0</span> <a href="https://2013.igem.org/Special:PopularPages">visitors</a><br />
</div><br />
<div style="float: left; text-align: right; width: 400px; height: 40px; margin: 5px 0px 5px 33px;"><br />
<span id="countdown" style="color: #502204; font: normal 24px/40px sketch_rockwell,Arial,sans-serif;"></span> left to World Wiki Freeze<br />
</div><br />
<a class="tour start" href="https://2013.igem.org/Team:TU-Munich/Project/Overview">Take the Tour</a><br />
</div><br />
<div style="height: 145px; margin: 5px 0px 5px;"><br />
<a class="button application" href="https://2013.igem.org/Team:TU-Munich/Results/Implementation#Our_swimming_remediation_raft">Application</a><br />
<a class="button autoannotator" href="https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">AutoAnnotator</a><br />
<a class="button entrepreneur" href="https://2013.igem.org/Team:TU-Munich/Results/Economics">Entrepreneur</a><br />
<a class="button physco" href="https://2013.igem.org/Team:TU-Munich/Project/Physcomitrella">Physco</a><br />
<a class="button safety" href="https://2013.igem.org/Team:TU-Munich/Project/Safety">Safety</a><br />
<a class="button judging" href="https://2013.igem.org/Team:TU-Munich/Team/Judging">Judging</a><br />
</div><br />
</html><br />
<br />
== PhyscoFilter &ndash; Clean different. ==<br />
The contamination of aquatic ecosystems with a multitude of anthropogenic pollutants has been a problem since the industrial revolution. Antibiotics, hormones and various noxious substances threaten environmental health and are not effectively removed by conventional waste water treatment. We propose to employ transgenic plants which produce effectors for enzymatic degradation ([https://2013.igem.org/Team:TU-Munich/Project/Biodegradation BioDegradation]) or specific binding ([https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation]) of pollutants. The autotrophic, sedentary, aquatic nature of the moss [https://2013.igem.org/Team:TU-Munich/Project/Physcomitrella ''Physcomitrella patens''] makes it an optimal chassis for a self-renewing, low-maintenance and cheap water filter. A light-triggered [https://2013.igem.org/Team:TU-Munich/Project/Killswitch kill switch] prevents unintended environmental spreading by limiting viability to places where the spectrum of sunlight is appropriately filtered. Furthermore, we have developed a device to [https://2013.igem.org/Team:TU-Munich/Results/Implementation implement our filter] in an aquatic environment, investigated the application of this new technology and examined its [https://2013.igem.org/Team:TU-Munich/Results/Economics economic feasibility]. Based on our results, the PhyscoFilter may become a game-changing approach to improve global water quality in an affordable and sustainable fashion.<br />
<br />
<html><br />
<right><iframe style="box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.2);padding: 5px;margin: 5px;background-color: white;" src="http://player.vimeo.com/video/76195786" width="900" height="510" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe></right></html><br />
<br />
== Achievements ==<br />
<br />
At the European Jamboree our team achieved the following:<br />
<div class="achievements"><br />
*We won a gold medal.<br />
*We advanced to the World Championship Jamboree.<br />
*We won the Best Wiki prize.<br />
*We were the first runner up in the undergrad section.<br />
</div><br />
<br />
== Sponsors ==<br />
<html><br />
<a class="sponsor" href="http://www.tum.de/"><img src="https://static.igem.org/mediawiki/2013/9/97/Logo_TU-Muenchen_01.png" width="190px"></a><br />
<a class="sponsor" href="http://wzw.tum.de/"><img src="https://static.igem.org/mediawiki/2013/a/ac/Wzwlogo2.png" width="210px"></a><br />
<a class="sponsor" href="http://biologische-chemie.userweb.mwn.de/index.html"><img src="https://static.igem.org/mediawiki/2013/0/05/Unbenannt.PNG" width="190px"></a><br />
<a class="sponsor" href="http://www.daad.de/de/index.html"><img src="https://static.igem.org/mediawiki/2013/f/f7/TUM13_DAAD.jpg" width="120px"></a><br />
<a class="sponsor" href="http://www.geneious.com/"><img src="https://static.igem.org/mediawiki/2012/8/82/TUM_Geneious.png" width="190px"></a><br />
<a class="sponsor" href="http://www.eurofins.de/"><img src="https://static.igem.org/mediawiki/2013/b/bc/TUM_Eurofins.png" width="200px"></a><br />
<a class="sponsor" href="http://www.mathworks.de/"><img src="https://static.igem.org/mediawiki/2013/0/0c/TUM13_MathWorks.png" width="200px"></a><br />
<a class="sponsor" href="http://www.ika.com/"><img src="https://static.igem.org/mediawiki/2013/9/9d/TUM13_IKA.png" width="105px"></a><br />
<a class="sponsor" href="http://www.neb.com/"><img src="https://static.igem.org/mediawiki/2013/5/50/TUM13_Sponsor_NEB.jpg" width="155px"></a><br />
<a class="sponsor" href="http://www.promega.de/"><img src="https://static.igem.org/mediawiki/2013/f/f0/Promega-300.jpg" width="175px"></a><br />
<a class="sponsor" href="http://www.qiagen.com/"><img src="https://static.igem.org/mediawiki/2013/6/60/TUM13_Sponsor_Qiagen.png" width="100px"></a> <br />
<a class="sponsor" href="http://www.iba-lifesciences.com/"><img src="https://static.igem.org/mediawiki/2013/9/9c/Iba_logo_claim_r_farbe.jpg" width="180px"></a> <br />
<a class="sponsor" href="http://eu.idtdna.com/site/"><img src="https://static.igem.org/mediawiki/2013/1/13/Bonn_sponsor_idt.jpg" width="180px"></a> <br />
<a class="sponsor" href="http://www.thermoscientific.com"><img src="https://static.igem.org/mediawiki/2013/e/ed/TUM13_Sponsor_logo_Thermo.jpg" width="140px"></a><br />
<a class="sponsor" href="http://www.erasynbio.eu/"><img src="https://static.igem.org/mediawiki/2013/5/58/Logo_ERASynBio.png" width="180px"></a><br />
<div class="visualClear"></div><br />
<a class="sponsor" style="float: none; margin: 10px auto;" href="http://www.roche.com/"><img src="https://static.igem.org/mediawiki/2013/d/d2/TUM13_Roche.jpg" height="80px"></a><br />
<br />
<center style="margin-top: 10px;"><a href="http://www2.clustrmaps.com/user/c81109e0d" id="clustrMapsLink"><img src="http://www2.clustrmaps.com/stats/maps-no_clusters/2013.igem.org-Team-TU-Munich-thumb.jpg" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com';" width="150" /></a></center><br />
</html><br />
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<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/TUM13_ScriptTeam:TU-Munich/TUM13 Script2013-10-29T02:11:44Z<p>PSchneider: </p>
<hr />
<div>function myWikiReady() {<br />
<br />
<br />
// audio<br />
if ($('div#blubberkolben').length > 0) {<br />
preload('https://static.igem.org/mediawiki/2013/4/42/TUM13_blubber.gif');<br />
$('div#blubberkolben img').hover(function(e){<br />
$('div#blubberkolben img')[0].src = "https://static.igem.org/mediawiki/2013/4/42/TUM13_blubber.gif";<br />
$('div#blubberkolben').append($('<audio autobuffer autoplay loop><source src="https://static.igem.org/mediawiki/2013/b/b3/TUM13_blubbern.mp3" type="audio/mpeg"></audio>'));<br />
}, function(e){<br />
$('div#blubberkolben img')[0].src = "https://static.igem.org/mediawiki/2013/a/ab/TUM13_blubbern-stop.gif";<br />
$('div#blubberkolben audio').remove();<br />
});<br />
}<br />
<br />
<br />
// put the footer in the right place<br />
<br />
$("#footer-box").prepend($("#social-footer"));<br />
<br />
<br />
// animate top button<br />
<br />
function gotop(e){<br />
if ($(window).scrollTop() != 0) {<br />
$("a#gotop").fadeIn(400);<br />
} else {<br />
$("a#gotop").fadeOut(400);<br />
}<br />
}<br />
<br />
$("a#gotop").hide(0);<br />
gotop();<br />
<br />
$(window).scroll(gotop);<br />
$("a#gotop").click(function(e){<br />
e.preventDefault();<br />
$(window).off('scroll', gotop);<br />
$('html, body').animate({scrollTop : 0},500,'swing',function(){$(window).scroll(gotop);$("a#gotop").fadeOut(400);});<br />
});<br />
<br />
<br />
// GET parsing<br />
<br />
$.urlParam = function(name){<br />
var results = new RegExp('[\\?&]' + name + '=([^&#]*)').exec(window.location.href);<br />
if (results==null){<br />
return null;<br />
}<br />
else{<br />
while (results[1].indexOf('+') != -1) {<br />
results[1] = results[1].replace('+', ' ');<br />
}<br />
return results[1] || 0;<br />
}<br />
};<br />
<br />
<br />
// implement image preloading<br />
<br />
function preload() {<br />
var images = new Array()<br />
for (i = 0; i < preload.arguments.length; i++) {<br />
images[i] = new Image()<br />
images[i].src = preload.arguments[i]<br />
}<br />
}<br />
<br />
// FilterModel<br />
<br />
if ($('#rafts').length > 0) {<br />
initFilterModel();<br />
}<br />
<br />
// preload menu backgrounds<br />
<br />
preload( "https://static.igem.org/mediawiki/2013/9/95/TUM13_menu-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/4/4e/TUM13_submenu-bg.png",<br />
"https://static.igem.org/mediawiki/2013/d/db/TUM13_submenu-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/5/5f/TUM13_tour-start-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/6/6e/TUM13_tour-previous-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/3/35/TUM13_tour-next-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/4/44/TUM13_button-application-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/a/a7/TUM13_button-autoannotator-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/d/d5/TUM13_button-physco-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/e/e6/TUM13_button-entrepreneur-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/0/01/TUM13_button-safety-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/d/d6/TUM13_button-judging-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/c/c5/TUM13_gotop-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/2/2d/TUM13_gotop.png",<br />
"https://static.igem.org/mediawiki/2013/b/b4/TUM13_ajax-loading.gif",<br />
"https://static.igem.org/mediawiki/2013/2/29/TUM13_ajax-bg.png" );<br />
<br />
// preload footer links<br />
<br />
preload( "https://static.igem.org/mediawiki/2013/0/05/TUM13_address-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/c/c7/TUM13_contact-icon-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/9/9f/TUM13_facebook-icon-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/2/22/TUM13_twitter-icon-highlight.png",<br />
"https://static.igem.org/mediawiki/2013/a/a1/TUM13_youtube-icon-highlight.png" );<br />
<br />
// preload team pictures<br />
<br />
if ( $("div#teamfield").length > 0 ) {<br />
preload( "https://static.igem.org/mediawiki/2013/9/95/TUM13_moos.png",<br />
"https://static.igem.org/mediawiki/2013/b/b6/TUM13_katrin-front.png", // Katrin<br />
"https://static.igem.org/mediawiki/2013/1/13/TUM13_katrin-t.png",<br />
"https://static.igem.org/mediawiki/2013/a/a8/TUM13_katrin-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/7/72/TUM13_katrin-l.png",<br />
"https://static.igem.org/mediawiki/2013/7/7f/TUM13_katrin-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/c/cf/TUM13_katrin-b.png",<br />
"https://static.igem.org/mediawiki/2013/2/28/TUM13_katrin-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/3/3e/TUM13_katrin-r.png",<br />
"https://static.igem.org/mediawiki/2013/8/8e/TUM13_katrin-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/b/b6/TUM13_rosario-front.png", // Rosario<br />
"https://static.igem.org/mediawiki/2013/2/2e/TUM13_rosario-t.png",<br />
"https://static.igem.org/mediawiki/2013/4/42/TUM13_rosario-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/9/91/TUM13_rosario-l.png",<br />
"https://static.igem.org/mediawiki/2013/6/66/TUM13_rosario-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/0/05/TUM13_rosario-b.png",<br />
"https://static.igem.org/mediawiki/2013/8/8e/TUM13_rosario-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/1/1a/TUM13_rosario-r.png",<br />
"https://static.igem.org/mediawiki/2013/3/38/TUM13_rosario-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/5/55/TUM13_fabian-front.png", // Fabian<br />
"https://static.igem.org/mediawiki/2013/0/0a/TUM13_fabian-t.png",<br />
"https://static.igem.org/mediawiki/2013/8/87/TUM13_fabian-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/b/b7/TUM13_fabian-l.png",<br />
"https://static.igem.org/mediawiki/2013/0/0b/TUM13_fabian-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/2/24/TUM13_fabian-b.png",<br />
"https://static.igem.org/mediawiki/2013/5/51/TUM13_fabian-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/0/01/TUM13_fabian-r.png",<br />
"https://static.igem.org/mediawiki/2013/5/51/TUM13_fabian-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/d/de/TUM13_andreas-front.png", // Andreas<br />
"https://static.igem.org/mediawiki/2013/6/67/TUM13_andreas-t.png",<br />
"https://static.igem.org/mediawiki/2013/d/da/TUM13_andreas-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/8/84/TUM13_andreas-l.png",<br />
"https://static.igem.org/mediawiki/2013/d/d6/TUM13_andreas-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/9/9c/TUM13_andreas-b.png",<br />
"https://static.igem.org/mediawiki/2013/2/21/TUM13_andreas-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/5/55/TUM13_andreas-r.png",<br />
"https://static.igem.org/mediawiki/2013/8/81/TUM13_andreas-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/5/50/TUM13_louise-front.png", // Louise<br />
"https://static.igem.org/mediawiki/2013/5/58/TUM13_louise-t.png",<br />
"https://static.igem.org/mediawiki/2013/8/86/TUM13_louise-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/4/4f/TUM13_louise-l.png",<br />
"https://static.igem.org/mediawiki/2013/b/b1/TUM13_louise-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/a/ad/TUM13_louise-b.png",<br />
"https://static.igem.org/mediawiki/2013/3/3f/TUM13_louise-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/b/bc/TUM13_louise-r.png",<br />
"https://static.igem.org/mediawiki/2013/f/fe/TUM13_louise-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/4/47/TUM13_johanna-front.png", // Johanna<br />
"https://static.igem.org/mediawiki/2013/f/fc/TUM13_johanna-t.png",<br />
"https://static.igem.org/mediawiki/2013/1/10/TUM13_johanna-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/8/8c/TUM13_johanna-l.png",<br />
"https://static.igem.org/mediawiki/2013/b/b1/TUM13_johanna-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/4/4a/TUM13_johanna-b.png",<br />
"https://static.igem.org/mediawiki/2013/3/32/TUM13_johanna-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/8/89/TUM13_johanna-r.png",<br />
"https://static.igem.org/mediawiki/2013/d/d2/TUM13_johanna-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/2/29/TUM13_meike-front.png", // Meike<br />
"https://static.igem.org/mediawiki/2013/8/85/TUM13_meike-t.png",<br />
"https://static.igem.org/mediawiki/2013/3/3e/TUM13_meike-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/0/07/TUM13_meike-l.png",<br />
"https://static.igem.org/mediawiki/2013/7/79/TUM13_meike-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/6/63/TUM13_meike-b.png",<br />
"https://static.igem.org/mediawiki/2013/a/af/TUM13_meike-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/e/e3/TUM13_meike-r.png",<br />
"https://static.igem.org/mediawiki/2013/c/c1/TUM13_meike-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/d/db/TUM13_volker-front.png", // Volker<br />
"https://static.igem.org/mediawiki/2013/1/1a/TUM13_volker-t.png",<br />
"https://static.igem.org/mediawiki/2013/0/0a/TUM13_volker-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/4/4f/TUM13_volker-l.png",<br />
"https://static.igem.org/mediawiki/2013/f/fb/TUM13_volker-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/5/57/TUM13_volker-b.png",<br />
"https://static.igem.org/mediawiki/2013/8/86/TUM13_volker-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/2/2c/TUM13_volker-r.png",<br />
"https://static.igem.org/mediawiki/2013/2/27/TUM13_volker-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/3/3c/TUM13_polte-front.png", // Polte<br />
"https://static.igem.org/mediawiki/2013/9/9e/TUM13_polte-t.png",<br />
"https://static.igem.org/mediawiki/2013/9/9c/TUM13_polte-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/0/03/TUM13_polte-l.png",<br />
"https://static.igem.org/mediawiki/2013/5/58/TUM13_polte-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/9/99/TUM13_polte-b.png",<br />
"https://static.igem.org/mediawiki/2013/0/0f/TUM13_polte-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/b/b9/TUM13_polte-r.png",<br />
"https://static.igem.org/mediawiki/2013/6/61/TUM13_polte-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/d/da/TUM13_leonie-front.png", // Leonie<br />
"https://static.igem.org/mediawiki/2013/7/79/TUM13_leonie-t.png",<br />
"https://static.igem.org/mediawiki/2013/9/9c/TUM13_leonie-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/7/78/TUM13_leonie-l.png",<br />
"https://static.igem.org/mediawiki/2013/2/26/TUM13_leonie-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/8/8a/TUM13_leonie-b.png",<br />
"https://static.igem.org/mediawiki/2013/c/cc/TUM13_leonie-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/8/81/TUM13_leonie-r.png",<br />
"https://static.igem.org/mediawiki/2013/2/25/TUM13_leonie-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/0/0c/TUM13_philipp-front.png", // Philipp<br />
"https://static.igem.org/mediawiki/2013/a/a4/TUM13_philipp-t.png",<br />
"https://static.igem.org/mediawiki/2013/2/2d/TUM13_philipp-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/c/cf/TUM13_philipp-l.png",<br />
"https://static.igem.org/mediawiki/2013/8/82/TUM13_philipp-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/3/3a/TUM13_philipp-b.png",<br />
"https://static.igem.org/mediawiki/2013/1/1e/TUM13_philipp-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/f/ff/TUM13_philipp-r.png",<br />
"https://static.igem.org/mediawiki/2013/6/68/TUM13_philipp-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/2/25/TUM13_jeff-front.png", // Jeff<br />
"https://static.igem.org/mediawiki/2013/4/41/TUM13_jeff-t.png",<br />
"https://static.igem.org/mediawiki/2013/9/90/TUM13_jeff-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/2/21/TUM13_jeff-l.png",<br />
"https://static.igem.org/mediawiki/2013/b/bf/TUM13_jeff-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/e/ec/TUM13_jeff-b.png",<br />
"https://static.igem.org/mediawiki/2013/f/f4/TUM13_jeff-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/3/3e/TUM13_jeff-r.png",<br />
"https://static.igem.org/mediawiki/2013/a/a5/TUM13_jeff-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/a/a1/TUM13_chris-front.png", // Chris<br />
"https://static.igem.org/mediawiki/2013/4/42/TUM13_chris-t.png",<br />
"https://static.igem.org/mediawiki/2013/a/a4/TUM13_chris-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/4/4d/TUM13_chris-l.png",<br />
"https://static.igem.org/mediawiki/2013/e/ec/TUM13_chris-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/9/9b/TUM13_chris-b.png",<br />
"https://static.igem.org/mediawiki/2013/c/c6/TUM13_chris-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/7/72/TUM13_chris-r.png",<br />
"https://static.igem.org/mediawiki/2013/0/05/TUM13_chris-t-r.png",<br />
"https://static.igem.org/mediawiki/2013/0/03/TUM13_flo-front.png", // Flo<br />
"https://static.igem.org/mediawiki/2013/b/b4/TUM13_flo-t.png",<br />
"https://static.igem.org/mediawiki/2013/c/ce/TUM13_flo-t-l.png",<br />
"https://static.igem.org/mediawiki/2013/0/06/TUM13_flo-l.png",<br />
"https://static.igem.org/mediawiki/2013/1/11/TUM13_flo-b-l.png",<br />
"https://static.igem.org/mediawiki/2013/6/6b/TUM13_flo-b.png",<br />
"https://static.igem.org/mediawiki/2013/4/4b/TUM13_flo-b-r.png",<br />
"https://static.igem.org/mediawiki/2013/3/30/TUM13_flo-r.png"/*,<br />
"https://static.igem.org/mediawiki/2013/5/5d/TUM13_jeff-anim.gif", // Gifs<br />
"https://static.igem.org/mediawiki/2013/f/f9/TUM13_rosario-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/d/d1/TUM13_fabian-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/a/aa/TUM13_philipp-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/f/ff/TUM13_johanna-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/a/a5/TUM13_andi-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/e/ea/TUM13_flo-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/6/6c/TUM13_polte-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/7/70/TUM13_leonie-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/2/24/TUM13_louise-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/9/9b/TUM13_chris-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/6/6c/TUM13_katrin-anim.gif",<br />
"https://static.igem.org/mediawiki/2013/5/5e/TUM13_meike-anim.gif" */ );<br />
}<br />
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description = el.title + el.alt;<br />
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if ($('span#counter').length > 0) {<br />
$.ajax({<br />
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dom = $.parseHTML(html);<br />
visitors = $(dom).find('a[title="Team:TU-Munich"]').parent().text();<br />
visitors = visitors.substring(visitors.indexOf('(')+1);<br />
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visitors = visitors.replace(',', '');<br />
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clock = window.setInterval(function(){<br />
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time_left = Date.UTC(2013, 9, 29, 4, 0, 0) - Date.UTC(jetzt.getUTCFullYear(), jetzt.getUTCMonth(), jetzt.getUTCDate(), jetzt.getUTCHours(), jetzt.getUTCMinutes(), jetzt.getUTCSeconds());<br />
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$(document).ready(myWikiReady);</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/SummaryTeam:TU-Munich/Results/Summary2013-10-29T02:06:22Z<p>PSchneider: /* Implementation */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Start of content --><br />
<br />
==Our Project for this summer: Remediation.==<br />
<html><center><iframe style="box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.2);padding: 5px;margin: 5px;background-color: white;" src="http://player.vimeo.com/video/76195786" width="400" height="240" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe></center></html> <br><br />
During this summer we wanted to work on an iGEM project, which has the potential to become a real world application, since we believe that it is an important step for Synthetic Biology to provide alternative solutions for global problems. For this reason we focused on Bioremediation: The use of organisms to remove emissions caused by humans and bring the environment back to its natural state. As water is a resource which is absolutely essential for all living organisms, we decided to focus on the pollution of aquatic ecosystems.<br />
<br />
==Choice of the appropriate chassis for a water filter==<br />
Remediation is not new to iGEM, in fact it is a topic the iGEM community has worked on for nearly 10 years now. Therefore a set of promising BioBricks were already available in the Parts Registry, which we wanted to use in order to increase the knowledge on these effector proteins. Having found suitable effector proteins, we discussed about the most suitable chassis for our application. Most of the previous projects on Bioremediation were based on ''E. coli'', whereas we decided to use a plant instead. Photosynthesis carried out by the plants will allow the water filter to maintain and renew itself without the addition of any nutrients. We considered algae such as ''Chlamydomonas reinhardtii'', Bryophytes such as ''Physcomitrella patens'' and higher plants like ''Arabidopsis thaliana''. In the end ''Physcomitrella patens'' was the chassis of choice as it already grows in a filter-like structure and can be cultivated in terrestric as well as in aquatic conditions. Additionally it is a well established organism in biotechnology. Working with ''Physcomitrella patens'' is not easy considering the 1-2 months it takes from the transformation process to the experiments with stable transfected plants and the doubling times of 3-6 days. As nobody at the TU Munich works with the moss ''Physcomitrella patens'', we looked for an expert and found Prof. Reski who occupies a professorship at Freiburg University. We were very happy to gain him as an advisor during our project. For the use of ''Physcomitrella patens'' in iGEM we created a strong constitutive promoter ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159306 BBa_K1159306]), a plant terminator ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159307 BBa_K1159307]) and an antibiotic selection marker ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159308 BBa_K1159308]), which were all used to transform and select 21 different transgenic moss lines.<br />
<br />
==Localization of effector proteins==<br />
[[File:Localization_general.jpg|thumb|right|500px|'''Figure 1:''' Cytosolic protein expression and our modularized receptor for ''Physcomitrella'' work as expected.]]<br />
The actual remediation of pollutants is accomplished by effector proteins which function with quite different mechanisms. Thus it was important to enable the localization of effector proteins at different cellular sites. Cytosolic effector proteins are easily expressed, whereas for secretion a signal peptide BioBrick is cloned ahead of the effector protein. Several receptor signal peptides from ''Physcomitrella patens'' and other organisms were analyzed by using [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions bioinformatics tools]. The signal peptide of the Somatic Embryogenesis Receptor-like Kinase (SERK) from ''Physcomitrella patens''and the IgK signal peptide from ''Mus musculus'', which is described in literature to function in ''Physcomitrella'', were chosen. The secretion of a newly introduced luciferase with both of these signal peptides was investigated for 8 clones each. No detectable secretion for the IgKappa but a high secretion rate for the SERK signal peptide was shown. Successful secretion could be achieved using the SERK signal peptide. Because the secreted effector proteins are not attached to the moss cell, they diffuse into the water, which is suboptimal, for example if you want to remove pollutants by simply binding them. Therefore we designed a modular receptor for ''Physcomitrella'', which can carry effector proteins at the outer side of the cell membrane. For this purpose [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions bioinformatics methods] were used again and the SERK transmembrane domain was chosen to be the best one. A receptor composed of (1) the SERK signal peptide, (2) an extracellularly located effector protein, (3) a linker with a Strep-tag II and a TEV protease cleavage site, (4) the SERK transmembrane domain, (5) a short linker domain and (6) a green fluorescent protein were assembled using the RFC[25] standard. This highly modular receptor was successfully transformed into ''Physcomitrella patens'' and stable cell lines were selected. These stable cell lines were used for experiments. The localization of the membrane-bound GFP could be detected clearly on the surface of the moss cells (see figure 1), whereas expressing GFP cytosolically in the moss, showed a uniform fluorescence over the whole cell. Further we incubated the moss cells with recombinant TEV protease, which diffused through the cell wall, cleaved the TEV site within the extracellular domain of the receptor and liberated the NanoLuc luciferase. The luciferase assay of the supernatant at the beginning of this incubation and after 16 hours showed a dramatic increase in luminescence, which is an evidence that our modular receptor is located in the membrane and - even better - in the right orientation, exposed to the extracellular space. Beyond the possibility to locate an effector protein in the extracellular part of the receptor, we thought about further applications and found the SypCatcher-SpyTag System to be a perfect tool for our needs [[http://www.ncbi.nlm.nih.gov/pubmed/22366317 Zakeri et al., 2012]]. In this system a peptide bond is formed between the side chains of two protein domains in an efficient manner. With this system it is not necessary to fuse effector proteins to a specific terminus of the receptor any more, it becomes possible to immobilize effector proteins which are active as multimeric proteins and it would also be possible to express a single receptor carrying a SpyCatcher domain at the outer side of the membrane which subsequently binds a set of different effector proteins which are secreted and become immobilized afterwards. Constructs were created for a His-tagged SypCatcher, a SypTag with a N-terminal or C-terminal SpyTag or with protein domains on both termini of the SpyTag. These constructs were produced recombinantly in ''E. coli'' and the proteins were then purified. Protein coupling experiments were performed and afterwards the formation of isopeptide bond was confirmed by pull-down experiments and in reducing SDS-PAGE. This system enables you as a potential user of our modular receptor to customize our receptor to any need an effector protein could have. Taken together all our intended localization BioBricks worked in ''Physcomitrella'' empowering the iGEM community to work creatively with Phsycomitrella as a chassis.<br />
<br />
==BioDegradation==<br />
[[File:TUM13_EreB_LCMS.png|thumb|right|350px|'''Figure 2''': Degradation of erythromycin by recombinant protein and our PhyscoFilter [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Erythromycin read more].]]<br />
Under the headline [https://2013.igem.org/Team:TU-Munich/Project/Biodegradation BioDegradation] we investigated effector proteins which degrade pollutants by enzymatic catalysis. For this purpose we introduced the new enzyme BioBrick Erythromycin Esterase (EreB) which degrades macrolide antibiotics. On the other hand we used well established BioBricks for BioDegradation. We improved the Laccase from Bacillus pumilus by converting it to RFC[25] in order to be able to integrate it into the extracellular portion of our receptor. Both enzymes were produced as recombinant proteins and were purified. Enzymatic characterization was carried out concerning substrate dependency, salt tolerance and pH dependency. For the laccase additionally the temperature dependency and the half-life was estimated in river water. All data was fitted in our enzyme kinetic modeling. The aim was to analyze these data and to provide a solid base for our filter calculator. This calculator uses all data produced in our enzyme characterization to extrapolate for the use of transgenic PhyscoFilter in waste water treatment plants or rivers. We assumed the secretory production of laccase by our moss as the laccase degrades a wide variety of important pollutants such as the pain killer diclofenac, the oral contraceptive ethinylestradiol or iodined x-ray contrast media which are all present in nature and are hardly degradable by conventional methods. From the [https://2013.igem.org/Team:TU-Munich/Modeling/Filter modeling with this calculator] we learned that factor such as the degree of pollution of a river, the average temperature in a specific country, the enzyme half-life as well as the actual amount of secreted protein play an important role for the efficacy of our PhyscoFilter. Generally the results show that approximately an area of 20 football field would be required to produce enough laccase to reduce the contamination of a river with the mentioned pharmaceutical compounds. Beside this result we also produced several different stable transgenic moss lines for our BioDegradation module and could show that our cytoplasmatically expressed Erythromycin Esterase B enables our moss to degrade the macrolide antibiotic Erythromycin which is normally only degraded poorly. This experiment was measured with mass spectrometry coupled to liquid chromatography (LC-MS) and worked for the recombinant protein as well as for the transgenic plant giving the proof of principle for ''Physcomirella'' as a bioremediation organism.<br />
<br />
==BioAccumulation==<br />
<html><center><iframe style="box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.2);padding: 5px;margin: 5px;background-color: white;" src="http://player.vimeo.com/video/77974681" width="400" height="255" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe></center></html> <br><br />
Beside the enzymatic degradation of pollutants we found different methods to bind pollutants to our moss filter which we called [https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation]. The most obvious idea was to use binding proteins which are developed for human therapy such as antibodies for example. To investigate this idea we used an alternative binding protein (Anticalin) engineered to bind fluorescein as it has a very high affinity, a small size and a robust fold [[http://www.ncbi.nlm.nih.gov/pubmed/16307475 Vopel et al., 2005]]. Beside this engineered binding protein we also found the idea of [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration%20with%20Dundee%20iGEM%20team%202013 Dundee iGEM 2013] quite interesting to use the protein which is affected in the toxicity mechanism of microcystein and to use it as a binding partner which then absorbs the pollutant from the water. Thus we [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration%20with%20Dundee%20iGEM%20team%202013 contacted Dundee iGEM], told them about our idea of an collaboration, got their BioBrick sent, converted it to RFC[25], assembled it into our modular receptor and finally transformed and selected stable transfected moss lines which we characterized finally. Basically the limitation of BioAccumulation applications is that they only can bind one pollutant per binding protein and thus an extremely high number of binding proteins is required to achieve a reduction of environmental pollutants. We transformed and selected transgenic moss lines with all three effector proteins and checked the cellular localization of these proteins using light microscopy. For the moss lines with a receptor harboring an Anticalin which binds fluorescein a [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Fluorescein membrane bound localization could be confirmed] whereas the moss lines with a receptor carrying the protein phosphatase 1 (PP1) from our collaboration partner Dundee showed a [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Microcystin localization in cytosolic vesicles] and not on the membrane. This is in good agreement with the result presented by Dundee that the SEC-pathway secretion is not working for this BioBrick. This might be because of surface exposed cystein residues which tend to aggregation in the oxidizing milieu, therefore it would be necessary to perform protein engineering to exchange these cystein residues for other amino acid residues in order to increase the stability of this protein.<br />
<br />
==Kill-Switch==<br />
Safety is one of the most important issues in synthetic biology and we therefore implemented a kill switch into our project. For us it was important to use a trigger which is ubiquitously present in the environment and no action of humans is required. We therefore developed a light-triggered kill switch. With this system the transgenic moss could be cultivated under blue filter foil. As long as the moss grows under this blue foil no red light reaches the moss and the moss stays alive. As soon as the moss escapes from this protected environment the red light is present and the kill switch becomes triggered. The system was modularized into a sensor module and a suicide module. The sensor domain consists of a splitted TEV protease which is attached to either PhyB or PIF. The later two proteins dimerized when red light is present and therefore lead to the reconstitution of the TEV protease. The suicide module consists of nuclease which is localized at the cellular membrane by a linker which contains a nuclear localization signal (NLS) and a TEV cleavage site. As soon as the sensor module is reconstituted by red light, the TEV protease cleaves its cleavage site inside the suicide module. Thereby the nuclease is liberated, becomes transported to the nucleus because of the nuclear localization signal and fragments the genome. The choice to use a nuclease instead of siRNA for example was driven by our modeling in which we found the siRNA suicide module to be less effective as there is a negative feedback loop which avoids the efficient killing of moss cells. <br />
We have transformed moss cells with this kill switch and have protected the resulting cells by the blue foil mentioned before. When we opened the blue foil after the selection process, all moss cells were dead. This can be explained by a drastically reduced transformation efficacy as the kill switch DNA was >10 kDa or by the fact that the kill switch is reliably killing the cells even without a trigger. In order to test the sensor module in vitro we have produced the two fusion proteins in vitro as recombinant proteins and have attempted to purify them which was not successful as the proteins are most probably not stable in vitro. Although we only had a single shot to test our kill switch in ''Physcomitrella'' we have discussed by far more about this system compared to the other parts of our project that worked very well in first experiments. During these discussions on our kill switch we have learned a lot about this system and we described these findings in order to help subsequent iGEM teams which are aiming to design a comparable kill switch.<br />
<br />
==Implementation==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|400px|'''Figure 3''': Remediation rafts in front of the MIT]]<br />
Projects in iGEM must not stop at the lab door and therefore it is immensely important to think about technical solutions to implement the transgenic organisms in order to show highest efficacy. For this reason we convinced experts like Prof. Dr. Posten to join our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews#Expert_Counsel:_An_overview advisery board] and have evaluated different cultivation methods for moss such as closed tube reactors, open pond reactors and floating remediation rafts. We came to the conclusion that in the case of immobilized effector proteins an open pond or closed tube reactor will be the superior technology as the degradation requires a close contact between the moss and a the pollutant to degrade. As a second possibility we evaluated the secretion of effector proteins such as laccase, which would then be implemented best on floating remediation rafts which are cheap to produce, mobile and could also be applied in third world countries. PhyscoFilter moss could be grown on these rafts and would secrete recombinant protein which then is liberated and can degrade pollutants in the environment. For all these cultivation methods we built model reactors, tried the cultivation of moss within them and tested the flow characteristics of the systems. For the triangular remediation raft we constructed a life-size prototype which costed only US$ 70. Additionally we developed a measurement device based on an [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device Arduino microcontroller] which measures environmental parameters, sends the data via WiFi to a webserver from where the actual data can be monitored with any smart phone or computer at any place in the world. To get an idea how such remediation rafts could look like on our rivers, we [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration_with_Op.N talked to architects] and also rendered an 3D-CAD-model in front of the MIT (see figure 3).<br />
<br />
==The iGEM Community==<br />
It is really amazing to see how the iGEM community advanced over the last years and we also invested some effort to advance the iGEM community. We programed a software tool which translates protein coding BioBricks in the registry to amino acid sequences, calculates various parameters and does alignments with various data banks. In the end all collected information for a BioBrick is collected in a standardized table which can easily be integrated into the part description of a BioBricks. We submitted a RFC for this [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator] which obtained the number RFC[96].<br><br />
Beside this software toll we have written tutorials on wiki programming, creation of animated gifs of protein structures and the usage of Arduino microcontrollers for iGEM projects.<br />
<br />
==References:==<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/16307475 Vopel et al., 2005]] Vopel S, Mühlbach H, Skerra A. (2005) Rational engineering of a fluorescein-binding anticalin for improved ligand affinity. ''Biol. Chem.'', 386(11):1097-104.<br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/22366317 Zakeri et al., 2012]] Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M. (2012). Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. ''Proc Natl Acad Sci U S A''. 20;109(12)<br><br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/SummaryTeam:TU-Munich/Results/Summary2013-10-29T02:04:43Z<p>PSchneider: /* Implementation */</p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
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==Our Project for this summer: Remediation.==<br />
<html><center><iframe style="box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.2);padding: 5px;margin: 5px;background-color: white;" src="http://player.vimeo.com/video/76195786" width="400" height="240" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe></center></html> <br><br />
During this summer we wanted to work on an iGEM project, which has the potential to become a real world application, since we believe that it is an important step for Synthetic Biology to provide alternative solutions for global problems. For this reason we focused on Bioremediation: The use of organisms to remove emissions caused by humans and bring the environment back to its natural state. As water is a resource which is absolutely essential for all living organisms, we decided to focus on the pollution of aquatic ecosystems.<br />
<br />
==Choice of the appropriate chassis for a water filter==<br />
Remediation is not new to iGEM, in fact it is a topic the iGEM community has worked on for nearly 10 years now. Therefore a set of promising BioBricks were already available in the Parts Registry, which we wanted to use in order to increase the knowledge on these effector proteins. Having found suitable effector proteins, we discussed about the most suitable chassis for our application. Most of the previous projects on Bioremediation were based on ''E. coli'', whereas we decided to use a plant instead. Photosynthesis carried out by the plants will allow the water filter to maintain and renew itself without the addition of any nutrients. We considered algae such as ''Chlamydomonas reinhardtii'', Bryophytes such as ''Physcomitrella patens'' and higher plants like ''Arabidopsis thaliana''. In the end ''Physcomitrella patens'' was the chassis of choice as it already grows in a filter-like structure and can be cultivated in terrestric as well as in aquatic conditions. Additionally it is a well established organism in biotechnology. Working with ''Physcomitrella patens'' is not easy considering the 1-2 months it takes from the transformation process to the experiments with stable transfected plants and the doubling times of 3-6 days. As nobody at the TU Munich works with the moss ''Physcomitrella patens'', we looked for an expert and found Prof. Reski who occupies a professorship at Freiburg University. We were very happy to gain him as an advisor during our project. For the use of ''Physcomitrella patens'' in iGEM we created a strong constitutive promoter ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159306 BBa_K1159306]), a plant terminator ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159307 BBa_K1159307]) and an antibiotic selection marker ([http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159308 BBa_K1159308]), which were all used to transform and select 21 different transgenic moss lines.<br />
<br />
==Localization of effector proteins==<br />
[[File:Localization_general.jpg|thumb|right|500px|'''Figure 1:''' Cytosolic protein expression and our modularized receptor for ''Physcomitrella'' work as expected.]]<br />
The actual remediation of pollutants is accomplished by effector proteins which function with quite different mechanisms. Thus it was important to enable the localization of effector proteins at different cellular sites. Cytosolic effector proteins are easily expressed, whereas for secretion a signal peptide BioBrick is cloned ahead of the effector protein. Several receptor signal peptides from ''Physcomitrella patens'' and other organisms were analyzed by using [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions bioinformatics tools]. The signal peptide of the Somatic Embryogenesis Receptor-like Kinase (SERK) from ''Physcomitrella patens''and the IgK signal peptide from ''Mus musculus'', which is described in literature to function in ''Physcomitrella'', were chosen. The secretion of a newly introduced luciferase with both of these signal peptides was investigated for 8 clones each. No detectable secretion for the IgKappa but a high secretion rate for the SERK signal peptide was shown. Successful secretion could be achieved using the SERK signal peptide. Because the secreted effector proteins are not attached to the moss cell, they diffuse into the water, which is suboptimal, for example if you want to remove pollutants by simply binding them. Therefore we designed a modular receptor for ''Physcomitrella'', which can carry effector proteins at the outer side of the cell membrane. For this purpose [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions bioinformatics methods] were used again and the SERK transmembrane domain was chosen to be the best one. A receptor composed of (1) the SERK signal peptide, (2) an extracellularly located effector protein, (3) a linker with a Strep-tag II and a TEV protease cleavage site, (4) the SERK transmembrane domain, (5) a short linker domain and (6) a green fluorescent protein were assembled using the RFC[25] standard. This highly modular receptor was successfully transformed into ''Physcomitrella patens'' and stable cell lines were selected. These stable cell lines were used for experiments. The localization of the membrane-bound GFP could be detected clearly on the surface of the moss cells (see figure 1), whereas expressing GFP cytosolically in the moss, showed a uniform fluorescence over the whole cell. Further we incubated the moss cells with recombinant TEV protease, which diffused through the cell wall, cleaved the TEV site within the extracellular domain of the receptor and liberated the NanoLuc luciferase. The luciferase assay of the supernatant at the beginning of this incubation and after 16 hours showed a dramatic increase in luminescence, which is an evidence that our modular receptor is located in the membrane and - even better - in the right orientation, exposed to the extracellular space. Beyond the possibility to locate an effector protein in the extracellular part of the receptor, we thought about further applications and found the SypCatcher-SpyTag System to be a perfect tool for our needs [[http://www.ncbi.nlm.nih.gov/pubmed/22366317 Zakeri et al., 2012]]. In this system a peptide bond is formed between the side chains of two protein domains in an efficient manner. With this system it is not necessary to fuse effector proteins to a specific terminus of the receptor any more, it becomes possible to immobilize effector proteins which are active as multimeric proteins and it would also be possible to express a single receptor carrying a SpyCatcher domain at the outer side of the membrane which subsequently binds a set of different effector proteins which are secreted and become immobilized afterwards. Constructs were created for a His-tagged SypCatcher, a SypTag with a N-terminal or C-terminal SpyTag or with protein domains on both termini of the SpyTag. These constructs were produced recombinantly in ''E. coli'' and the proteins were then purified. Protein coupling experiments were performed and afterwards the formation of isopeptide bond was confirmed by pull-down experiments and in reducing SDS-PAGE. This system enables you as a potential user of our modular receptor to customize our receptor to any need an effector protein could have. Taken together all our intended localization BioBricks worked in ''Physcomitrella'' empowering the iGEM community to work creatively with Phsycomitrella as a chassis.<br />
<br />
==BioDegradation==<br />
[[File:TUM13_EreB_LCMS.png|thumb|right|350px|'''Figure 2''': Degradation of erythromycin by recombinant protein and our PhyscoFilter [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Erythromycin read more].]]<br />
Under the headline [https://2013.igem.org/Team:TU-Munich/Project/Biodegradation BioDegradation] we investigated effector proteins which degrade pollutants by enzymatic catalysis. For this purpose we introduced the new enzyme BioBrick Erythromycin Esterase (EreB) which degrades macrolide antibiotics. On the other hand we used well established BioBricks for BioDegradation. We improved the Laccase from Bacillus pumilus by converting it to RFC[25] in order to be able to integrate it into the extracellular portion of our receptor. Both enzymes were produced as recombinant proteins and were purified. Enzymatic characterization was carried out concerning substrate dependency, salt tolerance and pH dependency. For the laccase additionally the temperature dependency and the half-life was estimated in river water. All data was fitted in our enzyme kinetic modeling. The aim was to analyze these data and to provide a solid base for our filter calculator. This calculator uses all data produced in our enzyme characterization to extrapolate for the use of transgenic PhyscoFilter in waste water treatment plants or rivers. We assumed the secretory production of laccase by our moss as the laccase degrades a wide variety of important pollutants such as the pain killer diclofenac, the oral contraceptive ethinylestradiol or iodined x-ray contrast media which are all present in nature and are hardly degradable by conventional methods. From the [https://2013.igem.org/Team:TU-Munich/Modeling/Filter modeling with this calculator] we learned that factor such as the degree of pollution of a river, the average temperature in a specific country, the enzyme half-life as well as the actual amount of secreted protein play an important role for the efficacy of our PhyscoFilter. Generally the results show that approximately an area of 20 football field would be required to produce enough laccase to reduce the contamination of a river with the mentioned pharmaceutical compounds. Beside this result we also produced several different stable transgenic moss lines for our BioDegradation module and could show that our cytoplasmatically expressed Erythromycin Esterase B enables our moss to degrade the macrolide antibiotic Erythromycin which is normally only degraded poorly. This experiment was measured with mass spectrometry coupled to liquid chromatography (LC-MS) and worked for the recombinant protein as well as for the transgenic plant giving the proof of principle for ''Physcomirella'' as a bioremediation organism.<br />
<br />
==BioAccumulation==<br />
<html><center><iframe style="box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.2);padding: 5px;margin: 5px;background-color: white;" src="http://player.vimeo.com/video/77974681" width="400" height="255" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe></center></html> <br><br />
Beside the enzymatic degradation of pollutants we found different methods to bind pollutants to our moss filter which we called [https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation]. The most obvious idea was to use binding proteins which are developed for human therapy such as antibodies for example. To investigate this idea we used an alternative binding protein (Anticalin) engineered to bind fluorescein as it has a very high affinity, a small size and a robust fold [[http://www.ncbi.nlm.nih.gov/pubmed/16307475 Vopel et al., 2005]]. Beside this engineered binding protein we also found the idea of [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration%20with%20Dundee%20iGEM%20team%202013 Dundee iGEM 2013] quite interesting to use the protein which is affected in the toxicity mechanism of microcystein and to use it as a binding partner which then absorbs the pollutant from the water. Thus we [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration%20with%20Dundee%20iGEM%20team%202013 contacted Dundee iGEM], told them about our idea of an collaboration, got their BioBrick sent, converted it to RFC[25], assembled it into our modular receptor and finally transformed and selected stable transfected moss lines which we characterized finally. Basically the limitation of BioAccumulation applications is that they only can bind one pollutant per binding protein and thus an extremely high number of binding proteins is required to achieve a reduction of environmental pollutants. We transformed and selected transgenic moss lines with all three effector proteins and checked the cellular localization of these proteins using light microscopy. For the moss lines with a receptor harboring an Anticalin which binds fluorescein a [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Fluorescein membrane bound localization could be confirmed] whereas the moss lines with a receptor carrying the protein phosphatase 1 (PP1) from our collaboration partner Dundee showed a [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss#The_PhyscoFilter_for_Microcystin localization in cytosolic vesicles] and not on the membrane. This is in good agreement with the result presented by Dundee that the SEC-pathway secretion is not working for this BioBrick. This might be because of surface exposed cystein residues which tend to aggregation in the oxidizing milieu, therefore it would be necessary to perform protein engineering to exchange these cystein residues for other amino acid residues in order to increase the stability of this protein.<br />
<br />
==Kill-Switch==<br />
Safety is one of the most important issues in synthetic biology and we therefore implemented a kill switch into our project. For us it was important to use a trigger which is ubiquitously present in the environment and no action of humans is required. We therefore developed a light-triggered kill switch. With this system the transgenic moss could be cultivated under blue filter foil. As long as the moss grows under this blue foil no red light reaches the moss and the moss stays alive. As soon as the moss escapes from this protected environment the red light is present and the kill switch becomes triggered. The system was modularized into a sensor module and a suicide module. The sensor domain consists of a splitted TEV protease which is attached to either PhyB or PIF. The later two proteins dimerized when red light is present and therefore lead to the reconstitution of the TEV protease. The suicide module consists of nuclease which is localized at the cellular membrane by a linker which contains a nuclear localization signal (NLS) and a TEV cleavage site. As soon as the sensor module is reconstituted by red light, the TEV protease cleaves its cleavage site inside the suicide module. Thereby the nuclease is liberated, becomes transported to the nucleus because of the nuclear localization signal and fragments the genome. The choice to use a nuclease instead of siRNA for example was driven by our modeling in which we found the siRNA suicide module to be less effective as there is a negative feedback loop which avoids the efficient killing of moss cells. <br />
We have transformed moss cells with this kill switch and have protected the resulting cells by the blue foil mentioned before. When we opened the blue foil after the selection process, all moss cells were dead. This can be explained by a drastically reduced transformation efficacy as the kill switch DNA was >10 kDa or by the fact that the kill switch is reliably killing the cells even without a trigger. In order to test the sensor module in vitro we have produced the two fusion proteins in vitro as recombinant proteins and have attempted to purify them which was not successful as the proteins are most probably not stable in vitro. Although we only had a single shot to test our kill switch in ''Physcomitrella'' we have discussed by far more about this system compared to the other parts of our project that worked very well in first experiments. During these discussions on our kill switch we have learned a lot about this system and we described these findings in order to help subsequent iGEM teams which are aiming to design a comparable kill switch.<br />
<br />
==Implementation==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|400px|'''Figure 3''': Remediation rafts in front of the MIT]]<br />
Projects in iGEM must not stop at the lab door and therefore it is immensely important to think about technical solutions to implement the transgenic organisms in order to show highest efficacy. For this reason we convinced experts like Prof. Dr. Posten to join our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews#Expert_Counsel:_An_overview advisery board] and have evaluated different cultivation methods for moss such as closed tube reactors, open pond reactors and floating remediation rafts. We came to the conclusion that in the case of immobilized effector proteins an open pond or closed tube reactor will be the superior technology as the degradation requires a close contact between the moss and a the pollutant to degrade. As a second possibility we evaluated the secretion of effector proteins such as laccase, which would then be implemented best on floating remediation rafts which are cheap to produce, mobile and could also be applied in third world countries. PhyscoFilter moss could be grown on these rafts and would secrete recombinant protein which then is liberated and can degrade pollutants in the environment. For all these cultivation methods we built model reactors, tried the cultivation of moss within them and tested the flow characteristics of the systems. For the triangular remediation raft we constructed a life-size prototype which costed only US$ 70. Additionally we developed a measurement device based on an [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device Arduino microcontroller] which measures environmental parameters, sends the data via WiFi to a webserver from where the actual data can be monitored with any smart phone or computer at any place in the world. To get an idea how such remediation rafts could look like on our rivers we [https://2013.igem.org/Team:TU-Munich/Team/Collaborations#Collaboration_with_Op.N talked to architects] and also rendered an 3D-CAD-model in front of the MIT (see figure 3).<br />
<br />
==The iGEM Community==<br />
It is really amazing to see how the iGEM community advanced over the last years and we also invested some effort to advance the iGEM community. We programed a software tool which translates protein coding BioBricks in the registry to amino acid sequences, calculates various parameters and does alignments with various data banks. In the end all collected information for a BioBrick is collected in a standardized table which can easily be integrated into the part description of a BioBricks. We submitted a RFC for this [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator] which obtained the number RFC[96].<br><br />
Beside this software toll we have written tutorials on wiki programming, creation of animated gifs of protein structures and the usage of Arduino microcontrollers for iGEM projects.<br />
<br />
==References:==<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/16307475 Vopel et al., 2005]] Vopel S, Mühlbach H, Skerra A. (2005) Rational engineering of a fluorescein-binding anticalin for improved ligand affinity. ''Biol. Chem.'', 386(11):1097-104.<br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/22366317 Zakeri et al., 2012]] Zakeri B, Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M. (2012). Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. ''Proc Natl Acad Sci U S A''. 20;109(12)<br><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/How_ToTeam:TU-Munich/Results/How To2013-10-29T01:21:19Z<p>PSchneider: /* Code */</p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
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==Our Tutorials==<br />
During our iGEM summer we have acquired many skills which are useful for iGEMers and for every synthetic biologist. In order to spread this knowledge we created some tutorials. We hope that these tutorials enable future iGEM teams to present their project in a more colorful fashion.<br />
<br />
== Wiki Tips & Tricks ==<br />
<br />
Below is a list of iGEM wiki related tips and tutorials for future teams.<br />
<br />
=== Picture viewer ===<br />
<br />
Maybe you have not noticed it yet, but if you clicked any of the pictures on our wiki, you were not redirected to the ugly wiki page of the file. Instead a nice picture viewer opened and after you closed it, you did not have to go back to the site you saw the picture on. To get the same effect on your wiki follow the steps listed below:<br />
<br />
* '''Get the files!'''<br />We modified the original slimbox 2 viewer to work with the wiki and to not exceed the browser viewport, so it is recommended to use our versions, which can be found at [[Team:TU-Munich/TUM13_slimbox2.css]] and [[Team:TU-Munich/TUM13_slimbox2.js]].<br />
* '''Embed the files in your wiki!'''<br />The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the picture viewer.<br />
* '''Include the autoload code block!'''<br />A bit of JavaScript code that attaches the viewer to the right pictures needs to be executed on all the pages that use it. This code attaches the picture viewer to all images on the page which are embedded with the <code><nowiki>[[File:xxx.png|thumb|caption]]</nowiki></code> wiki code and it adds the corresponding caption to the viewer.<br />
<nowiki>$(document).ready(function(){<br />
$("div.thumbinner > a img").slimbox({/* Put custom options here */}, function(el) {<br />
url = el.src;<br />
if (url.indexOf('thumb') != -1) {<br />
url = url.substring(0, url.lastIndexOf('/'));<br />
url = url.replace('/thumb/', '/');<br />
}<br />
description = $(el).parents("div.thumbinner").children("div.thumbcaption").text();<br />
return [url, description];<br />
}, function(el) {<br />
return (this == el);<br />
});<br />
});</nowiki><br />
* '''Test it!'''<br />Below is an example picture, click on it to see what the picture viewer looks like.<br />
[[File:TUM13_physco-logo.png|thumb|center|350px|'''Figure 1:''' The logo of our project.]]<br />
<br />
=== Slideshow ===<br />
<br />
To create a good looking slideshow just follow the instructions below:<br />
<br />
* '''Get the files!'''<br />You can get the Stylesheet and Javascript for the slideshow either from [http://bxslider.com/ bxSlider] or from our wiki: [[Team:TU-Munich/TUM13_bxslider.css]] and [[Team:TU-Munich/TUM13_bxslider.js]].<br />
<br />
* '''Embed the files in your wiki!'''<br />The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the slideshow.<br />
<br />
* '''Include the initializing code block!'''<br />A bit of JavaScript code that activates the slideshow needs to be executed on all the pages that use it. This code changes all unordered lists of the class bxslider into slideshows.<br />
<nowiki>$(document).ready(function(){<br />
$('.bxslider').bxSlider({<br />
responsive: false,<br />
auto: true,<br />
autoHover: true<br />
});<br />
});</nowiki><br />
<br />
* '''Add the slideshow to the page!'''<br />To add a slideshow just put the pictures you want to include in an unordered list like shown below:<br />
<nowiki><html><br />
<ul class="bxslider"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li><br />
</ul><br />
</html></nowiki><br />
<br />
* '''Test it!'''<br />Below is an example of the slideshow.<br />
<br />
<html><br />
<ul class="bxslider"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li><br />
</ul><br />
</html><br />
<br />
==Generation of Rotating Protein Structures==<br />
Animated gifs of rotating protein structures have been used for some time in the iGEM competition. Here we present an easy to reproduce tutorial for iGEMers which are interested in similar images.<br />
*If there is no PDB file available for your protein of interest, you can use a homology search to find the most homologous structure. A good homology search tool is [http://toolkit.tuebingen.mpg.de/hhpred HHpred].<br />
*The entry for the best matching structure was used for the figure. If it is only a homologous structure please cite this together with the homology when presenting the resulting image.<br />
*You can save the PDB file of the homologous structure on your computer.<br />
*If you do not have [http://www.pymol.org/ PyMol] (freeware) installed on your computer download and install it.<br />
*Start PyMol software and open the PDB file by clicking File -> Open.<br />
*The following approach was adapted from a PyMol tutorial [[http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong]].<br />
*The following commands were entered into the command line:<br />
<code><br />
PyMOL> orient<br><br />
PyMOL> hide everything, all<br><br />
PyMOL> show cartoon, all<br><br />
PyMol> bg_color white<br><br />
click> Settings>Rendering>Shadows>Occlusion<br><br />
PyMOL> color purple, ss h; color yellow, ss s; color green, ss ""<br><br />
PyMOL> show surface, all<br><br />
PyMOL> set transparency, 0.75<br><br />
PyMOL> set surface_quality, 1 (command will prolongue the process significantly, you may skip it)<br> <br />
PyMOL> set ray_trace_frames=1 (command will prolongue the process significantly, you may skip it)<br> <br />
PyMOL> mset 1 x180<br><br />
PyMOL> util.mroll 1,180<br><br />
PyMOL> mpng frame<br><br />
</code><br />
*Afterwards the *.png files were automatically converted to *.tif files using [http://www.xnview.com/de/xnconvert/ XnConvert].<br />
*The program [http://www.animake.de/gif-animation.htm Animake] was used to generate the annimated gifs.<br />
**The Animake software was started<br />
**A new working folder was generated (File -> New) and the *.tif files were imported (Edit -> Import_from_file)<br />
**The background was set to white (Animation -> Settings)<br />
**The range of colors was set to 256 (Edit -> Select_all and Edit -> Change_Color)<br />
**The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit -> Change_size. We suggest a size of 320x240 px or even smaller if the resulting gif becomes to big.<br />
**Finally the animated gif can be saved in the program format (.abp) and as gif (File -> Save_as)<br />
**If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)<br />
<center>This is how your protein of interest could look like:</center><br />
<br />
[[File:TUM13_Annimated_test.gif|thumb|center|320px|'''Figure 2:''' Protein]]<br />
<br />
==Setting up a basic Arduino measuring device==<br />
===Introduction===<br />
[[File:TUM13_Arduino_Assembly_Animation.gif|thumb|left|400px|'''Figure 3:''' Assembly Order]]<br />
<br />
Since the Arduino Due was released in autumn 2012, this is the first iGEM year this '''very powerful''' device can be used. We found it a useful '''supervising tool''' for short and long-term experiments. It can be used in as well as outside the lab. The improvements that were made from Uno to Due are considerable.<br />
<br />
It is capable of handling many things at once, such as a WiFi shield, a display, a SD-Card and multiple sensors.<br />
At this point the Uno did not match up any longer. <br />
<br />
To establish the usage of Arduino in iGEM even more we want to share our experiences and help you building up a '''basic device''' that can '''collect''' and '''view sensor data''' on its '''display''' and '''upload''' them to a server.<br />
<br />
===Part Description===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/0e/TUM13_Arduino_Due.png" alt="Figure 4: Arduino Due" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/5/58/Arduino_WiFi.png" alt="Figure 5: Arduino WiFi Shield" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/e7/Arduino_Mega_MSD.png" alt="Figure 6: Mega MSD Shield" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/d/de/Arduino_MI0283.png" alt="Figure 7: MI0283 Display" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/Arduino_Tsl2561.png" alt="Figure 8: TSL2561 light sensor" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a5/Arduino_Tsl2561_Curve.png" alt="Figure 9: TSL2561 absorption curve" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/3d/Arduino_Watersensor.png" alt="Figure 10: Water sensor" /></li><br />
</ul><br />
</div><br />
</html><br />
====Arduino Due====<br />
<br />
The Arduino Due is the most powerful Arduino board. Its underlying 32bit-processor is the Atmel SAM3X8E. <br />
Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficient.<br />
It was released in October 2012.<br />
<br />
'''Data:'''<br />
<br />
84 Mhz CPU Clock<br />
96 KBytes of SRAM.<br />
512 KBytes of Flash memory. <br />
54 Digital I/O Pins<br />
12 Analog Input Pins<br />
2 (DAC)Analog Outputs Pins<br />
<br />
====Arduino WiFi Shield====<br />
<br />
The Arduino WiFi Shield is an attachable shield that provides Wireless LAN 802.11b/g to the Arduino. <br />
It scans and connects to networks and opens TCP and UDP sockets for data transfer. It also supports WEP and WPA2 encryption. It was released in August 2012.<br />
The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi library. <br />
There is also an on-board SD-card socket to store received data. <br />
As the SD-card is accessible separately, it can also be used as a storage for any data generated by the Arduino.<br />
The SD-card socket is also supported by a stock library. The communication between Arduino Due and the WiFi Shield runs via an SPI/ICSP interface.<br />
<br />
'''Pin usage:'''<br />
Pin 4 SS for SD card (Slave Select)<br />
Pin 7 Handshake between Arduino and WiFi Shield<br />
Pin 10 SS for WiFi<br />
Pin 74 SPI MISO (Master in, Slave out)<br />
Pin 75 SPI MOSI (Master out, Slave in)<br />
Pin 76 SPI SCK (Serial clock)<br />
gnd<br />
3.3V<br />
5V<br />
<br />
====Watterott Mega MSD-Shield====<br />
<br />
The Mega MSD-Shield was designed by Watterott and consists of a couple of components. <br />
The components are one real time clock, one SD-card socket (we will not use), a small battery and a socket for a touch display.<br />
To get it ready to run, the shield must be assembled. The stackable headers and the clock's quartz must be soldered to the board and the battery must be inserted.<br />
Unluckily the Mega MSD-Shield and therefore also the MI0283QT-9 touch display don't come with a working library for the Arduino Due. The existing library only supports all boards up to the Arduino Uno.<br />
Therefore all libraries had to be rewritten.<br />
The touch display and the SD-card slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmits its data via I²C.<br />
<br />
'''Pin usage:'''<br />
Pin 4 SS for SD card<br />
Pin 6 SS for the touch of the touch display<br />
Pin 8 reset LCD<br />
Pin 9 LCD LED<br />
Pin 20 RTC (real time clock) I²C SDA (Serial Data Line)<br />
Pin 21 RTC I²C SCL (Serial Clock)<br />
Pin 25 SS (7) for the LCD (Workarround of the double usage of pin 7 by the WIFI Shield)<br />
Pin 50 SPI MISO<br />
Pin 51 SPI MOSI<br />
Pin 52 SPI SCK<br />
gnd<br />
3.3V<br />
<br />
====Display MI0283QT-9====<br />
<br />
The MI0283QT-9 is a multicolor touch display. It comes already attached to a board, where only the pin headers are left to be soldered.<br />
Once assembled it can easily be plugged into the Mega MSD-Shield. It has an on-board touch controller (TI ADS7846).<br />
The display size is 2.83"(43.2 x 57.6mm) with a resolution of 240x320. It supports 262k colors. <br />
The pin usage is already considered in the Mega MSD-Shield description.<br />
<br />
====Light Sensor TSL2561====<br />
<br />
The light sensor is a small, so called, breakout board. It is usually connected by wires instead of directly plugged into the Arduino's headers.<br />
The light sensor has two photo diodes on-board that measure visible and infrared light. Similar to the RTC, the TSL2561 is addressed via I²C.<br />
Once you get the I²C library working on your Arduino Due working it takes only little effort to integrate additional I²C devices.<br />
Just very few lines of the library have to be rewritten here.<br />
The photo diodes can be addressed separately or both at one. Their output is already converted to Lux.<br />
<br />
'''Pin usage:'''<br />
<br />
Pin 20 TSL2561 I²C SDA (Serial Data Line)<br />
Pin 21 TSL2561 I²C SCL (Serial Clock)<br />
gnd<br />
3.3V<br />
<br />
====Temperature Sensor DS18B20====<br />
<br />
The temperature sensor is embedded into a water proof cable. It is addressed via a OneWire interface. <br />
The provided data are digital raw data, which need to be converted into degree Celsius. Information about the conversion are given by the manufacturer.<br />
Similar to the I²C (TwoWire) bus, you only have to get the OneWire interface working once. After that, you can easily set up more OneWire devices.<br />
Again, just very few lines of the library have to be rewritten.<br />
<br />
'''Pin usage:'''<br />
<br />
Pin 14 One-Wire DS18B20 (pin was randomly chosen)<br />
Pin gnd<br />
Pin 3.3V<br />
<br />
====Water Sensor====<br />
<br />
Setting up the water sensor is very easy. If and how much water the sensor registered can be measured via an analog pin.<br />
<br />
'''pin usage:'''<br />
<br />
Pin A5 Water sensor<br />
gnd<br />
3.3V<br />
<br />
===Tools===<br />
*Breadboard<br />
*Soldering bolt<br />
*Solder<br />
<br />
===Assembly===<br />
<br />
<br />
Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code (e.g. red cable for 3.3V etc.) otherwise troubleshooting can get nasty.<br />
<br />
All '''steps''' you need to follow building up your own Arduino measuring device are '''explained below''' in the '''slide show''' and the image descriptions.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d7/TUM13_Arduiono_Assembly_1.png/350px-TUM13_Arduiono_Assembly_1.png" alt="Figure 11: Place your Arduino Due on your desk"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/c/c4/TUM13_Arduiono_Assembly_2.png/350px-TUM13_Arduiono_Assembly_2.png" alt="Figure 12: Connect ground and 3.3V to two different lines of you breadboard"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/2/21/TUM13_Arduiono_Assembly_3.png/350px-TUM13_Arduiono_Assembly_3.png" alt="Figure 13: Connect the light sensor's ground and the 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/9b/TUM13_Arduiono_Assembly_4.png/350px-TUM13_Arduiono_Assembly_4.png" alt="Figure 14: Connect the sda line of your light sensor to pin 20 and scl to pin 21"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/9c/TUM13_Arduiono_Assembly_5.png/350px-TUM13_Arduiono_Assembly_5.png" alt="Figure 15: Connect the temperature sensor's ground and the 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Arduiono_Assembly_6.png/350px-TUM13_Arduiono_Assembly_6.png" alt="Figure 16: Connect the signal line of your temp sensor via the breadbroad to pin 14" /></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/8/83/TUM13_Arduiono_Assembly_7.png/350px-TUM13_Arduiono_Assembly_7.png" alt="Figure 17: Place a ~50kOhm resistor between the 3.3V line and the temps sensor's signal line on your breadboard" /></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/b/b0/TUM13_Arduiono_Assembly_8.png/350px-TUM13_Arduiono_Assembly_8.png" alt="Figure 18: Connect the water sensor to the ground and 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/e/e4/TUM13_Arduiono_Assembly_9.png/350px-TUM13_Arduiono_Assembly_9.png" alt="Figure 19: Connect the signal line of your water sensor to pin A5"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/8/86/TUM13_Arduiono_Assembly_10.png/350px-TUM13_Arduiono_Assembly_10.png" alt="Figure 20: Voila! You are done with the basic connection of your three sensors. The next steps explain how to connect the WiFi shield, the msd shield and the display. You can connect all the sensors to the shield's and header's pins the same way, you connected them to the Arduino Due"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_11.png/350px-TUM13_Arduiono_Assembly_11.png" alt="Figure 21: First solder a short copper cable to the msd shield, connecting its pin 25 to pin 7"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/1/18/TUM13_Arduiono_Assembly_12.png/350px-TUM13_Arduiono_Assembly_12.png" alt="Figure 22: Then bend pin 7 and pin 4, so they don't connect to the WiFi shield's pins. Pin 4 would be a double usage of the msd shield's and the wifi shield's sd card. Pin 7 (lcd slave select) interferes with the wifi handshake pin"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/99/TUM13_Arduiono_Assembly_13.png/350px-TUM13_Arduiono_Assembly_13.png" alt="Figure 23: This is just an explanation of how the shield's sub-devices are connected. A deeper understanding of the following diagrams goes along with a deeper understanding of the program's source code and the additional libraries. All shields are of course connected to the Arduino Due's ground and 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/e/e8/TUM13_Arduiono_Assembly_14.png/350px-TUM13_Arduiono_Assembly_14.png" alt="Figure 24: The yellow link shows the spi interface between Arduino Due and the WiFi shield"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Arduiono_Assembly_15.png/350px-TUM13_Arduiono_Assembly_15.png" alt="Figure 25: The thinner yellow lines are the WiFi handshake and the wifi slave select connections"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_16.png/350px-TUM13_Arduiono_Assembly_16.png" alt="Figure 26: The blue link is the sd reader's slave select"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/6/6d/TUM13_Arduiono_Assembly_17.png/350px-TUM13_Arduiono_Assembly_17.png" <br />
alt="Figure 27: The green link represents the connection to the real time clock"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Arduiono_Assembly_18.png/350px-TUM13_Arduiono_Assembly_18.png" alt="Figure 28: The pink link represents the spi interface between the msd shield and the Arduino Due, required for the communication with the lcd and its touch functions (pins 50, 51 and pin 52)"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/4/4b/TUM13_Arduiono_Assembly_19.png/350px-TUM13_Arduiono_Assembly_19.png" alt="Figure 29: Lcd slave select, lcd reset and lcd LED"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Arduiono_Assembly_20.png/350px-TUM13_Arduiono_Assembly_20.png" alt="Figure 30: Lcd's touch slave select"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/5c/TUM13_Arduiono_Assembly_21.png/350px-TUM13_Arduiono_Assembly_21.png" alt="Figure 31: the power supply can be established with a 9V block battery"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ef/TUM13_Arduiono_Assembly_22.png/350px-TUM13_Arduiono_Assembly_22.png" alt="Figure 32: At last: an overview"/></li><br />
<br />
</ul><br />
</div><br />
</html><br />
[[File:TUM13_Arduino_in_action.gif|thumb|500px|left|'''Figure 33:''' Arduino in action]]<br />
For more explaining photos visit our [[#Arduino_photo_gallery|photo gallery]]. On the left you see the Arduino as it boots up, connects to a WiFi hotspot and collects data.<br />
<br />
===Code===<br />
<br />
We strongly recommend the usage of '''Microsoft Visual Studio''' with the '''"visual micro"''' plugin. Microsoft Intellisense helps you a lot, when you are unfamiliar with the manufacturer provided libraries (automatic code completion). In order to compile the code properly you need the latest beta version of [http://arduino.cc/en/Main/Software Arduino's software]. In the visual micro settings, choose the path to the Arduino IDE on your hard drive, also disable "Upload using programmer". In the settings of the Arduino IDE, select "use external software".<br />
<br />
Now you are ready to start programming. Below we share our code, feel free to use, edit and play around with it!<br />
But '''wait''' first you need our '''[[#Libraries|libraries]]'''! They're exclusively '''fitted''' to the Arduino Due, mostly based on the existing manufacturer's libraries for the Arduino Uno.<br />
<br />
Since Arduino released a new version of its IDE and software, and extended its support on the Arduino Due, we have rewritten our previews code. Both, the old and the new code can be found in our '''[https://github.com/VonAlphaBisZulu/IGEM_ARDUINO GitHub repo]'''.<br />
<br />
Assuming you followed our tutorial until here.<br />
Once you adapted the code to your WiFi and server settings and uploaded it to the Arduino it does the following:<br />
#it starts up and the '''screen''' stays black, but turns its lights on<br />
#if you have pressed the screen, the calibration process starts<br />
#it '''searches for networks''' and displays the total number of found networks on its screen<br />
#it displays some '''WiFi stations''' that were found<br />
#it tries to '''connect''' to the WiFi station you have set<br />
#if a connection was established it shows the '''Arduino's IP address''' and the SSID (name) of the WiFi it is connected to<br />
#then it idles until you you press the screen<br />
#after you pressed the screen it jumps to the '''"loop"-section''' of the code<br />
#it continuously runs and displays:<br />
##the current '''time'''<br />
##the '''temperature'''<br />
##the measured '''infrared''' and '''broadband light'''<br />
##the '''coordinates''' of the point you '''pressed''' on the screen<br />
#it builds up a '''connection to a server, calling a PHP script, passing on the collected data'''<br />
<br />
<nowiki><br />
#include "SPI.h" // SPI library (stock)<br />
#include "Wire.h" // TwoWire library (stock) sda-scl<br />
#include "RTClib.h" // Real time clock library (original library, slightly rewritten to fit the Due)<br />
#include "SPI.h"<br />
#include "MI0283QT9Due.h" // LCD library (quite much had to be rewritten). Pins were changed, usage of Software SPI... quite a mess but it works great<br />
#include "ADS7846Due.h" // Touch controller (same story as at the lcd library)<br />
#include "Adafruit_TSL2561.h" // light sensor library (had to be rewritten in some parts to fit the Due) functions were added to correct the lux-output that wasn't always correct with the stock library<br />
#include "OneWire.h" // OneWire (I don't know, but I guess it's the stock library)<br />
#include "avr/dtostrf.h" // optional library to workaround some compatibility problems with the Due<br />
#include "math.h" // standard C-maths library<br />
#include "SD.h" // SD reader (stock)<br />
#include "WiFi.h" // (stock)<br />
#include "time.h" // standard C-time library<br />
#include "math.h"<br />
<br />
#define ledW (11)<br />
#define ledR (12)<br />
#define ledG (13)<br />
#define Poti (A0)<br />
#define Button (A1)<br />
#define Temp (14)<br />
#define Wat (A5)<br />
<br />
#define shift8to32(a,b,c,d) (d << 24) | (c << 16) | (b << 8) | a<br />
#define shift8to16(a,b) (b << 8) | a<br />
<br />
MI0283QT9 lcd;<br />
ADS7846 tp;<br />
RTC_DS1307 rtc;<br />
OneWire tempsen(Temp);<br />
Adafruit_TSL2561 lightsen(TSL2561_ADDR_FLOAT,12345);<br />
File bitmap;<br />
WiFiClient client(0);<br />
<br />
float valueWater=0, valueTemp=0, valueLight=0, valueLightIR=0; // sensor values (avaredged)<br />
uint32_t valueTime=0,valueCounter[3]={0,0,0};<br />
uint16_t counter=1,potValue=0; // vlauecounter 0:Water 1:Temp 2:Light/IR<br />
uint8_t cursorY=1,cursorX=0;<br />
bool buttonValue=0,logging=0,wifiConnection,mossstatus=0,firstreceive=1;<br />
<br />
int waitForTap(){<br />
tp.service();<br />
while(tp.getPressure()==0) // Idle until the touchscreen is pressed to continue<br />
{<br />
delay(20);<br />
tp.service();<br />
if(digitalRead(Button)==0)<br />
return 1;<br />
}<br />
return 0;<br />
}<br />
<br />
void continueText(String drawtext, int cursY=cursorY-1, int cursX=cursorX,int maxlen=38){<br />
maxlen=maxlen-cursX;<br />
<br />
lcd.drawText(15+cursX*8,cursY*15,drawtext,1,COLOR_WHITE,COLOR_BLACK);<br />
<br />
cursorX=drawtext.length()+1;<br />
}<br />
<br />
void drawText(String drawtext="", int cursY=cursorY,int maxlen=38){<br />
continueText(drawtext,cursY,0);<br />
cursorY=cursY+1;<br />
}<br />
<br />
void OpenBMPFile(char *file, int16_t x, int16_t y)<br />
{<br />
uint8_t pad;<br />
uint8_t buf[54]; //read buf (min. size = sizeof(BMP_DIPHeader))<br />
int16_t width, height, w, h;<br />
<br />
if(!SD.exists(file))<br />
{<br />
Serial.println(String(file)+"not found");<br />
return;<br />
}<br />
else<br />
bitmap = SD.open(file, FILE_READ);<br />
if(!bitmap.available())<br />
{<br />
Serial.println("not reading image file");<br />
return;<br />
}<br />
else<br />
Serial.println("reading image file");<br />
<br />
//BMP Header<br />
for(int i=0;i<14;i++)<br />
{<br />
buf[i]=bitmap.read();<br />
}<br />
<br />
if((buf[0] == 'B') && (buf[1] == 'M') && (buf[10] == 54))<br />
{<br />
Serial.println("Bitmap recognized");<br />
//BMP DIP-Header<br />
for(int i=14;i<54;i++)<br />
buf[i]=bitmap.read();<br />
if(<br />
Serial.println(shift8to32(buf[14],buf[15],buf[16],buf[17]))&& // size<br />
Serial.println(shift8to16(buf[28],buf[29]))&& // bitspp<br />
Serial.println(shift8to32(buf[30],buf[31],buf[32],buf[33]))) // compress<br />
{<br />
Serial.println("DIP recognized");<br />
//BMP data (1. pixel = bottom left)<br />
width = shift8to32(buf[18],buf[19],buf[20],buf[21]); // width<br />
height = shift8to32(buf[22],buf[23],buf[24],buf[25]); // height<br />
pad = width % 4; //padding (line is multiply of 4)<br />
Serial.println("printing");<br />
if((x+width) <= lcd.getWidth() && (y+height) <= lcd.getHeight())<br />
{<br />
lcd.setArea(x, y, x+width-1, y+height-1);<br />
for(h=(y+height-1); h >= y; h--) //for every line<br />
{<br />
uint8_t pix[320][3];<br />
bitmap.read(pix,width*3);<br />
for(w=0; w < width; w++) //for every pixel in line<br />
{<br />
lcd.drawPixel(x+w, h, RGB(pix[w][2],pix[w][1],pix[w][0]));<br />
}<br />
if(pad)<br />
{<br />
bitmap.read(pix, pad);<br />
}<br />
}<br />
}<br />
else<br />
{<br />
lcd.drawTextPGM(x, y, PSTR("Pic out of screen!"), 1, RGB(0,0,0), RGB(255,255,255));<br />
}<br />
}<br />
}<br />
bitmap.close();<br />
}<br />
<br />
void initDisplay()<br />
{<br />
lcd.init();<br />
lcd.setOrientation(180);<br />
lcd.led(100);<br />
lcd.clear(COLOR_BLACK);<br />
}<br />
<br />
void initSD(){<br />
if (!SD.begin(4)) {<br />
continueText("failed");<br />
return;<br />
} else {<br />
continueText("succeeded");;<br />
}<br />
}<br />
<br />
void initLightSen() // initialize the light sensor<br />
{<br />
lightsen.setIntegrationTime(TSL2561_INTEGRATIONTIME_101MS);<br />
lightsen.enableAutoGain(true); <br />
lightsen.begin();<br />
}<br />
<br />
void initWiFi()<br />
{<br />
lcd.clear(COLOR_BLACK);<br />
cursorY=1;<br />
WiFi.disconnect();<br />
drawText("number of networks:");<br />
uint8_t nnet=WiFi.scanNetworks();<br />
continueText(String(nnet));<br />
for(int i=0;i<nnet;i++)<br />
drawText(WiFi.SSID(i));<br />
drawText();<br />
drawText("connecting to YOURWIFI..");<br />
for(int i=0;WL_CONNECTED!=WiFi.begin("YOURWIFI","yourpassword")&&i<3;i++)<br />
{<br />
WiFi.scanNetworks();<br />
drawText(String("connection failed ")+String(2-i)+String(" left.."));<br />
}<br />
if(WiFi.status()==WL_CONNECTED)<br />
{<br />
continueText(" succeeded");<br />
drawText("local IP address: "+String(WiFi.localIP()[0])+"."+String(WiFi.localIP()[1])+"."+String(WiFi.localIP()[2])+"."+String(WiFi.localIP()[3]));<br />
}<br />
else<br />
drawText("connection failed");<br />
logging=0;<br />
drawText();<br />
drawText("continue to data display & logging ..");<br />
waitForTap();<br />
lcd.clear(COLOR_BLACK);<br />
drawText("button: off",6);<br />
continueText("logging: off",1,25);<br />
String s="potentiometer: "+String((((float)analogRead(Poti))*0.0977517106549))+" ";<br />
drawText(s,7);<br />
}<br />
<br />
void updateTP(){<br />
tp.service();<br />
drawText("x: "+String(tp.getX())+" y: "+String(tp.getY())+" ",2);<br />
}<br />
<br />
void updateButtonAndPoti(){<br />
bool butv=(!digitalRead(Button));<br />
if(buttonValue!=butv)<br />
{<br />
if(wifiConnection==0)<br />
{<br />
initWiFi();<br />
counter=1;<br />
return;<br />
}<br />
if(butv)<br />
{<br />
logging=!logging;<br />
if(logging)<br />
{<br />
continueText("logging: on ",1,25);<br />
WiFiSend();<br />
counter=1;<br />
}<br />
else<br />
{<br />
continueText("logging: off",1,25);<br />
WiFiReceive();<br />
counter=1025;<br />
}<br />
}<br />
if(!butv)<br />
drawText("button: off",6);<br />
else<br />
drawText("button: on ",6);<br />
buttonValue=!buttonValue;<br />
}<br />
uint16_t potv=analogRead(Poti);<br />
if(potValue!=potv)<br />
{<br />
String s="potentiometer: "+String((((float)potv)*0.0977517106549))+" ";<br />
drawText(s,7);<br />
potValue=potv;<br />
}<br />
<br />
}<br />
<br />
void updateRTC() // update the time from the clock<br />
{<br />
DateTime tm=rtc.now();<br />
if(valueTime != tm.unixtime()) // Only refresh the values on the display if they changed (when the seconds value has changed since the last call)<br />
{<br />
char s[30];<br />
sprintf(s,"%02i:%02i:%02i %02i.%02i:%04i",tm.hour(),tm.minute(),tm.second(),tm.day(),tm.month(),tm.year());<br />
drawText(s,1);<br />
}<br />
valueTime = tm.unixtime();<br />
}<br />
<br />
void updateSenLight() // get current light values<br />
{<br />
uint16_t lsbroadband,lsinfrared; // definition<br />
float flsbroadband,flsinfrared;<br />
lightsen.getLuminosity(&lsbroadband,&lsinfrared); // the full function is implemented in the library<br />
flsbroadband=((float)lsbroadband*lightsen.getMultiplier());<br />
flsinfrared=((float)lsinfrared*lightsen.getMultiplier()); // getMultipier is a function I added. I believe the developers just missed something out in their lib<br />
valueLight=(((float)valueCounter[2]*valueLight)+(float)flsbroadband)/(float)(valueCounter[2]+1.0); // Calculate the avaredged values<br />
valueLightIR=(((float)valueCounter[2]*valueLightIR)+(float)flsinfrared)/(float)(valueCounter[2]+1.0);<br />
valueCounter[2]++;<br />
drawText(String("visible light: ")+String(flsbroadband,1)+" ",4);<br />
drawText(String("infrared light: ")+String(flsinfrared,1)+" ",5);<br />
float lratio=flsinfrared/flsbroadband;<br />
continueText(String("ratio: ")+String(lratio,4),5,25);<br />
uint8_t ledvw=-0.0000307574013*pow((double)log(flsbroadband)*25.5,3.0)+0.0117647055*pow((double)log(flsbroadband)*25.5,2.0);<br />
analogWrite(ledW,ledvw);<br />
uint8_t ledvr=-0.0000307574013*pow((lratio-0.2)*425.0,3.0)+0.0117647055*pow((lratio-0.2)*425.0,2.0);<br />
analogWrite(ledR,ledvr);<br />
uint8_t ledvg=-0.0000307574013*pow(255.0-((lratio-0.2)*425.0),3.0)+0.0117647055*pow(255.0-((lratio-0.2)*425.0),2.0);<br />
analogWrite(ledG,ledvg);<br />
bool alive;<br />
if(flsinfrared<30.0&&flsbroadband>50)<br />
alive=1;<br />
else<br />
alive=0;<br />
mossstatus=alive;<br />
}<br />
<br />
}<br />
<br />
void updateSenWater() // get current water values<br />
{<br />
float water = (0.0977517106549*(float)analogRead(Wat)); // The water sensor doesn't really work lineary. Here is my approximation for correction.<br />
valueWater=((valueCounter[0]*valueWater)+water)/(valueCounter[0]+1); // avaredged value<br />
valueCounter[0]++;<br />
String s="water level: "+String(water)+"% ";<br />
drawText(s,6);<br />
}<br />
<br />
void updateSenTemp(){ // get current temperature data<br />
byte data[12]; // array the incoming values should be stored to<br />
byte addr[8] = {0x28,0x1D,0xF1,0xB0,0x04,0x00,0x00,0x6B}; // OneWire temperature sensor address<br />
<br />
tempsen.reset(); // build up a connection and request data<br />
tempsen.select(addr);<br />
tempsen.write(0x44,1);<br />
tempsen.depower();<br />
tempsen.reset();<br />
tempsen.select(addr);<br />
tempsen.write(0xBE);<br />
for(byte z = 0; z < 9; z++) data[z] = tempsen.read(); // read out the return and store it byte per byte to the array<br />
unsigned int raw = (data[1] << 8) | data[0];<br />
valueTemp=(float)((valueCounter[1]*valueTemp)+((float)raw / 16.0)-1.5)/(float)(valueCounter[1]+1); // Take the current temperature into account for the avaredged value<br />
valueCounter[1]++;<br />
String s="temperature: "+String(((float)raw / 16.0)-1.5)+" ";<br />
drawText(s,3);<br />
}<br />
<br />
void updateWiFiConnection(){<br />
uint8_t wstat;<br />
if(!client.connected())<br />
client.stop();<br />
if(WiFi.status()==WL_CONNECTED)<br />
wstat=1;<br />
else<br />
wstat=0;<br />
if(wstat!=wifiConnection)<br />
{<br />
logging=0;<br />
continueText("logging: off",1,25);<br />
wifiConnection=wstat;<br />
if(wstat)<br />
{<br />
continueText("WiFi: con",2,25);<br />
continueText(" ",3,25);<br />
}<br />
else<br />
{<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
continueText("WiFi: dis",2,25);<br />
continueText("button: recn",3,25);<br />
<br />
}<br />
}<br />
}<br />
<br />
void WiFiSend()<br />
{<br />
if(!client.connected())<br />
client.stop();<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
drawText("client connecting.. ",10);<br />
cursorX-=11;<br />
if(!wifiConnection)<br />
{<br />
updateWiFiConnection();<br />
return;<br />
}<br />
if(client.connect("your.website.here",80))<br />
{<br />
continueText("connected");<br />
drawText("sending data..",11);<br />
<br />
client.print("GET http://your.website.here/save.php?key=yourkey");<br />
client.print(String("&water=")+String(valueWater,3) + "&temp="+String(valueTemp,3) + "&light1="+String(valueLight,3) + "&light2="+String(valueLightIR,3) +"&time="+String(valueTime));<br />
client.println(/*" HTTP/1.1"*/);<br />
client.println("Host: your.website.here");<br />
client.println("User-Agent: arduino-ethernet");<br />
client.println("Connection: close");<br />
client.println();<br />
<br />
continueText("done");<br />
for(int i=0;i<3;i++)<br />
valueCounter[i]=0; // Reset all counters and values for the avaredging process<br />
valueWater=0.0;<br />
valueTemp=0.0;<br />
valueLight=0.0;<br />
valueLightIR=0.0;<br />
firstreceive=1;<br />
}<br />
else<br />
{<br />
client.stop();<br />
continueText("failed");<br />
firstreceive=0;<br />
return;<br />
}<br />
}<br />
<br />
void WiFiReceive()<br />
{<br />
int i=0;<br />
if(firstreceive)<br />
{<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
drawText("listening..",10);<br />
firstreceive=0;<br />
}<br />
String response = "";<br />
while(client.connected() && i++<200)<br />
{<br />
if(client.available())<br />
{<br />
while(client.available())<br />
{<br />
response.concat((char)client.read()); <br />
}<br />
i=200;<br />
client.flush();<br />
}<br />
else<br />
delay(1);<br />
}<br />
if(i==200)<br />
Serial.println();<br />
Serial.print(response);<br />
drawText(String(response),10);<br />
}<br />
<br />
void setup()<br />
{<br />
initDisplay();<br />
Serial.begin(9600);<br />
Serial.println("serial ready");<br />
drawText("WiFi initialized");<br />
drawText("serial ready");<br />
drawText("init SD card reader.. ");<br />
initSD();<br />
drawText("init some pins");<br />
analogReadResolution(10);<br />
pinMode(Poti,INPUT);<br />
pinMode(Button,INPUT);<br />
pinMode(Temp,INPUT);<br />
pinMode(Wat,INPUT);<br />
pinMode(ledW,OUTPUT);<br />
pinMode(ledR,OUTPUT);<br />
pinMode(ledG,OUTPUT);<br />
digitalWrite(Poti,HIGH);<br />
digitalWrite(Button,HIGH);<br />
analogWrite(ledW,255);<br />
analogWrite(ledR,255);<br />
analogWrite(ledG,255);<br />
drawText("init touchpad");<br />
tp.init();<br />
tp.setOrientation(180);<br />
drawText("init real time clock");<br />
rtc.begin();<br />
drawText("init light sensor");<br />
initLightSen();<br />
drawText("done");<br />
drawText();<br />
drawText("Tap for WiFi search and connection\n..");<br />
drawText("Press button to proceed without WiFi..");<br />
if(waitForTap()==0)<br />
{<br />
initWiFi();<br />
}<br />
else<br />
{<br />
lcd.clear(COLOR_BLACK);<br />
drawText("button: off",6);<br />
continueText("logging: off",1,25);<br />
String s="potentiometer: "+String((((float)analogRead(Poti))*0.0977517106549))+" ";<br />
drawText(s,7);<br />
wifiConnection=0;<br />
continueText("WiFi: dis",2,25);<br />
continueText("button: recn",3,25);<br />
}<br />
}<br />
<br />
void loop()<br />
{<br />
if(counter%8==1) updateButtonAndPoti();<br />
if(counter%8==5) updateTP();<br />
if(counter%64==19) updateRTC();<br />
if(counter%64==37) updateSenWater();<br />
if(counter%128==11) updateSenLight();<br />
if(counter%128==73) updateSenTemp();<br />
if(counter%256==7) updateWiFiConnection();<br />
if(counter%4096==0&&logging) WiFiSend();<br />
if(counter%512==320&&logging) WiFiReceive();<br />
counter++;<br />
delay(1);<br />
}<br />
</nowiki><br />
<br />
====Libraries====<br />
<br />
Since it is not possible uploading files of the type file'''.h''' or file'''.cpp''', we zipped our libraries, named the suffix '''.zip.txt''' and uploaded '''[[Media:TUM13_arduino_libraries.zip.txt|THEM]]''' to the wiki. To unzip the libraries simply remove the '''.txt'''. We're very sorry but it was simply to much code to locate it as text on our pages.<br />
Unzip the archive into your ./arduino/libraries folder.<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
Please also visit our [https://github.com/VonAlphaBisZulu/IGEM_ARDUINO GitHub repo.]<br />
<br />
====Arduino photo gallery====<br />
<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/9c/Bent_pins.png" alt="Figure 34: bend pins 4 and 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/e6/Copper_cable.png" alt="Figure 35: solder copper cable: pins 7 and 24"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/2/29/Display.png" alt="Figure 36: display"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/6b/Side.png" alt="Figure 37: sideview"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/f/fb/Wifi_and_msd.png" alt="Figure 38: wifi and msd shield"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="Figure 39: <a href='http://igem.wzw.tum.de/arduino/'>light curve"</a>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="Figure 40: <a href='http://igem.wzw.tum.de/arduino/'>temperature curve</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References==<br />
<br />
The 2D Graphic of the Arduino Due was taken from a open source software called "fritzing"<br />
<br />
<div class="visualClear"></div><br />
<br />
<!-- End of content--><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/How_ToTeam:TU-Munich/Results/How To2013-10-29T01:20:32Z<p>PSchneider: /* Code */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Start of content --><br />
<br />
==Our Tutorials==<br />
During our iGEM summer we have acquired many skills which are useful for iGEMers and for every synthetic biologist. In order to spread this knowledge we created some tutorials. We hope that these tutorials enable future iGEM teams to present their project in a more colorful fashion.<br />
<br />
== Wiki Tips & Tricks ==<br />
<br />
Below is a list of iGEM wiki related tips and tutorials for future teams.<br />
<br />
=== Picture viewer ===<br />
<br />
Maybe you have not noticed it yet, but if you clicked any of the pictures on our wiki, you were not redirected to the ugly wiki page of the file. Instead a nice picture viewer opened and after you closed it, you did not have to go back to the site you saw the picture on. To get the same effect on your wiki follow the steps listed below:<br />
<br />
* '''Get the files!'''<br />We modified the original slimbox 2 viewer to work with the wiki and to not exceed the browser viewport, so it is recommended to use our versions, which can be found at [[Team:TU-Munich/TUM13_slimbox2.css]] and [[Team:TU-Munich/TUM13_slimbox2.js]].<br />
* '''Embed the files in your wiki!'''<br />The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the picture viewer.<br />
* '''Include the autoload code block!'''<br />A bit of JavaScript code that attaches the viewer to the right pictures needs to be executed on all the pages that use it. This code attaches the picture viewer to all images on the page which are embedded with the <code><nowiki>[[File:xxx.png|thumb|caption]]</nowiki></code> wiki code and it adds the corresponding caption to the viewer.<br />
<nowiki>$(document).ready(function(){<br />
$("div.thumbinner > a img").slimbox({/* Put custom options here */}, function(el) {<br />
url = el.src;<br />
if (url.indexOf('thumb') != -1) {<br />
url = url.substring(0, url.lastIndexOf('/'));<br />
url = url.replace('/thumb/', '/');<br />
}<br />
description = $(el).parents("div.thumbinner").children("div.thumbcaption").text();<br />
return [url, description];<br />
}, function(el) {<br />
return (this == el);<br />
});<br />
});</nowiki><br />
* '''Test it!'''<br />Below is an example picture, click on it to see what the picture viewer looks like.<br />
[[File:TUM13_physco-logo.png|thumb|center|350px|'''Figure 1:''' The logo of our project.]]<br />
<br />
=== Slideshow ===<br />
<br />
To create a good looking slideshow just follow the instructions below:<br />
<br />
* '''Get the files!'''<br />You can get the Stylesheet and Javascript for the slideshow either from [http://bxslider.com/ bxSlider] or from our wiki: [[Team:TU-Munich/TUM13_bxslider.css]] and [[Team:TU-Munich/TUM13_bxslider.js]].<br />
<br />
* '''Embed the files in your wiki!'''<br />The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the slideshow.<br />
<br />
* '''Include the initializing code block!'''<br />A bit of JavaScript code that activates the slideshow needs to be executed on all the pages that use it. This code changes all unordered lists of the class bxslider into slideshows.<br />
<nowiki>$(document).ready(function(){<br />
$('.bxslider').bxSlider({<br />
responsive: false,<br />
auto: true,<br />
autoHover: true<br />
});<br />
});</nowiki><br />
<br />
* '''Add the slideshow to the page!'''<br />To add a slideshow just put the pictures you want to include in an unordered list like shown below:<br />
<nowiki><html><br />
<ul class="bxslider"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li><br />
</ul><br />
</html></nowiki><br />
<br />
* '''Test it!'''<br />Below is an example of the slideshow.<br />
<br />
<html><br />
<ul class="bxslider"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li><br />
</ul><br />
</html><br />
<br />
==Generation of Rotating Protein Structures==<br />
Animated gifs of rotating protein structures have been used for some time in the iGEM competition. Here we present an easy to reproduce tutorial for iGEMers which are interested in similar images.<br />
*If there is no PDB file available for your protein of interest, you can use a homology search to find the most homologous structure. A good homology search tool is [http://toolkit.tuebingen.mpg.de/hhpred HHpred].<br />
*The entry for the best matching structure was used for the figure. If it is only a homologous structure please cite this together with the homology when presenting the resulting image.<br />
*You can save the PDB file of the homologous structure on your computer.<br />
*If you do not have [http://www.pymol.org/ PyMol] (freeware) installed on your computer download and install it.<br />
*Start PyMol software and open the PDB file by clicking File -> Open.<br />
*The following approach was adapted from a PyMol tutorial [[http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong]].<br />
*The following commands were entered into the command line:<br />
<code><br />
PyMOL> orient<br><br />
PyMOL> hide everything, all<br><br />
PyMOL> show cartoon, all<br><br />
PyMol> bg_color white<br><br />
click> Settings>Rendering>Shadows>Occlusion<br><br />
PyMOL> color purple, ss h; color yellow, ss s; color green, ss ""<br><br />
PyMOL> show surface, all<br><br />
PyMOL> set transparency, 0.75<br><br />
PyMOL> set surface_quality, 1 (command will prolongue the process significantly, you may skip it)<br> <br />
PyMOL> set ray_trace_frames=1 (command will prolongue the process significantly, you may skip it)<br> <br />
PyMOL> mset 1 x180<br><br />
PyMOL> util.mroll 1,180<br><br />
PyMOL> mpng frame<br><br />
</code><br />
*Afterwards the *.png files were automatically converted to *.tif files using [http://www.xnview.com/de/xnconvert/ XnConvert].<br />
*The program [http://www.animake.de/gif-animation.htm Animake] was used to generate the annimated gifs.<br />
**The Animake software was started<br />
**A new working folder was generated (File -> New) and the *.tif files were imported (Edit -> Import_from_file)<br />
**The background was set to white (Animation -> Settings)<br />
**The range of colors was set to 256 (Edit -> Select_all and Edit -> Change_Color)<br />
**The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit -> Change_size. We suggest a size of 320x240 px or even smaller if the resulting gif becomes to big.<br />
**Finally the animated gif can be saved in the program format (.abp) and as gif (File -> Save_as)<br />
**If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)<br />
<center>This is how your protein of interest could look like:</center><br />
<br />
[[File:TUM13_Annimated_test.gif|thumb|center|320px|'''Figure 2:''' Protein]]<br />
<br />
==Setting up a basic Arduino measuring device==<br />
===Introduction===<br />
[[File:TUM13_Arduino_Assembly_Animation.gif|thumb|left|400px|'''Figure 3:''' Assembly Order]]<br />
<br />
Since the Arduino Due was released in autumn 2012, this is the first iGEM year this '''very powerful''' device can be used. We found it a useful '''supervising tool''' for short and long-term experiments. It can be used in as well as outside the lab. The improvements that were made from Uno to Due are considerable.<br />
<br />
It is capable of handling many things at once, such as a WiFi shield, a display, a SD-Card and multiple sensors.<br />
At this point the Uno did not match up any longer. <br />
<br />
To establish the usage of Arduino in iGEM even more we want to share our experiences and help you building up a '''basic device''' that can '''collect''' and '''view sensor data''' on its '''display''' and '''upload''' them to a server.<br />
<br />
===Part Description===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/0e/TUM13_Arduino_Due.png" alt="Figure 4: Arduino Due" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/5/58/Arduino_WiFi.png" alt="Figure 5: Arduino WiFi Shield" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/e7/Arduino_Mega_MSD.png" alt="Figure 6: Mega MSD Shield" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/d/de/Arduino_MI0283.png" alt="Figure 7: MI0283 Display" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/Arduino_Tsl2561.png" alt="Figure 8: TSL2561 light sensor" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/a/a5/Arduino_Tsl2561_Curve.png" alt="Figure 9: TSL2561 absorption curve" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/3/3d/Arduino_Watersensor.png" alt="Figure 10: Water sensor" /></li><br />
</ul><br />
</div><br />
</html><br />
====Arduino Due====<br />
<br />
The Arduino Due is the most powerful Arduino board. Its underlying 32bit-processor is the Atmel SAM3X8E. <br />
Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficient.<br />
It was released in October 2012.<br />
<br />
'''Data:'''<br />
<br />
84 Mhz CPU Clock<br />
96 KBytes of SRAM.<br />
512 KBytes of Flash memory. <br />
54 Digital I/O Pins<br />
12 Analog Input Pins<br />
2 (DAC)Analog Outputs Pins<br />
<br />
====Arduino WiFi Shield====<br />
<br />
The Arduino WiFi Shield is an attachable shield that provides Wireless LAN 802.11b/g to the Arduino. <br />
It scans and connects to networks and opens TCP and UDP sockets for data transfer. It also supports WEP and WPA2 encryption. It was released in August 2012.<br />
The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi library. <br />
There is also an on-board SD-card socket to store received data. <br />
As the SD-card is accessible separately, it can also be used as a storage for any data generated by the Arduino.<br />
The SD-card socket is also supported by a stock library. The communication between Arduino Due and the WiFi Shield runs via an SPI/ICSP interface.<br />
<br />
'''Pin usage:'''<br />
Pin 4 SS for SD card (Slave Select)<br />
Pin 7 Handshake between Arduino and WiFi Shield<br />
Pin 10 SS for WiFi<br />
Pin 74 SPI MISO (Master in, Slave out)<br />
Pin 75 SPI MOSI (Master out, Slave in)<br />
Pin 76 SPI SCK (Serial clock)<br />
gnd<br />
3.3V<br />
5V<br />
<br />
====Watterott Mega MSD-Shield====<br />
<br />
The Mega MSD-Shield was designed by Watterott and consists of a couple of components. <br />
The components are one real time clock, one SD-card socket (we will not use), a small battery and a socket for a touch display.<br />
To get it ready to run, the shield must be assembled. The stackable headers and the clock's quartz must be soldered to the board and the battery must be inserted.<br />
Unluckily the Mega MSD-Shield and therefore also the MI0283QT-9 touch display don't come with a working library for the Arduino Due. The existing library only supports all boards up to the Arduino Uno.<br />
Therefore all libraries had to be rewritten.<br />
The touch display and the SD-card slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmits its data via I²C.<br />
<br />
'''Pin usage:'''<br />
Pin 4 SS for SD card<br />
Pin 6 SS for the touch of the touch display<br />
Pin 8 reset LCD<br />
Pin 9 LCD LED<br />
Pin 20 RTC (real time clock) I²C SDA (Serial Data Line)<br />
Pin 21 RTC I²C SCL (Serial Clock)<br />
Pin 25 SS (7) for the LCD (Workarround of the double usage of pin 7 by the WIFI Shield)<br />
Pin 50 SPI MISO<br />
Pin 51 SPI MOSI<br />
Pin 52 SPI SCK<br />
gnd<br />
3.3V<br />
<br />
====Display MI0283QT-9====<br />
<br />
The MI0283QT-9 is a multicolor touch display. It comes already attached to a board, where only the pin headers are left to be soldered.<br />
Once assembled it can easily be plugged into the Mega MSD-Shield. It has an on-board touch controller (TI ADS7846).<br />
The display size is 2.83"(43.2 x 57.6mm) with a resolution of 240x320. It supports 262k colors. <br />
The pin usage is already considered in the Mega MSD-Shield description.<br />
<br />
====Light Sensor TSL2561====<br />
<br />
The light sensor is a small, so called, breakout board. It is usually connected by wires instead of directly plugged into the Arduino's headers.<br />
The light sensor has two photo diodes on-board that measure visible and infrared light. Similar to the RTC, the TSL2561 is addressed via I²C.<br />
Once you get the I²C library working on your Arduino Due working it takes only little effort to integrate additional I²C devices.<br />
Just very few lines of the library have to be rewritten here.<br />
The photo diodes can be addressed separately or both at one. Their output is already converted to Lux.<br />
<br />
'''Pin usage:'''<br />
<br />
Pin 20 TSL2561 I²C SDA (Serial Data Line)<br />
Pin 21 TSL2561 I²C SCL (Serial Clock)<br />
gnd<br />
3.3V<br />
<br />
====Temperature Sensor DS18B20====<br />
<br />
The temperature sensor is embedded into a water proof cable. It is addressed via a OneWire interface. <br />
The provided data are digital raw data, which need to be converted into degree Celsius. Information about the conversion are given by the manufacturer.<br />
Similar to the I²C (TwoWire) bus, you only have to get the OneWire interface working once. After that, you can easily set up more OneWire devices.<br />
Again, just very few lines of the library have to be rewritten.<br />
<br />
'''Pin usage:'''<br />
<br />
Pin 14 One-Wire DS18B20 (pin was randomly chosen)<br />
Pin gnd<br />
Pin 3.3V<br />
<br />
====Water Sensor====<br />
<br />
Setting up the water sensor is very easy. If and how much water the sensor registered can be measured via an analog pin.<br />
<br />
'''pin usage:'''<br />
<br />
Pin A5 Water sensor<br />
gnd<br />
3.3V<br />
<br />
===Tools===<br />
*Breadboard<br />
*Soldering bolt<br />
*Solder<br />
<br />
===Assembly===<br />
<br />
<br />
Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code (e.g. red cable for 3.3V etc.) otherwise troubleshooting can get nasty.<br />
<br />
All '''steps''' you need to follow building up your own Arduino measuring device are '''explained below''' in the '''slide show''' and the image descriptions.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d7/TUM13_Arduiono_Assembly_1.png/350px-TUM13_Arduiono_Assembly_1.png" alt="Figure 11: Place your Arduino Due on your desk"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/c/c4/TUM13_Arduiono_Assembly_2.png/350px-TUM13_Arduiono_Assembly_2.png" alt="Figure 12: Connect ground and 3.3V to two different lines of you breadboard"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/2/21/TUM13_Arduiono_Assembly_3.png/350px-TUM13_Arduiono_Assembly_3.png" alt="Figure 13: Connect the light sensor's ground and the 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/9b/TUM13_Arduiono_Assembly_4.png/350px-TUM13_Arduiono_Assembly_4.png" alt="Figure 14: Connect the sda line of your light sensor to pin 20 and scl to pin 21"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/9c/TUM13_Arduiono_Assembly_5.png/350px-TUM13_Arduiono_Assembly_5.png" alt="Figure 15: Connect the temperature sensor's ground and the 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Arduiono_Assembly_6.png/350px-TUM13_Arduiono_Assembly_6.png" alt="Figure 16: Connect the signal line of your temp sensor via the breadbroad to pin 14" /></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/8/83/TUM13_Arduiono_Assembly_7.png/350px-TUM13_Arduiono_Assembly_7.png" alt="Figure 17: Place a ~50kOhm resistor between the 3.3V line and the temps sensor's signal line on your breadboard" /></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/b/b0/TUM13_Arduiono_Assembly_8.png/350px-TUM13_Arduiono_Assembly_8.png" alt="Figure 18: Connect the water sensor to the ground and 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/e/e4/TUM13_Arduiono_Assembly_9.png/350px-TUM13_Arduiono_Assembly_9.png" alt="Figure 19: Connect the signal line of your water sensor to pin A5"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/8/86/TUM13_Arduiono_Assembly_10.png/350px-TUM13_Arduiono_Assembly_10.png" alt="Figure 20: Voila! You are done with the basic connection of your three sensors. The next steps explain how to connect the WiFi shield, the msd shield and the display. You can connect all the sensors to the shield's and header's pins the same way, you connected them to the Arduino Due"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_11.png/350px-TUM13_Arduiono_Assembly_11.png" alt="Figure 21: First solder a short copper cable to the msd shield, connecting its pin 25 to pin 7"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/1/18/TUM13_Arduiono_Assembly_12.png/350px-TUM13_Arduiono_Assembly_12.png" alt="Figure 22: Then bend pin 7 and pin 4, so they don't connect to the WiFi shield's pins. Pin 4 would be a double usage of the msd shield's and the wifi shield's sd card. Pin 7 (lcd slave select) interferes with the wifi handshake pin"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/9/99/TUM13_Arduiono_Assembly_13.png/350px-TUM13_Arduiono_Assembly_13.png" alt="Figure 23: This is just an explanation of how the shield's sub-devices are connected. A deeper understanding of the following diagrams goes along with a deeper understanding of the program's source code and the additional libraries. All shields are of course connected to the Arduino Due's ground and 3.3V line"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/e/e8/TUM13_Arduiono_Assembly_14.png/350px-TUM13_Arduiono_Assembly_14.png" alt="Figure 24: The yellow link shows the spi interface between Arduino Due and the WiFi shield"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Arduiono_Assembly_15.png/350px-TUM13_Arduiono_Assembly_15.png" alt="Figure 25: The thinner yellow lines are the WiFi handshake and the wifi slave select connections"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_16.png/350px-TUM13_Arduiono_Assembly_16.png" alt="Figure 26: The blue link is the sd reader's slave select"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/6/6d/TUM13_Arduiono_Assembly_17.png/350px-TUM13_Arduiono_Assembly_17.png" <br />
alt="Figure 27: The green link represents the connection to the real time clock"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Arduiono_Assembly_18.png/350px-TUM13_Arduiono_Assembly_18.png" alt="Figure 28: The pink link represents the spi interface between the msd shield and the Arduino Due, required for the communication with the lcd and its touch functions (pins 50, 51 and pin 52)"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/4/4b/TUM13_Arduiono_Assembly_19.png/350px-TUM13_Arduiono_Assembly_19.png" alt="Figure 29: Lcd slave select, lcd reset and lcd LED"/></li><li><img src="<br />
https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Arduiono_Assembly_20.png/350px-TUM13_Arduiono_Assembly_20.png" alt="Figure 30: Lcd's touch slave select"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/5c/TUM13_Arduiono_Assembly_21.png/350px-TUM13_Arduiono_Assembly_21.png" alt="Figure 31: the power supply can be established with a 9V block battery"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ef/TUM13_Arduiono_Assembly_22.png/350px-TUM13_Arduiono_Assembly_22.png" alt="Figure 32: At last: an overview"/></li><br />
<br />
</ul><br />
</div><br />
</html><br />
[[File:TUM13_Arduino_in_action.gif|thumb|500px|left|'''Figure 33:''' Arduino in action]]<br />
For more explaining photos visit our [[#Arduino_photo_gallery|photo gallery]]. On the left you see the Arduino as it boots up, connects to a WiFi hotspot and collects data.<br />
<br />
===Code===<br />
<br />
We strongly recommend the usage of '''Microsoft Visual Studio''' with the '''"visual micro"''' plugin. Microsoft Intellisense helps you a lot, when you are unfamiliar with the manufacturer provided libraries (automatic code completion). In order to compile the code properly you need the latest beta version of [http://arduino.cc/en/Main/Software Arduino's software]. In the visual micro settings, choose the path to the Arduino IDE on your hard drive, also disable "Upload using programmer". In the settings of the Arduino IDE, select "use external software".<br />
<br />
Now you are ready to start programming. Below we share our code, feel free to use, edit and play around with it!<br />
But '''wait''' first you need our '''[[#Libraries|libraries]]'''! They're exclusively '''fitted''' to the Arduino Due, mostly based on the existing manufacturer's libraries for the Arduino Uno.<br />
<br />
Since Arduino released a new version of its IDE and software, and extended its support on the Arduino Due, we have rewritten our previews code. Both, the old and the new code can be found in our [https://github.com/VonAlphaBisZulu/IGEM_ARDUINO GitHub repo].<br />
<br />
Assuming you followed our tutorial until here.<br />
Once you adapted the code to your WiFi and server settings and uploaded it to the Arduino it does the following:<br />
#it starts up and the '''screen''' stays black, but turns its lights on<br />
#if you have pressed the screen, the calibration process starts<br />
#it '''searches for networks''' and displays the total number of found networks on its screen<br />
#it displays some '''WiFi stations''' that were found<br />
#it tries to '''connect''' to the WiFi station you have set<br />
#if a connection was established it shows the '''Arduino's IP address''' and the SSID (name) of the WiFi it is connected to<br />
#then it idles until you you press the screen<br />
#after you pressed the screen it jumps to the '''"loop"-section''' of the code<br />
#it continuously runs and displays:<br />
##the current '''time'''<br />
##the '''temperature'''<br />
##the measured '''infrared''' and '''broadband light'''<br />
##the '''coordinates''' of the point you '''pressed''' on the screen<br />
#it builds up a '''connection to a server, calling a PHP script, passing on the collected data'''<br />
<br />
<nowiki><br />
#include "SPI.h" // SPI library (stock)<br />
#include "Wire.h" // TwoWire library (stock) sda-scl<br />
#include "RTClib.h" // Real time clock library (original library, slightly rewritten to fit the Due)<br />
#include "SPI.h"<br />
#include "MI0283QT9Due.h" // LCD library (quite much had to be rewritten). Pins were changed, usage of Software SPI... quite a mess but it works great<br />
#include "ADS7846Due.h" // Touch controller (same story as at the lcd library)<br />
#include "Adafruit_TSL2561.h" // light sensor library (had to be rewritten in some parts to fit the Due) functions were added to correct the lux-output that wasn't always correct with the stock library<br />
#include "OneWire.h" // OneWire (I don't know, but I guess it's the stock library)<br />
#include "avr/dtostrf.h" // optional library to workaround some compatibility problems with the Due<br />
#include "math.h" // standard C-maths library<br />
#include "SD.h" // SD reader (stock)<br />
#include "WiFi.h" // (stock)<br />
#include "time.h" // standard C-time library<br />
#include "math.h"<br />
<br />
#define ledW (11)<br />
#define ledR (12)<br />
#define ledG (13)<br />
#define Poti (A0)<br />
#define Button (A1)<br />
#define Temp (14)<br />
#define Wat (A5)<br />
<br />
#define shift8to32(a,b,c,d) (d << 24) | (c << 16) | (b << 8) | a<br />
#define shift8to16(a,b) (b << 8) | a<br />
<br />
MI0283QT9 lcd;<br />
ADS7846 tp;<br />
RTC_DS1307 rtc;<br />
OneWire tempsen(Temp);<br />
Adafruit_TSL2561 lightsen(TSL2561_ADDR_FLOAT,12345);<br />
File bitmap;<br />
WiFiClient client(0);<br />
<br />
float valueWater=0, valueTemp=0, valueLight=0, valueLightIR=0; // sensor values (avaredged)<br />
uint32_t valueTime=0,valueCounter[3]={0,0,0};<br />
uint16_t counter=1,potValue=0; // vlauecounter 0:Water 1:Temp 2:Light/IR<br />
uint8_t cursorY=1,cursorX=0;<br />
bool buttonValue=0,logging=0,wifiConnection,mossstatus=0,firstreceive=1;<br />
<br />
int waitForTap(){<br />
tp.service();<br />
while(tp.getPressure()==0) // Idle until the touchscreen is pressed to continue<br />
{<br />
delay(20);<br />
tp.service();<br />
if(digitalRead(Button)==0)<br />
return 1;<br />
}<br />
return 0;<br />
}<br />
<br />
void continueText(String drawtext, int cursY=cursorY-1, int cursX=cursorX,int maxlen=38){<br />
maxlen=maxlen-cursX;<br />
<br />
lcd.drawText(15+cursX*8,cursY*15,drawtext,1,COLOR_WHITE,COLOR_BLACK);<br />
<br />
cursorX=drawtext.length()+1;<br />
}<br />
<br />
void drawText(String drawtext="", int cursY=cursorY,int maxlen=38){<br />
continueText(drawtext,cursY,0);<br />
cursorY=cursY+1;<br />
}<br />
<br />
void OpenBMPFile(char *file, int16_t x, int16_t y)<br />
{<br />
uint8_t pad;<br />
uint8_t buf[54]; //read buf (min. size = sizeof(BMP_DIPHeader))<br />
int16_t width, height, w, h;<br />
<br />
if(!SD.exists(file))<br />
{<br />
Serial.println(String(file)+"not found");<br />
return;<br />
}<br />
else<br />
bitmap = SD.open(file, FILE_READ);<br />
if(!bitmap.available())<br />
{<br />
Serial.println("not reading image file");<br />
return;<br />
}<br />
else<br />
Serial.println("reading image file");<br />
<br />
//BMP Header<br />
for(int i=0;i<14;i++)<br />
{<br />
buf[i]=bitmap.read();<br />
}<br />
<br />
if((buf[0] == 'B') && (buf[1] == 'M') && (buf[10] == 54))<br />
{<br />
Serial.println("Bitmap recognized");<br />
//BMP DIP-Header<br />
for(int i=14;i<54;i++)<br />
buf[i]=bitmap.read();<br />
if(<br />
Serial.println(shift8to32(buf[14],buf[15],buf[16],buf[17]))&& // size<br />
Serial.println(shift8to16(buf[28],buf[29]))&& // bitspp<br />
Serial.println(shift8to32(buf[30],buf[31],buf[32],buf[33]))) // compress<br />
{<br />
Serial.println("DIP recognized");<br />
//BMP data (1. pixel = bottom left)<br />
width = shift8to32(buf[18],buf[19],buf[20],buf[21]); // width<br />
height = shift8to32(buf[22],buf[23],buf[24],buf[25]); // height<br />
pad = width % 4; //padding (line is multiply of 4)<br />
Serial.println("printing");<br />
if((x+width) <= lcd.getWidth() && (y+height) <= lcd.getHeight())<br />
{<br />
lcd.setArea(x, y, x+width-1, y+height-1);<br />
for(h=(y+height-1); h >= y; h--) //for every line<br />
{<br />
uint8_t pix[320][3];<br />
bitmap.read(pix,width*3);<br />
for(w=0; w < width; w++) //for every pixel in line<br />
{<br />
lcd.drawPixel(x+w, h, RGB(pix[w][2],pix[w][1],pix[w][0]));<br />
}<br />
if(pad)<br />
{<br />
bitmap.read(pix, pad);<br />
}<br />
}<br />
}<br />
else<br />
{<br />
lcd.drawTextPGM(x, y, PSTR("Pic out of screen!"), 1, RGB(0,0,0), RGB(255,255,255));<br />
}<br />
}<br />
}<br />
bitmap.close();<br />
}<br />
<br />
void initDisplay()<br />
{<br />
lcd.init();<br />
lcd.setOrientation(180);<br />
lcd.led(100);<br />
lcd.clear(COLOR_BLACK);<br />
}<br />
<br />
void initSD(){<br />
if (!SD.begin(4)) {<br />
continueText("failed");<br />
return;<br />
} else {<br />
continueText("succeeded");;<br />
}<br />
}<br />
<br />
void initLightSen() // initialize the light sensor<br />
{<br />
lightsen.setIntegrationTime(TSL2561_INTEGRATIONTIME_101MS);<br />
lightsen.enableAutoGain(true); <br />
lightsen.begin();<br />
}<br />
<br />
void initWiFi()<br />
{<br />
lcd.clear(COLOR_BLACK);<br />
cursorY=1;<br />
WiFi.disconnect();<br />
drawText("number of networks:");<br />
uint8_t nnet=WiFi.scanNetworks();<br />
continueText(String(nnet));<br />
for(int i=0;i<nnet;i++)<br />
drawText(WiFi.SSID(i));<br />
drawText();<br />
drawText("connecting to YOURWIFI..");<br />
for(int i=0;WL_CONNECTED!=WiFi.begin("YOURWIFI","yourpassword")&&i<3;i++)<br />
{<br />
WiFi.scanNetworks();<br />
drawText(String("connection failed ")+String(2-i)+String(" left.."));<br />
}<br />
if(WiFi.status()==WL_CONNECTED)<br />
{<br />
continueText(" succeeded");<br />
drawText("local IP address: "+String(WiFi.localIP()[0])+"."+String(WiFi.localIP()[1])+"."+String(WiFi.localIP()[2])+"."+String(WiFi.localIP()[3]));<br />
}<br />
else<br />
drawText("connection failed");<br />
logging=0;<br />
drawText();<br />
drawText("continue to data display & logging ..");<br />
waitForTap();<br />
lcd.clear(COLOR_BLACK);<br />
drawText("button: off",6);<br />
continueText("logging: off",1,25);<br />
String s="potentiometer: "+String((((float)analogRead(Poti))*0.0977517106549))+" ";<br />
drawText(s,7);<br />
}<br />
<br />
void updateTP(){<br />
tp.service();<br />
drawText("x: "+String(tp.getX())+" y: "+String(tp.getY())+" ",2);<br />
}<br />
<br />
void updateButtonAndPoti(){<br />
bool butv=(!digitalRead(Button));<br />
if(buttonValue!=butv)<br />
{<br />
if(wifiConnection==0)<br />
{<br />
initWiFi();<br />
counter=1;<br />
return;<br />
}<br />
if(butv)<br />
{<br />
logging=!logging;<br />
if(logging)<br />
{<br />
continueText("logging: on ",1,25);<br />
WiFiSend();<br />
counter=1;<br />
}<br />
else<br />
{<br />
continueText("logging: off",1,25);<br />
WiFiReceive();<br />
counter=1025;<br />
}<br />
}<br />
if(!butv)<br />
drawText("button: off",6);<br />
else<br />
drawText("button: on ",6);<br />
buttonValue=!buttonValue;<br />
}<br />
uint16_t potv=analogRead(Poti);<br />
if(potValue!=potv)<br />
{<br />
String s="potentiometer: "+String((((float)potv)*0.0977517106549))+" ";<br />
drawText(s,7);<br />
potValue=potv;<br />
}<br />
<br />
}<br />
<br />
void updateRTC() // update the time from the clock<br />
{<br />
DateTime tm=rtc.now();<br />
if(valueTime != tm.unixtime()) // Only refresh the values on the display if they changed (when the seconds value has changed since the last call)<br />
{<br />
char s[30];<br />
sprintf(s,"%02i:%02i:%02i %02i.%02i:%04i",tm.hour(),tm.minute(),tm.second(),tm.day(),tm.month(),tm.year());<br />
drawText(s,1);<br />
}<br />
valueTime = tm.unixtime();<br />
}<br />
<br />
void updateSenLight() // get current light values<br />
{<br />
uint16_t lsbroadband,lsinfrared; // definition<br />
float flsbroadband,flsinfrared;<br />
lightsen.getLuminosity(&lsbroadband,&lsinfrared); // the full function is implemented in the library<br />
flsbroadband=((float)lsbroadband*lightsen.getMultiplier());<br />
flsinfrared=((float)lsinfrared*lightsen.getMultiplier()); // getMultipier is a function I added. I believe the developers just missed something out in their lib<br />
valueLight=(((float)valueCounter[2]*valueLight)+(float)flsbroadband)/(float)(valueCounter[2]+1.0); // Calculate the avaredged values<br />
valueLightIR=(((float)valueCounter[2]*valueLightIR)+(float)flsinfrared)/(float)(valueCounter[2]+1.0);<br />
valueCounter[2]++;<br />
drawText(String("visible light: ")+String(flsbroadband,1)+" ",4);<br />
drawText(String("infrared light: ")+String(flsinfrared,1)+" ",5);<br />
float lratio=flsinfrared/flsbroadband;<br />
continueText(String("ratio: ")+String(lratio,4),5,25);<br />
uint8_t ledvw=-0.0000307574013*pow((double)log(flsbroadband)*25.5,3.0)+0.0117647055*pow((double)log(flsbroadband)*25.5,2.0);<br />
analogWrite(ledW,ledvw);<br />
uint8_t ledvr=-0.0000307574013*pow((lratio-0.2)*425.0,3.0)+0.0117647055*pow((lratio-0.2)*425.0,2.0);<br />
analogWrite(ledR,ledvr);<br />
uint8_t ledvg=-0.0000307574013*pow(255.0-((lratio-0.2)*425.0),3.0)+0.0117647055*pow(255.0-((lratio-0.2)*425.0),2.0);<br />
analogWrite(ledG,ledvg);<br />
bool alive;<br />
if(flsinfrared<30.0&&flsbroadband>50)<br />
alive=1;<br />
else<br />
alive=0;<br />
mossstatus=alive;<br />
}<br />
<br />
}<br />
<br />
void updateSenWater() // get current water values<br />
{<br />
float water = (0.0977517106549*(float)analogRead(Wat)); // The water sensor doesn't really work lineary. Here is my approximation for correction.<br />
valueWater=((valueCounter[0]*valueWater)+water)/(valueCounter[0]+1); // avaredged value<br />
valueCounter[0]++;<br />
String s="water level: "+String(water)+"% ";<br />
drawText(s,6);<br />
}<br />
<br />
void updateSenTemp(){ // get current temperature data<br />
byte data[12]; // array the incoming values should be stored to<br />
byte addr[8] = {0x28,0x1D,0xF1,0xB0,0x04,0x00,0x00,0x6B}; // OneWire temperature sensor address<br />
<br />
tempsen.reset(); // build up a connection and request data<br />
tempsen.select(addr);<br />
tempsen.write(0x44,1);<br />
tempsen.depower();<br />
tempsen.reset();<br />
tempsen.select(addr);<br />
tempsen.write(0xBE);<br />
for(byte z = 0; z < 9; z++) data[z] = tempsen.read(); // read out the return and store it byte per byte to the array<br />
unsigned int raw = (data[1] << 8) | data[0];<br />
valueTemp=(float)((valueCounter[1]*valueTemp)+((float)raw / 16.0)-1.5)/(float)(valueCounter[1]+1); // Take the current temperature into account for the avaredged value<br />
valueCounter[1]++;<br />
String s="temperature: "+String(((float)raw / 16.0)-1.5)+" ";<br />
drawText(s,3);<br />
}<br />
<br />
void updateWiFiConnection(){<br />
uint8_t wstat;<br />
if(!client.connected())<br />
client.stop();<br />
if(WiFi.status()==WL_CONNECTED)<br />
wstat=1;<br />
else<br />
wstat=0;<br />
if(wstat!=wifiConnection)<br />
{<br />
logging=0;<br />
continueText("logging: off",1,25);<br />
wifiConnection=wstat;<br />
if(wstat)<br />
{<br />
continueText("WiFi: con",2,25);<br />
continueText(" ",3,25);<br />
}<br />
else<br />
{<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
continueText("WiFi: dis",2,25);<br />
continueText("button: recn",3,25);<br />
<br />
}<br />
}<br />
}<br />
<br />
void WiFiSend()<br />
{<br />
if(!client.connected())<br />
client.stop();<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
drawText("client connecting.. ",10);<br />
cursorX-=11;<br />
if(!wifiConnection)<br />
{<br />
updateWiFiConnection();<br />
return;<br />
}<br />
if(client.connect("your.website.here",80))<br />
{<br />
continueText("connected");<br />
drawText("sending data..",11);<br />
<br />
client.print("GET http://your.website.here/save.php?key=yourkey");<br />
client.print(String("&water=")+String(valueWater,3) + "&temp="+String(valueTemp,3) + "&light1="+String(valueLight,3) + "&light2="+String(valueLightIR,3) +"&time="+String(valueTime));<br />
client.println(/*" HTTP/1.1"*/);<br />
client.println("Host: your.website.here");<br />
client.println("User-Agent: arduino-ethernet");<br />
client.println("Connection: close");<br />
client.println();<br />
<br />
continueText("done");<br />
for(int i=0;i<3;i++)<br />
valueCounter[i]=0; // Reset all counters and values for the avaredging process<br />
valueWater=0.0;<br />
valueTemp=0.0;<br />
valueLight=0.0;<br />
valueLightIR=0.0;<br />
firstreceive=1;<br />
}<br />
else<br />
{<br />
client.stop();<br />
continueText("failed");<br />
firstreceive=0;<br />
return;<br />
}<br />
}<br />
<br />
void WiFiReceive()<br />
{<br />
int i=0;<br />
if(firstreceive)<br />
{<br />
drawText(" ",10);<br />
drawText(" ",11);<br />
drawText(" ",12);<br />
drawText(" ",13);<br />
drawText(" ",14);<br />
drawText("listening..",10);<br />
firstreceive=0;<br />
}<br />
String response = "";<br />
while(client.connected() && i++<200)<br />
{<br />
if(client.available())<br />
{<br />
while(client.available())<br />
{<br />
response.concat((char)client.read()); <br />
}<br />
i=200;<br />
client.flush();<br />
}<br />
else<br />
delay(1);<br />
}<br />
if(i==200)<br />
Serial.println();<br />
Serial.print(response);<br />
drawText(String(response),10);<br />
}<br />
<br />
void setup()<br />
{<br />
initDisplay();<br />
Serial.begin(9600);<br />
Serial.println("serial ready");<br />
drawText("WiFi initialized");<br />
drawText("serial ready");<br />
drawText("init SD card reader.. ");<br />
initSD();<br />
drawText("init some pins");<br />
analogReadResolution(10);<br />
pinMode(Poti,INPUT);<br />
pinMode(Button,INPUT);<br />
pinMode(Temp,INPUT);<br />
pinMode(Wat,INPUT);<br />
pinMode(ledW,OUTPUT);<br />
pinMode(ledR,OUTPUT);<br />
pinMode(ledG,OUTPUT);<br />
digitalWrite(Poti,HIGH);<br />
digitalWrite(Button,HIGH);<br />
analogWrite(ledW,255);<br />
analogWrite(ledR,255);<br />
analogWrite(ledG,255);<br />
drawText("init touchpad");<br />
tp.init();<br />
tp.setOrientation(180);<br />
drawText("init real time clock");<br />
rtc.begin();<br />
drawText("init light sensor");<br />
initLightSen();<br />
drawText("done");<br />
drawText();<br />
drawText("Tap for WiFi search and connection\n..");<br />
drawText("Press button to proceed without WiFi..");<br />
if(waitForTap()==0)<br />
{<br />
initWiFi();<br />
}<br />
else<br />
{<br />
lcd.clear(COLOR_BLACK);<br />
drawText("button: off",6);<br />
continueText("logging: off",1,25);<br />
String s="potentiometer: "+String((((float)analogRead(Poti))*0.0977517106549))+" ";<br />
drawText(s,7);<br />
wifiConnection=0;<br />
continueText("WiFi: dis",2,25);<br />
continueText("button: recn",3,25);<br />
}<br />
}<br />
<br />
void loop()<br />
{<br />
if(counter%8==1) updateButtonAndPoti();<br />
if(counter%8==5) updateTP();<br />
if(counter%64==19) updateRTC();<br />
if(counter%64==37) updateSenWater();<br />
if(counter%128==11) updateSenLight();<br />
if(counter%128==73) updateSenTemp();<br />
if(counter%256==7) updateWiFiConnection();<br />
if(counter%4096==0&&logging) WiFiSend();<br />
if(counter%512==320&&logging) WiFiReceive();<br />
counter++;<br />
delay(1);<br />
}<br />
</nowiki><br />
<br />
====Libraries====<br />
<br />
Since it is not possible uploading files of the type file'''.h''' or file'''.cpp''', we zipped our libraries, named the suffix '''.zip.txt''' and uploaded '''[[Media:TUM13_arduino_libraries.zip.txt|THEM]]''' to the wiki. To unzip the libraries simply remove the '''.txt'''. We're very sorry but it was simply to much code to locate it as text on our pages.<br />
Unzip the archive into your ./arduino/libraries folder.<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
Please also visit our [https://github.com/VonAlphaBisZulu/IGEM_ARDUINO GitHub repo.]<br />
<br />
====Arduino photo gallery====<br />
<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/9c/Bent_pins.png" alt="Figure 34: bend pins 4 and 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/e/e6/Copper_cable.png" alt="Figure 35: solder copper cable: pins 7 and 24"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/2/29/Display.png" alt="Figure 36: display"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/6/6b/Side.png" alt="Figure 37: sideview"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/f/fb/Wifi_and_msd.png" alt="Figure 38: wifi and msd shield"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="Figure 39: <a href='http://igem.wzw.tum.de/arduino/'>light curve"</a>/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="Figure 40: <a href='http://igem.wzw.tum.de/arduino/'>temperature curve</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References==<br />
<br />
The 2D Graphic of the Arduino Due was taken from a open source software called "fritzing"<br />
<br />
<div class="visualClear"></div><br />
<br />
<!-- End of content--><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:56:37Z<p>PSchneider: </p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1650px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. <br />
<br />
This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1650px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
<br />
The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:55:58Z<p>PSchneider: </p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1640px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. <br />
<br />
This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1640px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
<br />
The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:54:30Z<p>PSchneider: </p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1700px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1700px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
<br />
The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:53:49Z<p>PSchneider: /* Open filter on felt base */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
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<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1500px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1500px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
<br />
The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
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<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:41:26Z<p>PSchneider: </p>
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<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1500px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1500px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:40:02Z<p>PSchneider: /* Closed tube reactor */</p>
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<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
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<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1500px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:36:52Z<p>PSchneider: /* Closed tube reactor */</p>
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==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
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===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.<br />
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===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
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==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
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===Images from our trip to the construction center===<br />
<html><br />
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<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
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==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
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=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
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<div class="box-center"><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
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In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
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<div class="box-center"><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
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==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:33:58Z<p>PSchneider: /* Our swimming remediation raft */</p>
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<!-- Star des Inhalts --><br />
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==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is no longer needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===New York PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
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<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/File:TUM13_RenderingMIT.jpgFile:TUM13 RenderingMIT.jpg2013-10-29T00:31:56Z<p>PSchneider: uploaded a new version of &quot;File:TUM13 RenderingMIT.jpg&quot;</p>
<hr />
<div></div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-29T00:31:18Z<p>PSchneider: /* Closed tube reactor */</p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
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<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values. This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is no longer needed.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
<br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': 3D-print of our remediation raft]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T22:51:47Z<p>PSchneider: /* Our swimming remediation raft */</p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
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<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': 3D-print of our remediation raft]]<br />
<br />
[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[http://bvt.blt.kit.edu/ Homepage about Institute of bioprocess Engineering (KIT)]<br />
<br />
[http://op-n.net/filter/work/PARALLEL-NETWORKS Homepage Op.N]<br />
<br />
[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]<br />
<br />
[http://www.bestmann-green-systems.de/ Homepage BGS Ingenieurbiologie und -ökologie GmbH]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/File:TUM13_RenderingMIT.jpgFile:TUM13 RenderingMIT.jpg2013-10-28T22:51:16Z<p>PSchneider: uploaded a new version of &quot;File:TUM13 RenderingMIT.jpg&quot;</p>
<hr />
<div></div>PSchneiderhttp://2013.igem.org/File:Raft.pngFile:Raft.png2013-10-28T22:49:53Z<p>PSchneider: uploaded a new version of &quot;File:Raft.png&quot;</p>
<hr />
<div></div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T21:25:34Z<p>PSchneider: /* Introduction */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
<br />
<!-- Ende des Inhalts --><br />
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</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T21:24:45Z<p>PSchneider: /* Introduction */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
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<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
<br />
<!-- Ende des Inhalts --><br />
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<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T21:24:00Z<p>PSchneider: /* Introduction */</p>
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<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|left|400px|'''Figure 21''': Idea for a measuring device]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Arduino Uno, released in September 2010]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
<br />
<!-- Ende des Inhalts --><br />
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</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T21:23:13Z<p>PSchneider: /* Introduction */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
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<div id="wikicontent-container"><br />
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<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:Arduino_Uno.png|thumb|right|200px|'''Figure 21''': Idea for a measuring device]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:TUM13_measuring_device.png|thumb|left|400px|'''Figure 22''': Arduino Uno, released in September 2010]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
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In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
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==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Team/AttributionsTeam:TU-Munich/Team/Attributions2013-10-28T21:11:56Z<p>PSchneider: /* Laboratory of Prof. Dr. Skerra */</p>
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== iGEM Team TU-Munich 2013 ==<br />
<br />
<br />
===Experimental measurements===<br />
All experiments and measurements were conducted by student members of the [https://2013.igem.org/Team:TU-Munich/Team/Members iGEM Team TU-Munich 2013]. The team could build on the knowledge of Jeffery Truong, Ingmar Polte and Katrin Fischer who had already participated in last year's competition and already knew the most important techniques and the laboratory. They implemented the lab management from last year from the first moment on, such as our extensive [https://2013.igem.org/Team:TU-Munich/Notebook/Labjournal Labjournal]. For the first usage of instruments we obtained an introduction into the lab techniques by an instructor. Measurement itself and the evaluation of the obtained data were done by us.<br />
<br />
====LC-MS Measurements====<br />
The LC-MS measurements were performed to confirm the successful degradation of pollutants by effector proteins which were produced recombinantly or which are expressed by transgenic moss plants. Here we contacted Prof. Dr. Thomas Hofmann, who already helped us in our last year's iGEM project with the detection of caffeine. The responsible team member for the LC-MS was in both years Ingmar Polte who performed the degradation experiment, established the contact to Prof. Hofmann and brought the samples to the [http://www.molekulare-sensorik.de Chair for Molecular Sensory]. At the chair, the student members Ingmar Polte or Andreas-David Brunner contacted the operator of the mass spectrometer (Mr. ???) with whom he did the sample preparation, the actual measurement and the data evaluation.<br />
<br />
====ESI-TOF Measurements====<br />
In order to confirm the correctness of recombinant proteins they were analyzed in the ESI-TOF mass spectrometer, which is present at our hosting laboratory. For this purpose a student team member did the sample preparation, calculated the theoretical mass using the '''[https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator]''' and brought the samples to Andreas Reichert who is a doctoral student at the chair and is responsible for the ESI-TOF mass spectrometer. He measured the samples together with a student team member and showed us the deconvolution of the primary data.<br />
<br />
====Fluorescense Microscopy====<br />
All fluorescense microscopy experiments were performed at the [http://plantdev.bio.wzw.tum.de/index.php?id=36 Chair for Plant Developmental Biology] (Prof. Dr. Schneitz) as plants (and especially ''P. patens'') exhibit a strong autofluorescence caused by the photosystem. Therefore an advanced microscope with appropriate filters is absolutely necessary which we could use at the Chair for Plant Developmental Biology. The experiments were performed by our student member [https://2013.igem.org/Team:TU-Munich/Team/Members Dong-Jiunn Jeffery Truong] who has worked during his bachelor thesis with fluorescense microscopy over several weeks and was therefore an essential experimentator for this part of the project. An introduction to the microscopes was given by Dr. Prasad Vaddepalli.<br />
<br />
====Transformation of ''Physcomitrella patens''====<br />
The transformation of ''Physcomitrella patens'' was one of the main concerns when we thought about working with ''Physcomitrella'' as it might cause some trouble which can only be handled by using the appropriate equipment and the advises of an experienced researcher. Therefore we contacted '''Prof. Dr. Reski''' (Freiburg University, 350 km distance) in May and could win him as an advisor for our team. After traveling several times to Freiburg we could perform the '''transformations''' in his lab. For this purpose we brought all buffers and the sterile linearized DNA from Munich and performed the transformation under the instructions of Dr. Gertrud Wiedemann. All steps of the transformation were conducted by student team members as it can be seen in our [https://2013.igem.org/Team:TU-Munich/Results/Moss#3._Transformation_of_Physcomitrella_patens Transformation Results] section.<br />
<br />
====Outreach====<br />
The [http://vimeo.com/76195786 introduction video for our team] created during this competition, was designed, produced and cut by the student team member Katrin Fischer.<br><br />
The group photos of our team were created by the press office of the TUM.<br />
<br />
== Laboratory of Prof. Dr. Skerra ==<br />
<br />
The research group at the [http://biologische-chemie.userweb.mwn.de/index.html Chair of Biological Chemistry] at TUM works in the field of biochemical protein engineering and design with a focus on therapeutic proteins and their application. The three main fields of research are (1) the development of '''anticalins''' which is an alternative binding scaffold and which are a promising alternative for conventional antibodies (2) the '''extension''' of the '''plasma half-life''' of therapeutic proteins using a poly-peptide polymer and (3) the '''site-specific conjugation''' of therapeutic proteins. Thus the focus of our hosting laboratory is biomedical engineering whereas our iGEM topic shows no intersection with this topic. <br><br />
The single negligible exception is that we used a '''higher engineered anticalin''' (<partinfo>K1159003</partinfo>) to bind fluorescein in our [https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation] subproject, compared to the conventional BioBrick (<partinfo>BBa_K157004</partinfo>). This higher engineered version has three additional amino acid exchanges and exhibits a 75-fold higher affinity for its binding partner (fluorescein). It was not essential to have this higher engineered version for our project but we wanted to supply the registry with this improved part.<br><br />
Beside this plasmid, we also obtained a plasmid for the TEV protease from the chair which we have used to generate the Split-TEV protease (<partinfo>BBa_K1159100</partinfo>, <partinfo>BBa_K1159101</partinfo> and <partinfo>BBa_K1159102</partinfo>).<br />
<br />
<br />
''Prof. Skerra kindly provided us with '''space in his laboratory''', and '''generously advanced us money''' to pay for team registration, travel expenses and laboratory resources. Moreover he '''participated approximately one a month in our team meetings''' and advised us on our project.''<br />
<br />
== Technical University Munich ==<br />
As we had to cover several different scientific aspects during our project we contacted several professors from our university to get their opinion on our plans, obtain reagents or access to measuring instruments such as mass spectrometers or microscopes.<br />
<br />
==== Laboratory of Prof. Dr. Helmreich ====<br />
[http://www.sww.bv.tum.de Sanitary Environmental Engineering] is a horizontal discipline comprised of civil engineering, process engineering and chemistry/biology. Research and teaching include the fields of water supply, sewage and rain water treatment, water quality and the modeling of aquatic systems.<br />
<br />
''In our interview with Prof. Helmreich, she explained us several '''characterization techniques''' to assess water quality. Furthermore she kindly provided us with '''water samples''' from sewage treatment plants.''<br />
<br />
==== Laboratory of Prof. Dr. Thomas Hofmann ====<br />
LCMS<br />
<br />
==== Laboratory of Prof. Dr. Langosch ====<br />
The [http://www.wzw.tum.de/biopolymere Chair for Chemistry of Biopolymers] focuses on the '''structural biochemistry''' of '''integral membrane proteins'''. Core themes are molecular interactions between membrane proteins, structural dynamics of membrane bound protein helices, membrane protein/lipid interactions and structure/function relationships of integral membrane protein complexes.<br />
<br />
''During the planning phase of our project we asked Prof. Langosch for advice concerning the design of the transmembrane domain of our constructs.''<br />
<br />
==== Laboratory of Prof. Dr. Rost ====<br />
Prof. Rost works in the field of '''bioinformatics''' and computer-based biology, focusing on the '''prediction of structure and function of proteins''' and genes. His team's specialty is the use of artificial intelligence and machine learning algorithms to predict structure and function of proteins.<br />
<br />
''After developing an early version of our [https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator AutoAnnotator], we presented our work to Prof. Rost and his group. He gave us some very helpful advice on features we could add and provided us with access to his [http://www.predictprotein.org/ PredictProtein] server. A special "thank you" goes to Manfred Roos for tailoring the access point of the server to our needs.''<br />
<br />
==== Laboratory of Prof. Dr. Schneitz ====<br />
The [http://plantdev.bio.wzw.tum.de/index.php?id=36 Chair for Plant Developmental Biology] is interested in the genetic and molecular basis of the '''regulatory pathways controlling organ development and tissue morphogenesis''' in plants. <br />
<br />
''The chair gave us great access to their '''microscopes''' and excellent support in how to use them. Many thanks for that, especially to Prasad Vaddepalli for his introduction into fluorescence microscopy.''<br />
<br />
==== Laboratory of Prof. Dr. Schwechheimer ====<br />
The [http://www.sysbiol.wzw.tum.de Chair for Systems Biology of Plants] investigates a range of '''queries''' concerning the '''ubiquitin proteasome''' system of plants applying a combination of genetics, molecular biology and cell biology with both '''genomic''' and '''proteomic''' approaches. <br />
<br />
''Together with Prof. Schwechheimer we discussed several different signal transduction pathways that could be utilised for our '''[https://2013.igem.org/Team:TU-Munich/Project/Killswitch kill-switch]'''. Moreover he kindly granted us access to a '''fluorescence microscope'''.''<br />
<br />
==== Laboratory of Prof. Dr. Scherer ====<br />
The [http://www.micbio.wzw.tum.de/index.php Chair for microbial ecology] conducts basic research in the field of '''molecular genetics and ecology of pathogenic microorganisms'''. Projects include the microbial characterization of food and microbial diagnostics and consulting in the food industry for prevention and clearance of contaminations.<br />
<br />
''The team kindly provided us with a culture of ''Micrococcus luteus'' for the '''[https://2013.igem.org/wiki/index.php?title=Team:TU-Munich/Results/Recombinant#Kirby-Bauer_Assay:_Measuring_remaining_erythromycin_on_a_pertri_dish Kirby-Bauer assay]''' and also helped out with a tube of restriction enzyme during an unexpected shortage.''<br />
<br />
== Other Universities ==<br />
The team also obtained help from other universities in order to complete the project. As nobody at our university works with ''Physcomitrella patens'' which the team chose to work with we had to find an advisor who could support us with the '''transformation procedure''' which is not really simple for plants. Additionally researches from other universities helped us by '''providing plasmids'''. <br />
<br />
==== Laboratory of [https://2013.igem.org/Team:TU-Munich/Team/Members#Prof._Dr._Ralf_Reski Prof. Dr. Reski] at Freiburg University (Germany) ====<br />
The team at the [http://www.plant-biotech.net/ Chair for Plant Biotechnology] is working on '''gene expression''' in the bryophyte model plant ''Physcomitrella patens'' (Hedw.) B.S.G. at different levels in correlation with phenotype analysis and additionally employs comparative genomic approaches.<br />
<br />
''The Reski team kindly supported us by supervising [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss our moss transformations at their lab] and by allowing us to use some of their equipment and materials for the process. Our special thanks go to [https://2013.igem.org/Team:TU-Munich/Team/Members#Dr._Gertrud_Wiedemann Dr. Gertrud Wiedemann].''<br />
<br />
==== Laboratory of Prof. Dr. Fussenegger at ETH Zurich (Switzerland)====<br />
The research group at the [http://www.bsse.ethz.ch/groups/group_fussenegger/index/ Chair for Biotechnology and Bioengineering] is implementing a progress in basic research to achieve generic and prototypic advances in '''human therapy''' by focusing on '''mammalian cells''' and capitalizing on an integrated interdisciplinary systems approach. Their current research initiatives include several programs interfacing with '''biopharmaceutical manufacturing''', '''gene therapy''' and '''tissue engineering'''.<br />
<br />
''They kindly provided us with the pSH21 plasmid which was used as template for the Polioviral Internal Ribosome Entry Site (<partinfo>BBa_K1159300</partinfo>).''<br />
<br />
==== Laboratory of Dr. G.D. Wright at McMaster University (Canada) ====<br />
<br />
The [http://www.thewrightlab.com Wright Lab] is trying to understand fundamental aspects of '''how antibiotics work''', their sources and '''how bacteria become resistant''' to them.<br />
<br />
''They kindly provided us with the plasmids pDEST14_ereA and pDEST14_ereB which was used as a template for the Erythromycin Esterase Type II (<partinfo>BBa_K1159000</partinfo>).''<br />
<br />
==== Laboratory of Prof. Dr. Arndt at Potsdam University (Germany)====<br />
The team at the [http://www.uni-potsdam.de/index.php?id=13895 Chair for Molecular Biotechnology] investigates the '''factors that mediate interactions in coiled-coil proteins''' in order to target coiled-coil domains of proteins e.g. involved in tumorigenesis, tumor proliferation and metastasis.<br />
<br />
''Sven Hagen who had participated several times in iGEM in the past kindly provided us with the pBad-mVenus (<nowiki>RFC 25</nowiki>) expression plasmid. This plasmid was used for the production of recombinant protein in '''E. coli'''. ''<br />
<br />
== Webdesign ==<br />
The webdesign was entirely done by Florian Albrecht who has programmed different websites before. He also wrote the [https://2013.igem.org/Team:TU-Munich/Results/How_To webdesign tutorial] we put online to explain other teams how to use the code, developed by our team. The graphic elements used on the website were created by several different student members (such as Ingmar Polte, Katrin Fischer, Jeffery Truong, Rosario Ciccone and others) using the open source vector software Inkscape. The only component that was bought are the two direction signs used in the header (obtained from [http://vector-images.de/clipart/clp217632/ http://vector-images.de/clipart/clp217632]).<br />
<br />
==== normalize.css ====<br />
<br />
[http://necolas.github.io/normalize.css/ Normalize.css] was used to reset the wiki style (version used: 2.1.3).<br />
<br />
==== jQuery ====<br />
<br />
[http://jquery.com/ jQuery] is a powerful JavaScript extension used by many Webdesigners (version used: 1.10.2).<br />
<br />
==== jQuery UI ====<br />
<br />
[http://jqueryui.com/ jQuery UI] is a GUI extension of jQuery and was used for the datepicker on the Arduino data page (version used: 1.10.3).<br />
<br />
==== History.js ====<br />
<br />
[https://github.com/browserstate/history.js/ History.js] was used to ensure compatibility with HTML4 browsers, that do not support history.pushState().<br />
<br />
==== Slimbox 2 ====<br />
<br />
[http://code.google.com/p/slimbox/ Slimbox 2] was used as a picture viewer (version used: 2.05). The code had to be adapted to work with the wiki and bxSlider and we added a feature that fits the viewer to the browser size.<br />
<br />
==== bxSlider ====<br />
<br />
[http://bxslider.com/ bxSlider] is a JavaScript content slider and powers the slideshows and picture galleries on our wiki (version used: 4.1.1). The code was modified so all the images are scaled to the same height in gallery mode.<br />
<br />
==== NVD3 ====<br />
<br />
[http://nvd3.org/ NVD3] is a JavaScript chart library and was used for the interactive chart of the Arduino data (version used: 1.1.13).<br />
<br />
== Software - The AutoAnnotator ==<br />
The software tool we have written to '''facilitate and improve the annotation''' of protein coding BioBricks (the [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator]) was developed and programmed by the student member [https://2013.igem.org/Team:TU-Munich/Team/Members Christopher Wolf]. He developed this idea himself to import, translate sequences and to compute important parameters. After this was completed he contacted the bioinformatics group of Prof. Rost and presented his idea and the program in a group seminar. In the seminar, ideas for further improvements were generated. The group advised Chrostopher to implement a bioinformatic module that does alignments to several databases and bioinformatic servers. The research group of Prof. Rost has a server that concentrates bioinformatic information and they enabled Christopher to use this tool. He implemented these information into the AutoAnnotator himself. It was also Chrostopher Wolf who has written the [http://dspace.mit.edu/handle/1721.1/81330 RFC 96] to describe the usage of the AutoAnnotator and who created the [http://vimeo.com/75965599 introduction video].<br><br />
For further information please see our [https://2013.igem.org/Team:TU-Munich/Results/Software Software page].<br />
<br />
====jQuery====<br />
Powerful extension of JavaScript<br />
<br />
====James Padolsey====<br />
''We used [http://james.padolsey.com James Padolsey´s] jQuery extension for [http://james.padolsey.com/javascript/cross-domain-requests-with-jquery/ Cross-domain AJAX requests] in the AutoAnnotator.''<br />
<br />
====Flot.js====<br />
Plotting Charts (see flotchart.org)<br />
<br />
<br />
====Flot-AxisLabels====<br />
Adds axis labels to Flot.js<br />
https://github.com/markrcote/flot-axislabels<br />
<br />
====Excanvas====<br />
Extend <canvas>-tag to IE 8.0 and earlier.<br />
<br />
====Paul Johnston====<br />
MD5 generator<br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Modeling/Protein_PredictionsTeam:TU-Munich/Modeling/Protein Predictions2013-10-28T21:06:56Z<p>PSchneider: /* Analysis of Receptor Sequences &ndash; Choosing the right template */</p>
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==Prediction of Protein Structures and Functions==<br />
'''Structural properties''' of '''effector proteins''' are often essential for their function, so it is advantageous to know about them. It is for example necessary to know whether '''termini are accessible''' for protein fusion or whether the protein is '''only functional in a multimeric fold'''. For this reason a structure based search was performed in the [http://www.rcsb.org/pdb/home/home.do protein database]. As the number of identified structures is still limited, it is a promising attempt to look for homologous proteins whose crystal structures have been determined.<br />
<br />
==Analysis of Receptor Sequences &ndash; Choosing the right template ==<br />
<br />
For several purposes of our project, we needed a synthetic receptor enabling us to integrate proteins into the membrane in the desired orientation, i.e. to express protein-domains on the intracellular or extracellular side of the cell membrane. We investigated several different plant-receptors from the well characterized dicotyledon ''Arabidopsis thaliana'' and the moss ''Physcomitrella patens'', our chassis. The receptors from ''Arabidopsis thaliana'' have the advantage that their transgenic expression has successfully been demonstrated [[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] whereas the native receptors from ''Physcomitrella patens'' bear only a small risk of failing [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]]<br><br />
Due to the fact that there were many different available receptors, which we could have used as template for our synthetic receptor, we used bioinformatical methods to evaluate the suitability of these receptors. The following three examples ERF, FLS2 and SERK shown in table 1 resulted from this equation.<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1:''' Examined Receptors<br />
!Receptor<br />
!Organism<br />
!Length (aa)<br />
!Sequence reference<br />
!Literature reference<br />
|-<br />
|ERF<br />
|''A. thaliana''<br />
|1031<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_197548.1 NP_197548.1]<br />
|<br />
|-<br />
|FLS2<br />
|''A. thaliana''<br />
|1173<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_199445.1 NP_199445.1]<br />
|<br />
|-<br />
|SERK<br />
|''P. patens''<br />
|625<br />
|[http://www.ncbi.nlm.nih.gov/protein/XP_001759122.1 XP_001759122.1]<br />
|[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]<br />
|-<br />
|}<br />
<br><br />
<br><br />
===Prediction of Signal Peptides===<br />
[[File:TUM13 Modeling_Signal-P.png|thumb|right|350px| '''Figure 1:''' Prediction and analysis of signal peptides]]<br />
'''Introduction'''<br><br />
A first analysis was performed to identify signal-peptides, which are bound by the cellular signal recognition particle and lead to the translocation of the bound polypeptide into the endoplasmic reticulum. Afterwards the signal peptide is cleaved by a signal peptide peptidase at a specific site. The analysis for signal peptides was done by using the [http://www.cbs.dtu.dk/services/SignalP SignalP 4.1 Server]. <br><br />
<br><br />
'''Results'''<br><br />
The program was run for different receptors and will be illustrated for the three examples mentioned above (see fig. 1). <br><br />
The figure shows the N-terminal sequence of the receptors, together with three scores: <br><br />
(1) The C-Score (raw cleavage site score) in red. <br><br />
(2) The S-Score (signal peptide score) in green. <br><br />
(3) The Y-Score (combined cleavage site score) in blue.<br><br />
<br><br />
The C-Score shows the most probable cleavage site identified by the peptidase. It was possible to identify the most probable cleavage site for all shown receptors with ambiguous cleavage sites for the SERK-receptor. The amino acid with the highest C-score is predicted to be the first amino acid of the primary structure of the cleaved receptor. <br><br />
The S-Score was developed to identify amino acid sequences which appear in a signal peptide and others that belong to the matured receptor. The course of this parameter is high for the first 23-28 amino acids of all receptors, identifying these residues as signal peptides. The amino acid residue, which lies at the greatest decrease of the S-Score, is the predicted border between the N-terminal signal peptide and the receptor. <br><br />
The Y-Score results from the geometrical structure of the protein and the previously determined scoring parameters. It illustrates that the two first parameters show a good fit for the identification of the signal peptide in all three indicated receptors.<br><br />
<br><br />
'''Discussion'''<br><br />
Summarizing these parameters, it can be concluded that all three pictured receptors seem to contain a sequence acting as a signal peptide. For many of the predicted receptors in the genome of ''Physcomitrella patens'' the prediction did not yield a positive result. With respect to the signal peptide, all mentioned receptors would be suitable as a template for our synthetic receptor. The predicted data show that the SERK-Receptor is favorable for our application, because its signal peptide is statistically the best recognized one and bears the smallest risk of failure.<br />
<br />
<br><br />
<br><br />
<br />
===Prediction of Transmembrane Regions===<br />
[[File:TUM13 Modeling_TMHMM.png|thumb|right|350px| '''Figure 2:''' Prediction and analysis of transmembrane regions]]<br />
'''Introduction'''<br><br />
Additional to the identification of the signal peptide, it was very important to identify transmembrane regions within the receptors, because we wanted to use a type I receptor as a template that contains a N-terminal extracellular domain, a transmembrane domain and a C-terminal intracellular domain (see [https://2013.igem.org/Team:TU-Munich/Project/Localisation our localization page]). To analyze this issue, the prediction tool [http://www.cbs.dtu.dk/services/TMHMM TMHMM] was used for several different receptors. Again the most suitable receptors were ERK, FLS2 and SERK.<br><br />
<br><br />
'''Results'''<br><br />
The analysis yields a signal peptide and a single transmembrane domain for all three depicted receptors (see fig. 2). The estimated reliability of the predictions was equally good for all examined receptors, whereas the signal peptide was most reliably predicted for the SERK receptor. <br><br />
<br><br />
'''Discussion'''<br><br />
Focussing on the membrane topology point of view, all the investigated receptors would be suitable blue prints for our synthetic receptor. As the SERK-Receptor yields the best prediction, it was chosen as the favorable template. Another reason to choose the SERK-Receptor was that it is derived from ''Physcomitrella patens''. The only problem, concerning this prediction, is that the N-terminus of this receptor is predicted to be extracellular. The falsification of this prediction was simple, because the SERK receptor contains a C-terminal kinase-domain, which is known to be involved in signal transduction.<br />
<br><br />
<br><br />
<br />
===Choice of the SERK Receptor===<br />
Finally we decided to use the SERK receptor as a template to generate our synthetic receptor. The final receptor was designed in RFC[25] standard, which allows in frame protein fusions. The final constructs were designed containing the SERK signal peptide ([http://parts.igem.org/Part:BBa_K1159303 BBa_K1159303]), an extracellularly located effector protein, the transmembrane domain of the SERK receptor ([http://parts.igem.org/Part:BBa_K1159305 BBa_K1159305]), a short linker and a GFP, to investigate the cellular localization of our receptor with the aid of fluorescence microscopy.<br />
<br />
==Searching for Homologous Structures using HHpred==<br />
====Aim:====<br />
====Approach:====<br />
====Results:====<br />
====Conclusion:====<br />
<br />
The search for homologous structures was performed by using the freely accessible web server [http://toolkit.tuebingen.mpg.de/hhpred HHpred] [[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]]. The amino acid sequences for the BioBricks were translated into amino acid sequences using the [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator] and was then inserted into the the search field. The results for all proteins investigated in our project are shown in table 2. <br />
{|cellspacing="0" border="1" right<br />
|+ '''Table 2:''' Predicted Structures<br />
!Protein<br />
!BioBrick<br />
!PDB-code<br />
!Identity<br />
!Similarity<br />
!Structure<br />
|-<br />
|XylE<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K147002 BBa_K147002]<br />
| [http://www.rcsb.org/pdb/explore.do?structureId=3hpy 3hpy_A]<br />
|50%<br />
|0.939<br />
|[[File:TUM13 small_XylE.png|85px]]<br />
|-<br />
|Laccase<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159002 BBa_K1159002]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2wsd 2wsd_A]<br />
|68%<br />
|1.223<br />
|[[File:TUM13 small_Laccase.png|85px]]<br />
|-<br />
|NanoLuc<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159001 BBa_K1159001]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3ppt 3ppt_A]<br />
|21%<br />
|0.359<br />
|[[File:TUM13 small_NanoLuc.png|85px]]<br />
|-<br />
|EreB<br />
|[http://parts.igem.org/Part:BBa_K1159000 BBa_K1159000]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3b55 3b55_A]<br />
|19%<br />
|0.318<br />
|[[File:TUM13_small_EreBx.png|85px]]<br />
|-<br />
|Spycatcher<br />
|[http://parts.igem.org/Part:BBa_K1159200 BBa_K1159200]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2x5p 2x5p_A]<br />
|97%<br />
|1.298<br />
|[[File:TUM13 small_SpyCatcher.png|85px]]<br />
|-<br />
|PP1<br />
|[http://parts.igem.org/Part:BBa_K1159004 Part:BBa_K1159004]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3e7a 3e7a_A]<br />
|96%<br />
|1.593<br />
|[[File:TUM13_small_PP1.png|85px]]<br />
|-<br />
|GFP<br />
|[http://parts.igem.org/Part:BBa_K1159311 BBa_K1159311]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2WUR 2WUR]<br />
|98%<br />
|1.477<br />
|[[File:TUM13 small_GFP.png|85px]]<br />
|-<br />
|Glutathiontransferase / DDT Dehydrochlorinase<br />
|<partinfo>BBa_K620000</partinfo><br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3F6D 3F6D]<br />
|68%<br />
|1.155<br />
|[[File:TUM13 small_GST.png|85px]]<br />
|-<br />
|SERK-TM<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159305 BBa_K1159305]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2ks1 2ks1_B]<br />
|24%<br />
|0.233<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|TEV Protease<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=1Q31 1Q31]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|Streptavidin<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3RY2 3RY2]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|}<br />
<br />
====Results====<br />
The homology search showed that some of our effector proteins have very closely related proteins with a known structure. For example there are very similar protein structures available for the SypCatcher, PP1 and GFP each with identities of over 90%. Some other effector proteins such as XylE, Laccase or the DDT Dehydrochlorinase have less homologous proteins, whose structures still give good hints on structural questions. However there are also effectors where only badly matched structures are known, which can only be used as a very rough indication of the fold. The NanoLuc luciferase, which is a highly engineered protein derived from shrimps and was only published this year, is an example of a protein with no known structural homologue.<br><br />
The structures obtained here were used to design our experiments. A homology modeling for the Laccase was performed to determine whether it contains disulphide bridges. The resulting homologous structures were used as illustrations, as explained in one of our [https://2013.igem.org/Team:TU-Munich/Results/How_To How-Tos] about animated GIFs.<br />
<br />
==References:==<br />
[[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] MARGARET T. Boylan, M.T. and Quail, P.H. (1991). PhytochromeA overexpression inhibits hypocotyl elongation in transgenic ''Arabidopsis''. ''Proc. Natl. Acad. Sci.'' 88:10806-10810.<br><br />
<br />
[[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Reski, R. (1998). Development, Genetics and Molecular Biology of Mosses. ''Bot. Acta'', 111:1-15.<br /><br />
<br />
[[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]] Lienhart, O. (2007). Untersuchungen zu einem Somatic-Embryogenesis-Receptor-like-Kinase-Homolog in ''Physcomitrella patens'' (Hedw.) B.S.G. PhD-thesis at Freiburg University<br />
<br />
[http://www.cbs.dtu.dk/services/SignalP/ SignalP41 Server]<br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]] Söding J, Biegert A, Lupas AN. (2005). The HHpred interactive server for protein homology detection and structure prediction. ''Nucleic Acids Res.'' 2005 Jul 1;33(Web Server issue):W244-8.<br><br />
<br />
<br />
<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Modeling/Protein_PredictionsTeam:TU-Munich/Modeling/Protein Predictions2013-10-28T20:31:22Z<p>PSchneider: /* Analysis of Receptor Sequences &ndash; Choosing the right template */</p>
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<!-- Start des Inhalts --><br />
<br />
==Prediction of Protein Structures and Functions==<br />
'''Structural properties''' of '''effector proteins''' are often essential for their function, so it is advantageous to know about them. It is for example necessary to know whether '''termini are accessible''' for protein fusion or whether the protein is '''only functional in a multimeric fold'''. For this reason a structure based search was performed in the [http://www.rcsb.org/pdb/home/home.do protein database]. As the number of identified structures is still limited, it is a promising attempt to look for homologous proteins whose crystal structures have been determined.<br />
<br />
==Analysis of Receptor Sequences &ndash; Choosing the right template ==<br />
<br />
For several purposes of our project, we needed a synthetic receptor enabling us to integrate proteins into the membrane in the desired orientation, i.e. to express protein-domains on the intracellular or extracellular side of the cell membrane. We investigated several different plant-receptors from the well characterized dicotyledon ''Arabidopsis thaliana'' and the moss ''Physcomitrella patens'', our chassis. The receptors from ''Arabidopsis thaliana'' have the advantage that their transgenic expression has successfully been demonstrated [[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] whereas the receptors from ''Physcomitrella patens'' bear less risk of failing [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]]<br><br />
Due to the fact that there were many different available receptors, which we could use as a template for our synthetic receptor, we used bioinformatical methods to evaluate the suitability of these receptors. The following three examples ERF, FLS2 and SERK shown in table 1 resulted from this equation.<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1:''' Examined Receptors<br />
!Receptor<br />
!Organism<br />
!Length (aa)<br />
!Sequence reference<br />
!Literature reference<br />
|-<br />
|ERF<br />
|''A. thaliana''<br />
|1031<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_197548.1 NP_197548.1]<br />
|<br />
|-<br />
|FLS2<br />
|''A. thaliana''<br />
|1173<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_199445.1 NP_199445.1]<br />
|<br />
|-<br />
|SERK<br />
|''P. patens''<br />
|625<br />
|[http://www.ncbi.nlm.nih.gov/protein/XP_001759122.1 XP_001759122.1]<br />
|[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]<br />
|-<br />
|}<br />
<br><br />
<br><br />
===Prediction of Signal Peptides===<br />
[[File:TUM13 Modeling_Signal-P.png|thumb|right|350px| '''Figure 1:''' Prediction and analysis of signal peptides]]<br />
'''Introduction'''<br><br />
A first analysis was performed to identify signal-peptides, which are bound by the cellular signal recognition particle and lead to the translocation of the bound polypeptide into the endoplasmic reticulum. Afterwards the signal peptide is cleaved by a signal peptide peptidase at a specific site. The analysis for signal peptides was done by using the [http://www.cbs.dtu.dk/services/SignalP SignalP 4.1 Server]. <br><br />
<br><br />
'''Results'''<br><br />
The program was run for different receptors and will be illustrated for the three examples mentioned above (see fig. 1). <br><br />
The figure shows the N-terminal sequence of the receptors, together with three scores: <br><br />
(1) The C-Score (raw cleavage site score) in red. <br><br />
(2) The S-Score (signal peptide score) in green. <br><br />
(3) The Y-Score (combined cleavage site score) in blue.<br><br />
<br><br />
The C-Score shows the most probable cleavage site identified by the peptidase. It was possible to identify the most probable cleavage site for all shown receptors with ambiguous cleavage sites for the SERK-receptor. The amino acid with the highest C-score is predicted to be the first amino acid of the primary structure of the cleaved receptor. <br><br />
The S-Score was developed to identify amino acid sequences which appear in a signal peptide and others that belong to the matured receptor. The course of this parameter is high for the first 23-28 amino acids of all receptors, identifying these residues as signal peptides. The amino acid residue, which lies at the greatest decrease of the S-Score, is the predicted border between the N-terminal signal peptide and the receptor. <br><br />
The Y-Score results from the geometrical structure of the protein and the previously determined scoring parameters. It illustrates that the two first parameters show a good fit for the identification of the signal peptide in all three indicated receptors.<br><br />
<br><br />
'''Discussion'''<br><br />
Summarizing these parameters, it can be concluded that all three pictured receptors seem to contain a sequence acting as a signal peptide. For many of the predicted receptors in the genome of ''Physcomitrella patens'' the prediction did not yield a positive result. With respect to the signal peptide, all mentioned receptors would be suitable as a template for our synthetic receptor. The predicted data show that the SERK-Receptor is favorable for our application, because its signal peptide is statistically the best recognized one and bears the smallest risk of failure.<br />
<br />
<br><br />
<br><br />
<br />
===Prediction of Transmembrane Regions===<br />
[[File:TUM13 Modeling_TMHMM.png|thumb|right|350px| '''Figure 2:''' Prediction and analysis of transmembrane regions]]<br />
'''Introduction'''<br><br />
Additional to the identification of the signal peptide, it was very important to identify transmembrane regions within the receptors, because we wanted to use a type I receptor as a template that contains a N-terminal extracellular domain, a transmembrane domain and a C-terminal intracellular domain (see [https://2013.igem.org/Team:TU-Munich/Project/Localisation our localization page]). To analyze this issue, the prediction tool [http://www.cbs.dtu.dk/services/TMHMM TMHMM] was used for several different receptors. Again the most suitable receptors were ERK, FLS2 and SERK.<br><br />
<br><br />
'''Results'''<br><br />
The analysis yields a signal peptide and a single transmembrane domain for all three depicted receptors (see fig. 2). The estimated reliability of the predictions was equally good for all examined receptors, whereas the signal peptide was most reliably predicted for the SERK receptor. <br><br />
<br><br />
'''Discussion'''<br><br />
Focussing on the membrane topology point of view, all the investigated receptors would be suitable blue prints for our synthetic receptor. As the SERK-Receptor yields the best prediction, it was chosen as the favorable template. Another reason to choose the SERK-Receptor was that it is derived from ''Physcomitrella patens''. The only problem, concerning this prediction, is that the N-terminus of this receptor is predicted to be extracellular. The falsification of this prediction was simple, because the SERK receptor contains a C-terminal kinase-domain, which is known to be involved in signal transduction.<br />
<br><br />
<br><br />
<br />
===Choice of the SERK Receptor===<br />
Finally we decided to use the SERK receptor as a template to generate our synthetic receptor. The final receptor was designed in RFC[25] standard, which allows in frame protein fusions. The final constructs were designed containing the SERK signal peptide ([http://parts.igem.org/Part:BBa_K1159303 BBa_K1159303]), an extracellularly located effector protein, the transmembrane domain of the SERK receptor ([http://parts.igem.org/Part:BBa_K1159305 BBa_K1159305]), a short linker and a GFP, to investigate the cellular localization of our receptor with the aid of fluorescence microscopy.<br />
<br />
==Searching for Homologous Structures using HHpred==<br />
====Aim:====<br />
====Approach:====<br />
====Results:====<br />
====Conclusion:====<br />
<br />
The search for homologous structures was performed by using the freely accessible web server [http://toolkit.tuebingen.mpg.de/hhpred HHpred] [[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]]. The amino acid sequences for the BioBricks were translated into amino acid sequences using the [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator] and was then inserted into the the search field. The results for all proteins investigated in our project are shown in table 2. <br />
{|cellspacing="0" border="1" right<br />
|+ '''Table 2:''' Predicted Structures<br />
!Protein<br />
!BioBrick<br />
!PDB-code<br />
!Identity<br />
!Similarity<br />
!Structure<br />
|-<br />
|XylE<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K147002 BBa_K147002]<br />
| [http://www.rcsb.org/pdb/explore.do?structureId=3hpy 3hpy_A]<br />
|50%<br />
|0.939<br />
|[[File:TUM13 small_XylE.png|85px]]<br />
|-<br />
|Laccase<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159002 BBa_K1159002]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2wsd 2wsd_A]<br />
|68%<br />
|1.223<br />
|[[File:TUM13 small_Laccase.png|85px]]<br />
|-<br />
|NanoLuc<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159001 BBa_K1159001]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3ppt 3ppt_A]<br />
|21%<br />
|0.359<br />
|[[File:TUM13 small_NanoLuc.png|85px]]<br />
|-<br />
|EreB<br />
|[http://parts.igem.org/Part:BBa_K1159000 BBa_K1159000]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3b55 3b55_A]<br />
|19%<br />
|0.318<br />
|[[File:TUM13_small_EreBx.png|85px]]<br />
|-<br />
|Spycatcher<br />
|[http://parts.igem.org/Part:BBa_K1159200 BBa_K1159200]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2x5p 2x5p_A]<br />
|97%<br />
|1.298<br />
|[[File:TUM13 small_SpyCatcher.png|85px]]<br />
|-<br />
|PP1<br />
|[http://parts.igem.org/Part:BBa_K1159004 Part:BBa_K1159004]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3e7a 3e7a_A]<br />
|96%<br />
|1.593<br />
|[[File:TUM13_small_PP1.png|85px]]<br />
|-<br />
|GFP<br />
|[http://parts.igem.org/Part:BBa_K1159311 BBa_K1159311]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2WUR 2WUR]<br />
|98%<br />
|1.477<br />
|[[File:TUM13 small_GFP.png|85px]]<br />
|-<br />
|Glutathiontransferase / DDT Dehydrochlorinase<br />
|<partinfo>BBa_K620000</partinfo><br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3F6D 3F6D]<br />
|68%<br />
|1.155<br />
|[[File:TUM13 small_GST.png|85px]]<br />
|-<br />
|SERK-TM<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159305 BBa_K1159305]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2ks1 2ks1_B]<br />
|24%<br />
|0.233<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|TEV Protease<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=1Q31 1Q31]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|Streptavidin<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3RY2 3RY2]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|}<br />
<br />
====Results====<br />
The homology search showed that some of our effector proteins have very closely related proteins with a known structure. For example there are very similar protein structures available for the SypCatcher, PP1 and GFP each with identities of over 90%. Some other effector proteins such as XylE, Laccase or the DDT Dehydrochlorinase have less homologous proteins, whose structures still give good hints on structural questions. However there are also effectors where only badly matched structures are known, which can only be used as a very rough indication of the fold. The NanoLuc luciferase, which is a highly engineered protein derived from shrimps and was only published this year, is an example of a protein with no known structural homologue.<br><br />
The structures obtained here were used to design our experiments. A homology modeling for the Laccase was performed to determine whether it contains disulphide bridges. The resulting homologous structures were used as illustrations, as explained in one of our [https://2013.igem.org/Team:TU-Munich/Results/How_To How-Tos] about animated GIFs.<br />
<br />
==References:==<br />
[[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] MARGARET T. Boylan, M.T. and Quail, P.H. (1991). PhytochromeA overexpression inhibits hypocotyl elongation in transgenic ''Arabidopsis''. ''Proc. Natl. Acad. Sci.'' 88:10806-10810.<br><br />
<br />
[[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Reski, R. (1998). Development, Genetics and Molecular Biology of Mosses. ''Bot. Acta'', 111:1-15.<br /><br />
<br />
[[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]] Lienhart, O. (2007). Untersuchungen zu einem Somatic-Embryogenesis-Receptor-like-Kinase-Homolog in ''Physcomitrella patens'' (Hedw.) B.S.G. PhD-thesis at Freiburg University<br />
<br />
[http://www.cbs.dtu.dk/services/SignalP/ SignalP41 Server]<br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]] Söding J, Biegert A, Lupas AN. (2005). The HHpred interactive server for protein homology detection and structure prediction. ''Nucleic Acids Res.'' 2005 Jul 1;33(Web Server issue):W244-8.<br><br />
<br />
<br />
<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Modeling/Protein_PredictionsTeam:TU-Munich/Modeling/Protein Predictions2013-10-28T20:03:52Z<p>PSchneider: /* Prediction of Protein Structures and Functions */</p>
<hr />
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<br />
==Prediction of Protein Structures and Functions==<br />
'''Structural properties''' of '''effector proteins''' are often essential for their function, so it is advantageous to know about them. It is for example necessary to know whether '''termini are accessible''' for protein fusion or whether the protein is '''only functional in a multimeric fold'''. For this reason a structure based search was performed in the [http://www.rcsb.org/pdb/home/home.do protein database]. As the number of identified structures is still limited, it is a promising attempt to look for homologous proteins whose crystal structures have been determined.<br />
<br />
==Analysis of Receptor Sequences &ndash; Choosing the right template ==<br />
<br />
For several purposes of our project, we needed a synthetic receptor enabling us to integrate proteins into the membrane in the desired orientation, i.e. to express protein-domains on the intracellular or extracellular side of the cell membrane. We investigated several different plant-receptors from the well characterized dicotyledon ''Arabidopsis thaliana'' and the moss ''Physcomitrella patens'', our chassis. The receptors from ''Arabidopsis thaliana'' have the advantage that their transgenic expression has successfully been demonstrated [[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] whereas the receptors from ''Physcomitrella patens'' bear less risk that they do not work in the evolutionary far distant moss [[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]]<br><br />
Due to the fact that there were many different available receptors, which we could use as a template for our synthetic receptor, we used bioinformatical methods to evaluate the suitability of these receptors. The following three examples ERF, FLS2 and SERK shown in table 1 resulted from this equation.<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1:''' Examined Receptors<br />
!Receptor<br />
!Organism<br />
!Length (aa)<br />
!Sequence reference<br />
!Literature reference<br />
|-<br />
|ERF<br />
|''A. thaliana''<br />
|1031<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_197548.1 NP_197548.1]<br />
|<br />
|-<br />
|FLS2<br />
|''A. thaliana''<br />
|1173<br />
|[http://www.ncbi.nlm.nih.gov/protein/NP_199445.1 NP_199445.1]<br />
|<br />
|-<br />
|SERK<br />
|''P. patens''<br />
|625<br />
|[http://www.ncbi.nlm.nih.gov/protein/XP_001759122.1 XP_001759122.1]<br />
|[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]<br />
|-<br />
|}<br />
<br><br />
<br><br />
===Prediction of Signal Peptides===<br />
[[File:TUM13 Modeling_Signal-P.png|thumb|right|350px| '''Figure 1:''' Prediction and analysis of signal peptides]]<br />
'''Introduction'''<br><br />
A first analysis was performed to identify signal-peptides, which are bound by the cellular signal recognition particle and lead to the translocation of the bound polypeptide into the endoplasmic reticulum. Afterwards the signal peptide is cleaved by a signal peptide peptidase at a specific site. The analysis for signal peptides was done by using the [http://www.cbs.dtu.dk/services/SignalP SignalP 4.1 Server]. <br><br />
<br><br />
'''Results'''<br><br />
The program was run for different receptors and will be illustrated for the three examples mentioned above (see fig. 1). <br><br />
The figure shows the N-terminal sequence of the receptors, together with three scores: <br><br />
(1) The C-Score (raw cleavage site score) in red. <br><br />
(2) The S-Score (signal peptide score) in green. <br><br />
(3) The Y-Score (combined cleavage site score) in blue.<br><br />
<br><br />
The C-Score shows the most probable cleavage site identified by the peptidase. It was possible to identify the most probable cleavage site for all shown receptors with ambiguous cleavage sites for the SERK-receptor. The amino acid with the highest C-score is predicted to be the first amino acid of the primary structure of the cleaved receptor. <br><br />
The S-Score was developed to identify amino acid sequences which appear in a signal peptide and others that belong to the matured receptor. The course of this parameter is high for the first 23-28 amino acids of all receptors, identifying these residues as signal peptides. The amino acid residue, which lies at the greatest decrease of the S-Score, is the predicted border between the N-terminal signal peptide and the receptor. <br><br />
The Y-Score results from the geometrical structure of the protein and the previously determined scoring parameters. It illustrates that the two first parameters show a good fit for the identification of the signal peptide in all three indicated receptors.<br><br />
<br><br />
'''Discussion'''<br><br />
Summarizing these parameters, it can be concluded that all three pictured receptors seem to contain a sequence acting as a signal peptide. For many of the predicted receptors in the genome of ''Physcomitrella patens'' the prediction did not yield a positive result. With respect to the signal peptide, all mentioned receptors would be suitable as a template for our synthetic receptor. The predicted data show that the SERK-Receptor is favorable for our application, because its signal peptide is statistically the best recognized one and bears the smallest risk of failure.<br />
<br />
<br><br />
<br><br />
<br />
===Prediction of Transmembrane Regions===<br />
[[File:TUM13 Modeling_TMHMM.png|thumb|right|350px| '''Figure 2:''' Prediction and analysis of transmembrane regions]]<br />
'''Introduction'''<br><br />
Additional to the identification of the signal peptide, it was very important to identify transmembrane regions within the receptors, because we wanted to use a type I receptor as a template that contains a N-terminal extracellular domain, a transmembrane domain and a C-terminal intracellular domain (see [https://2013.igem.org/Team:TU-Munich/Project/Localisation our localization page]). To analyze this issue, the prediction tool [http://www.cbs.dtu.dk/services/TMHMM TMHMM] was used for several different receptors. Again the most suitable receptors were ERK, FLS2 and SERK.<br><br />
<br><br />
'''Results'''<br><br />
The analysis yields a signal peptide and a single transmembrane domain for all three depicted receptors (see fig. 2). The estimated reliability of the predictions was equally good for all examined receptors, whereas the signal peptide was most reliably predicted for the SERK receptor. <br><br />
<br><br />
'''Discussion'''<br><br />
Focussing on the membrane topology point of view, all the investigated receptors would be suitable blue prints for our synthetic receptor. As the SERK-Receptor yields the best prediction, it was chosen as the favorable template. Another reason to choose the SERK-Receptor was that it is derived from ''Physcomitrella patens''. The only problem, concerning this prediction, is that the N-terminus of this receptor is predicted to be extracellular. The falsification of this prediction was simple, because the SERK receptor contains a C-terminal kinase-domain, which is known to be involved in signal transduction.<br />
<br><br />
<br><br />
<br />
===Choice of the SERK Receptor===<br />
Finally we decided to use the SERK receptor as a template to generate our synthetic receptor. The final receptor was designed in RFC[25] standard, which allows in frame protein fusions. The final constructs were designed containing the SERK signal peptide ([http://parts.igem.org/Part:BBa_K1159303 BBa_K1159303]), an extracellularly located effector protein, the transmembrane domain of the SERK receptor ([http://parts.igem.org/Part:BBa_K1159305 BBa_K1159305]), a short linker and a GFP, to investigate the cellular localization of our receptor with the aid of fluorescence microscopy.<br />
<br />
==Searching for Homologous Structures using HHpred==<br />
====Aim:====<br />
====Approach:====<br />
====Results:====<br />
====Conclusion:====<br />
<br />
The search for homologous structures was performed by using the freely accessible web server [http://toolkit.tuebingen.mpg.de/hhpred HHpred] [[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]]. The amino acid sequences for the BioBricks were translated into amino acid sequences using the [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator] and was then inserted into the the search field. The results for all proteins investigated in our project are shown in table 2. <br />
{|cellspacing="0" border="1" right<br />
|+ '''Table 2:''' Predicted Structures<br />
!Protein<br />
!BioBrick<br />
!PDB-code<br />
!Identity<br />
!Similarity<br />
!Structure<br />
|-<br />
|XylE<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K147002 BBa_K147002]<br />
| [http://www.rcsb.org/pdb/explore.do?structureId=3hpy 3hpy_A]<br />
|50%<br />
|0.939<br />
|[[File:TUM13 small_XylE.png|85px]]<br />
|-<br />
|Laccase<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159002 BBa_K1159002]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2wsd 2wsd_A]<br />
|68%<br />
|1.223<br />
|[[File:TUM13 small_Laccase.png|85px]]<br />
|-<br />
|NanoLuc<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159001 BBa_K1159001]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3ppt 3ppt_A]<br />
|21%<br />
|0.359<br />
|[[File:TUM13 small_NanoLuc.png|85px]]<br />
|-<br />
|EreB<br />
|[http://parts.igem.org/Part:BBa_K1159000 BBa_K1159000]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3b55 3b55_A]<br />
|19%<br />
|0.318<br />
|[[File:TUM13_small_EreBx.png|85px]]<br />
|-<br />
|Spycatcher<br />
|[http://parts.igem.org/Part:BBa_K1159200 BBa_K1159200]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2x5p 2x5p_A]<br />
|97%<br />
|1.298<br />
|[[File:TUM13 small_SpyCatcher.png|85px]]<br />
|-<br />
|PP1<br />
|[http://parts.igem.org/Part:BBa_K1159004 Part:BBa_K1159004]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3e7a 3e7a_A]<br />
|96%<br />
|1.593<br />
|[[File:TUM13_small_PP1.png|85px]]<br />
|-<br />
|GFP<br />
|[http://parts.igem.org/Part:BBa_K1159311 BBa_K1159311]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2WUR 2WUR]<br />
|98%<br />
|1.477<br />
|[[File:TUM13 small_GFP.png|85px]]<br />
|-<br />
|Glutathiontransferase / DDT Dehydrochlorinase<br />
|<partinfo>BBa_K620000</partinfo><br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3F6D 3F6D]<br />
|68%<br />
|1.155<br />
|[[File:TUM13 small_GST.png|85px]]<br />
|-<br />
|SERK-TM<br />
|[http://parts.igem.org/wiki/index.php?title=Part:BBa_K1159305 BBa_K1159305]<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=2ks1 2ks1_B]<br />
|24%<br />
|0.233<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|TEV Protease<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=1Q31 1Q31]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|Streptavidin<br />
|Commercial reagent<br />
|[http://www.rcsb.org/pdb/explore.do?structureId=3RY2 3RY2]<br />
|n.d.<br />
|n.d.<br />
|[[File:Blanko2.png|85px]]<br />
|-<br />
|}<br />
<br />
====Results====<br />
The homology search showed that some of our effector proteins have very closely related proteins with a known structure. For example there are very similar protein structures available for the SypCatcher, PP1 and GFP each with identities of over 90%. Some other effector proteins such as XylE, Laccase or the DDT Dehydrochlorinase have less homologous proteins, whose structures still give good hints on structural questions. However there are also effectors where only badly matched structures are known, which can only be used as a very rough indication of the fold. The NanoLuc luciferase, which is a highly engineered protein derived from shrimps and was only published this year, is an example of a protein with no known structural homologue.<br><br />
The structures obtained here were used to design our experiments. A homology modeling for the Laccase was performed to determine whether it contains disulphide bridges. The resulting homologous structures were used as illustrations, as explained in one of our [https://2013.igem.org/Team:TU-Munich/Results/How_To How-Tos] about animated GIFs.<br />
<br />
==References:==<br />
[[http://www.pnas.org/content/88/23/10806.full.pdf Quail et al., 1991]] MARGARET T. Boylan, M.T. and Quail, P.H. (1991). PhytochromeA overexpression inhibits hypocotyl elongation in transgenic ''Arabidopsis''. ''Proc. Natl. Acad. Sci.'' 88:10806-10810.<br><br />
<br />
[[http://www.plant-biotech.net/paper/Reski_1998_BotActa-111_1_scan.pdf Reski, 1998]] Reski, R. (1998). Development, Genetics and Molecular Biology of Mosses. ''Bot. Acta'', 111:1-15.<br /><br />
<br />
[[http://www.freidok.uni-freiburg.de/volltexte/5390/pdf/Lienhart_Dissertation_2008.pdf Lienhart, 2007]] Lienhart, O. (2007). Untersuchungen zu einem Somatic-Embryogenesis-Receptor-like-Kinase-Homolog in ''Physcomitrella patens'' (Hedw.) B.S.G. PhD-thesis at Freiburg University<br />
<br />
[http://www.cbs.dtu.dk/services/SignalP/ SignalP41 Server]<br />
<br />
[[http://www.ncbi.nlm.nih.gov/pubmed/15980461 Söding et al., 2005]] Söding J, Biegert A, Lupas AN. (2005). The HHpred interactive server for protein homology detection and structure prediction. ''Nucleic Acids Res.'' 2005 Jul 1;33(Web Server issue):W244-8.<br><br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Modeling/OverviewTeam:TU-Munich/Modeling/Overview2013-10-28T19:44:58Z<p>PSchneider: /* Modeling Overview */</p>
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== Modeling Overview ==<br />
<br />
In our modeling efforts, we tried to cover a very wide range of different methods, reaching from simple ordinary differential equations, over partial differential equations, to stochastic differential equations as well as bioinformatical methods. To gain the largest possible output, we stayed in close contact with our wetlab team, answered their design questions and fitted parameters which could then be used for implementation aspects.<br />
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===Protein Predictions===<br />
For the immobilization of effectors on the cell membrane, we needed to design a transmembrane domain. Using several bioinformatical methods we identified the transmembrane region of the SERK receptor which we later used as starting point for our constructs. [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions Read More]<br />
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===Enzyme Kinetics===<br />
For an effective implementation of our filter system it is essential to analyze the enzymatic activity of our effectors. Using experimental data we fitted the respective kinetic parameters and carried out rigorous uncertainty analysis to assess the reliability of the fitted parameters. [https://2013.igem.org/Team:TU-Munich/Modeling/Enzyme Read More]<br />
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<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/b/b0/TUM13_modeling-3.jpg" /></html><br />
===Kill Switch===<br />
During the planning stage of our project, we had several different ideas on how to efficiently implement a kill-switch in our moss. In this section of the wiki we documented our mathematical train of thought that eventually led us to our final design.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Kill_Switch Read More]<br />
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<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/25/TUM13_modeling-4.jpg" /></html><br />
===Filter Model===<br />
The filter model is designed to simulate different remediation scenarios. It should be used to calculate the necessary amount of PhyscoFilters, referring to the environmental parameters.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Filter Read More]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T19:30:32Z<p>PSchneider: </p>
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==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
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<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:TUM13_measuring_device.png|thumb|left|400px|'''Figure 21''': Idea for a measuring device]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:Arduino_Uno.png|thumb|right|200px|'''Figure 22''': Arduino Uno, released in September 2010]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T19:27:37Z<p>PSchneider: /* Our swimming remediation raft */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|center|910px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:TUM13_measuring_device.png|thumb|left|400px|'''Figure 20''': Idea for a measuring device]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:Arduino_Uno.png|thumb|right|200px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 22''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 23''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 24: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 25"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 28"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 29''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 30"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 36"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37</a>"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
<br />
<!-- Ende des Inhalts --><br />
</div><br />
</div><br />
<br />
{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/File:TUM13_RenderingMIT.jpgFile:TUM13 RenderingMIT.jpg2013-10-28T19:26:34Z<p>PSchneider: </p>
<hr />
<div></div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Results/ImplementationTeam:TU-Munich/Results/Implementation2013-10-28T19:25:59Z<p>PSchneider: /* Our swimming remediation raft */</p>
<hr />
<div>{{Team:TU-Munich/TUM13_Menu}}<br />
{{Team:TU-Munich/TUM13_Style}}<br />
<br />
<div id="wikicontent-container"><br />
<div id="wikicontent"><br />
<!-- Star des Inhalts --><br />
<br />
==Implementation of a Plant Biofilter==<br />
How does a '''biofilter''' look like?<br />
To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br><br />
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br><br />
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.<br />
<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg" alt="Figure 4"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg" alt="Figure 5"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg" alt="Figure 6"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg" alt="Figure 7"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg" alt="Figure 8"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
<div class="box-left" style="height: 1480px;"><br />
===Closed tube reactor===<br />
[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]<br />
[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]<br />
The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It is one tube with the length of 15m arranged as a spiral. A meander shape wasn't possible, due to limits to the tube's bending radius. It has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.<br />
<br />
The idea behind that solution was to grow the moss on a bigger textile fiber inside the tube. In this manner many parameters are set and degradation experiments could return significant values.<br />
</div><br />
<br />
<div class="box-right" style="height: 1480px;"><br />
===Open filter on felt base===<br />
[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]<br />
Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.<br />
</div><br />
<br />
==Our swimming remediation raft==<br />
[[File:TUM13_RenderingMIT.jpg|thumb|800px|'''Figure 12''': Rendering of Remediation rafts in front of the MIT]]<br />
[[File:TUM13_lowcost_energy_scale_diagram.png|thumb|right|200px|'''Figure 13''': minimizing]]<br />
<br />
At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. <br />
The '''tube reactor''' guarantees a big '''contact surface''' between water and moss which is an asset to the filter properties, but the '''carbon dioxide exchange''' is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary.<br />
The '''open pond''' model brings along a smaller water-moss surface, therefore the filter properties may suffer and a '''wider area''' is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.<br />
<br />
Slightly we return to the question how a '''biofilter''' could look like.<br />
It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable. <br />
<br />
[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]<br />
<br />
Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.<br />
<br />
Our answer to that is the '''remediation raft'''. <br><br />
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. <br />
The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.<br />
<br />
===Shopping for the remediation raft===<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 1''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price in € (per piece)<br />
!Price in € (sum)<br />
|-<br />
|PVC-tubes 1,5 m, ⌀ 75mm<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 4,69<br />
| align=right | 14,07<br />
|-<br />
|One-eight bend (45°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Bend (67°)<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 1,09<br />
| align=right | 3,27<br />
|-<br />
|Fleece<br />
| align=right | 1,3 m<sup>2</sup><br />
|Hardware Store<br />
| align=right | 3,99 (per m<sup>2</sup>)<br />
| align=right | 5,19<br />
|-<br />
|Clamps<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 2,30<br />
| align=right | 6,90<br />
|-<br />
|Carbon rod<br />
| align=right | 1 (1,25 m)<br />
|Hardware Store<br />
| align=right | 4,75<br />
| align=right | 4,75<br />
|-<br />
|Round eyelets<br />
| align=right | 3<br />
|Hardware Store<br />
| align=right | 0,34<br />
| align=right | 1,01<br />
|-<br />
|'''Total'''<br />
|<br />
|<br />
|<br />
| align=right | '''38,44'''<br />
|-<br />
|}<br />
<br />
===Images from our trip to the construction center===<br />
<html><br />
<div class="box-center"><br />
<ul class="bxgallery"><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li><br />
</ul><br />
</div><br />
</html><br />
<br />
==Monitoring by an Arduino Microcontroller==<br />
<br />
===Introduction===<br />
[[File:TUM13_measuring_device.png|thumb|left|400px|'''Figure 20''': Idea for a measuring device]]<br />
One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that<br />
the environmental parameters fit and a proper living space is provided.<br />
The main goal of our measurement device is to '''monitor''' these environmental parameters in real time. <br />
Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.<br />
Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.<br />
So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.<br />
[[File:Arduino_Uno.png|thumb|right|200px|'''Figure 21''': Arduino Uno, released in September 2010]]<br />
This is where '''Arduino''' comes into play.<br />
Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming, <br />
the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for<br />
multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.<br />
We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010. <br />
Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.<br />
Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. <br />
But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.<br />
<br />
Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.<br />
It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. <br />
At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).<br />
<br />
We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.<br />
For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed. <br />
<br />
[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 22''': How it works]]<br />
<br />
The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.<br />
<br />
Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.<br />
[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 23''': components]]<br />
<br />
{|cellspacing="0" border="1"<br />
|+ '''Table 2''': Shopping list for our Arduino-Project<br />
!Component<br />
!Quantity<br />
!Source<br />
!Price<br />
!Figure<br />
|-<br />
|Arduino Due microcontroller<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]<br />
|46.41 €<br />
|Fig. 1 A<br />
|-<br />
|Arduino WIFI Shield<br />
|1<br />
|[https://www.sparkfun.com/products/11287 sparkfun]<br />
|63.58 €<br />
|Fig. 1 B<br />
|-<br />
|Watterott mega msd-shield<br />
|1<br />
|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]<br />
|19.49 €<br />
|Fig. 1 C<br />
|-<br />
|Display MI0283QT-9<br />
|1<br />
|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]<br />
|36.00 €<br />
|Fig. 1 D<br />
|-<br />
|Light sensor TSL2561<br />
|1<br />
|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]<br />
|7.74 €<br />
|Fig. 1 E<br />
|-<br />
|Temperature sensor DS18B20<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]<br />
|8.80 €<br />
|Fig. 1 G<br />
|-<br />
|Water sensor<br />
|1<br />
|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]<br />
|2.90 €<br />
|Fig. 1 H<br />
|-<br />
|Lithium-Battery<br />
|1<br />
|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]<br />
|16.35 €<br />
|<br />
|-<br />
|Stackable Headers<br />
|3<br />
|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]<br />
|5.37 €<br />
|<br />
|-<br />
|Linking wires and resistors<br />
|<br />
|<br />
|1.00 €<br />
|<br />
|-<br />
|Photo-diodes<br />
|3<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|207.64 €<br />
|280.77 $<br />
|}<br />
<br />
=== Server side ===<br />
<br />
To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.<br />
<br />
==How could it look installed in a river?==<br />
<br />
===NY PARALLEL NETWORKS===<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 24: embedding the PhyscoFilter pod"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 25"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 26"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 27"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 28"/></li><br />
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<br />
In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods. <br />
As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.<br />
We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.<br />
<br />
===Commercially available rafts called "Kampen"===<br />
[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 29''': Commercially available rafts]]<br />
During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.<br />
<br />
==Swimming remediation raft in action==<br />
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<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 30"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 31"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 32"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 33"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 34"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 35"/></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 36"/></a></li><br />
<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37</a>"/></li><br />
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<br />
==References:==<br />
<!-- Ab hier richtige Referenzen einfügen --><br />
<br />
[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Modeling/OverviewTeam:TU-Munich/Modeling/Overview2013-10-28T18:39:31Z<p>PSchneider: /* Modeling Overview */</p>
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== Modeling Overview ==<br />
<br />
In our modeling efforts, we tried to cover a very wide range of different methods, reaching from simple ordinary differential equations, over partial differential equations, to stochastic differential equations as well as bioinformatical methods. To gain the largest possible output, we stayed in close contact with our wetlab team, answered their design questions and fitted parameters which could then be used for implementation aspects.<br />
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<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/9/91/TUM13_modeling-1.jpg" /></html><br />
===Protein Predictions===<br />
For the immobilization of effectors on the cell membrane, we needed to design a transmembrane domain. Using several bioinformatical methods we identified the transmembrane region of the SERK receptor which we later used as starting point for our constructs. [https://2013.igem.org/Team:TU-Munich/Modeling/Protein_Predictions Read More]<br />
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<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/28/TUM13_modeling-2.jpg" /></html><br />
===Enzyme Kinetics===<br />
For the effective implementation of our filter system it is essential to analyse the enzymatic activity of our effectors. Using experimental data we fitted the respective kinetic parameters and carried out rigorous uncertainty analysis to assess the reliability of the fitted parameters. [https://2013.igem.org/Team:TU-Munich/Modeling/Enzyme Read More]<br />
</div><br />
<br />
<div class="box-left overview"><html><img src="https://static.igem.org/mediawiki/2013/b/b0/TUM13_modeling-3.jpg" /></html><br />
===Kill Switch===<br />
During the planning stage of our project, we had several different ideas on how to efficiently implement a kill-switch in our moss. In this section of the wiki we documented our mathematical train of thought that eventually led us to our final design.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Kill_Switch Read More]<br />
</div><br />
<br />
<div class="box-right overview"><html><img src="https://static.igem.org/mediawiki/2013/2/25/TUM13_modeling-4.jpg" /></html><br />
===Filter Model===<br />
The filter model is aimed to simulate different remediation scenarios and should be used to calculate the perfectly fitting conditions of our Physco filter, referring to the needs of the environment.<br>[https://2013.igem.org/Team:TU-Munich/Modeling/Filter Read More]<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Team/JudgingTeam:TU-Munich/Team/Judging2013-10-28T16:36:29Z<p>PSchneider: /* Medal Criteria */</p>
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<br />
==Medal Criteria==<br />
<br />
===Bronze Criteria===<br />
<div class="achievements"><br />
* Team registration<br><br />
We successfully registered our team and paid the registration fee.<br />
* Complete Judging form<br><br />
We successfully entered all the required Information into the Judging Form.<br />
* Team Wiki<br><br />
As you can see right now, we successfully created a team wiki and documented all our work according to the [https://2013.igem.org/Requirements/Wiki Wiki Requirements].<br />
* Present a poster and a talk at the iGEM Jamboree<br><br />
We are eagerly awaiting the Jamboree in Lyon to present our Project Idea and our Results.<br />
* Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). A new application of and outstanding documentation (quantitative data showing the Part’s/ Device’s function) of a previously existing BioBrick part in the “Experience” section of that BioBrick's Registry entry also counts. Please note you must submit this new part to the iGEM Parts Registry<br />
<br>See <partinfo>BBa_K1159000</partinfo>, <partinfo>BBa_K1159001</partinfo> as well as a series of other parts.<br />
</div><br />
<br />
===Silver Criteria===<br />
<div class="achievements"><br />
* Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.<br />
<br>See <partinfo>BBa_K1159000</partinfo>, <partinfo>BBa_K1159001</partinfo> as well as a series of other parts.<br />
* Document the characterization of this part in the “Main Page” section of that Part’s/Device’s Registry entry.<br />
<br>See <partinfo>BBa_K1159000</partinfo>, <partinfo>BBa_K1159001</partinfo> as well as a series of other parts.<br />
* Submit this new part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).<br />
<br>See <partinfo>BBa_K1159000</partinfo>, <partinfo>BBa_K1159001</partinfo> as well as a series of other parts.<br />
* Your project may have implications for the environment, security, safety and ethics and/or ownership and sharing. Describe one or more ways in which these or other broader implications have been taken into consideration in the design and execution of your project.<br />
<br>See https://2013.igem.org/Team:TU-Munich/Project/Safety<br />
</div><br />
<br />
===Gold Criteria===<br />
<div class="achievements"><br />
* Improve the function of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry (in the “Experience” section of that BioBrick’s Registry entry), create a new registry page for the improved part, and submit this part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).<br><br />
We improved three previously existing parts:<br><br />
*'''Laccase:''' <partinfo>BBa_K863000</partinfo> to <partinfo>BBa_K1159002</partinfo><br><br />
We converted the part from <nowiki>RFC 10 to RFC 25</nowiki>.<br><br />
*'''FluA:''' <partinfo>BBa_K157004</partinfo> to <partinfo>BBa_K1159003</partinfo><br><br />
We submitted an engineered variant with three additional mutations which make it 75-times more affine to fluorescein (KD from 152 nM to 2 nM).<br><br />
*'''PP1:''' [http://parts.igem.org/Part:BBa_K1012001 BBa_K1012001] to [http://parts.igem.org/Part:BBa_K1159004 Part:BBa_K1159004]<br><br />
We converted the part from <nowiki>RFC 10 to RFC 25</nowiki>.<br />
* Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.<br><br />
We had close collaboration with the 2013 teams from Dundee and Paris-Saclay and exchanged Biobricks with the 2012 team from LMU Munich and the 2013 teams from Tübingen, Uppsala and Paris Saclay. See: https://2013.igem.org/Team:TU-Munich/Team/Collaborations<br />
* Your project may have implications for the environment, security, safety and ethics and/or ownership and sharing. Describe a novel approach that your team has used to help you and others consider these aspects of the design and outcomes of synthetic biology efforts. Please justify its novelty and how this approach might be adapted and scaled for others to use.<br><br />
We took a new approach to the problem of phytoremediation by introducing a new chassis to iGEM. We hope that this will serve as reference for future teams that work on bioremediation or related environmental problems. See [https://2013.igem.org/Team:TU-Munich/Project/Phytoremediation Phytoremediation] for more details.<br />
</div><br />
<!---<br />
<br />
===Social Event Prizes at the Regional Jamboree===<br />
[[File:TUM13_Social_event.png|thumb|right|550px| '''Figure 1:''' Best of]]<br />
We applied for the Awards given during the social event in Lyon. Our transmittals were:<br />
*[[www.igem.org Best Logo]]<br />
*[www.igem.org Best Team Photo]<br />
*[www.igem.org Best T-Shirt]<br />
*[www.igem.org Best Video]<br />
*[www.igem.org Best Goodies]<br />
<br />
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{{Team:TU-Munich/TUM13_Footer}}</div>PSchneiderhttp://2013.igem.org/Team:TU-Munich/Team/AttributionsTeam:TU-Munich/Team/Attributions2013-10-28T16:19:21Z<p>PSchneider: /* Software - The AutoAnnotator */</p>
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== iGEM Team TU-Munich 2013 ==<br />
<br />
<br />
===Experimental measurements===<br />
All experiments and measurements were conducted by student members of the [https://2013.igem.org/Team:TU-Munich/Team/Members iGEM Team TU-Munich 2013]. The team could build on the knowledge of Jeffery Truong, Ingmar Polte and Katrin Fischer who had already participated in last year's competition and already knew the most important techniques and the laboratory. They implemented the lab management from last year from the first moment on, such as our extensive [https://2013.igem.org/Team:TU-Munich/Notebook/Labjournal Labjournal]. For the first usage of instruments we obtained an introduction into the lab techniques by an instructor. Measurement itself and the evaluation of the obtained data were done by us.<br />
<br />
====LC-MS Measurements====<br />
The LC-MS measurements were performed to confirm the successful degradation of pollutants by effector proteins which were produced recombinantly or which are expressed by transgenic moss plants. Here we contacted Prof. Dr. Thomas Hofmann, who already helped us in our last year's iGEM project with the detection of caffeine. The responsible team member for the LC-MS was in both years Ingmar Polte who performed the degradation experiment, established the contact to Prof. Hofmann and brought the samples to the [http://www.molekulare-sensorik.de Chair for Molecular Sensory]. At the chair, the student members Ingmar Polte or Andreas-David Brunner contacted the operator of the mass spectrometer (Mr. ???) with whom he did the sample preparation, the actual measurement and the data evaluation.<br />
<br />
====ESI-TOF Measurements====<br />
In order to confirm the correctness of recombinant proteins they were analyzed in the ESI-TOF mass spectrometer, which is present at our hosting laboratory. For this purpose a student team member did the sample preparation, calculated the theoretical mass using the '''[https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator]''' and brought the samples to Andreas Reichert who is a doctoral student at the chair and is responsible for the ESI-TOF mass spectrometer. He measured the samples together with a student team member and showed us the deconvolution of the primary data.<br />
<br />
====Fluorescense Microscopy====<br />
All fluorescense microscopy experiments were performed at the [http://plantdev.bio.wzw.tum.de/index.php?id=36 Chair for Plant Developmental Biology] (Prof. Dr. Schneitz) as plants (and especially ''P. patens'') exhibit a strong autofluorescence caused by the photosystem. Therefore an advanced microscope with appropriate filters is absolutely necessary which we could use at the Chair for Plant Developmental Biology. The experiments were performed by our student member [https://2013.igem.org/Team:TU-Munich/Team/Members Dong-Jiunn Jeffery Truong] who has worked during his bachelor thesis with fluorescense microscopy over several weeks and was therefore an essential experimentator for this part of the project. An introduction to the microscopes was given by Dr. Prasad Vaddepalli.<br />
<br />
====Transformation of ''Physcomitrella patens''====<br />
The transformation of ''Physcomitrella patens'' was one of the main concerns when we thought about working with ''Physcomitrella'' as it might cause some trouble which can only be handled by using the appropriate equipment and the advises of an experienced researcher. Therefore we contacted '''Prof. Dr. Reski''' (Freiburg University, 350 km distance) in May and could win him as an advisor for our team. After traveling several times to Freiburg we could perform the '''transformations''' in his lab. For this purpose we brought all buffers and the sterile linearized DNA from Munich and performed the transformation under the instructions of Dr. Gertrud Wiedemann. All steps of the transformation were conducted by student team members as it can be seen in our [https://2013.igem.org/Team:TU-Munich/Results/Moss#3._Transformation_of_Physcomitrella_patens Transformation Results] section.<br />
<br />
====Outreach====<br />
The [http://vimeo.com/76195786 introduction video for our team] created during this competition, was designed, produced and cut by the student team member Katrin Fischer.<br><br />
The group photos of our team were created by the press office of the TUM.<br />
<br />
== Laboratory of Prof. Dr. Skerra ==<br />
<br />
The research group at the [http://biologische-chemie.userweb.mwn.de/index.html Chair of Biological Chemistry] at TUM works in the field of biochemical protein engineering and design with a focus on therapeutic proteins and their application. The three main fields of research are (1) the development of '''anticalins''' which is an alternative binding scaffold and which are a promising alternative for conventional antibodies (2) the '''extension''' of the '''plasma half-life''' of therapeutic proteins using a poly-peptide polymer and (3) the '''site-specific conjugation''' of therapeutic proteins. Thus the focus of our hosting laboratory is biomedical engineering whereas our iGEM topic shows no intersection with this topic. <br><br />
The single negligible exception is that we used a '''higher engineered anticalin''' (<partinfo>BBa_K1159003</partinfo>) to bind fluorescein in our [https://2013.igem.org/Team:TU-Munich/Project/Bioaccumulation BioAccumulation] subproject, compared to the conventional BioBrick (<partinfo>BBa_K157004</partinfo>). This higher engineered version has three additional amino acid exchanges and exhibits a 75-fold higher affinity for its binding partner (fluorescein). It was not essential to have this higher engineered version for our project but we wanted to supply the registry with this improved part.<br><br />
Beside this plasmid, we also obtained a plasmid for the TEV protease from the chair which we have used to generate the Split-TEV protease (<partinfo>BBa_K1159100</partinfo>, <partinfo>BBa_K1159101</partinfo> and <partinfo>BBa_K1159102</partinfo>).<br />
<br />
<br />
''Prof. Skerra kindly provided us with '''space in his laboratory''', and '''generously advanced us money''' to pay for team registration, travel expenses and laboratory resources. Moreover he '''participated approximately one a month in our team meetings''' and advised us on our project.''<br />
<br />
== Technical University Munich ==<br />
As we had to cover several different scientific aspects during our project we contacted several professors from our university to get their opinion on our plans, obtain reagents or access to measuring instruments such as mass spectrometers or microscopes.<br />
<br />
==== Laboratory of Prof. Dr. Helmreich ====<br />
[http://www.sww.bv.tum.de Sanitary Environmental Engineering] is a horizontal discipline comprised of civil engineering, process engineering and chemistry/biology. Research and teaching include the fields of water supply, sewage and rain water treatment, water quality and the modeling of aquatic systems.<br />
<br />
''In our interview with Prof. Helmreich, she explained us several '''characterization techniques''' to assess water quality. Furthermore she kindly provided us with '''water samples''' from sewage treatment plants.''<br />
<br />
==== Laboratory of Prof. Dr. Thomas Hofmann ====<br />
LCMS<br />
<br />
==== Laboratory of Prof. Dr. Langosch ====<br />
The [http://www.wzw.tum.de/biopolymere Chair for Chemistry of Biopolymers] focuses on the '''structural biochemistry''' of '''integral membrane proteins'''. Core themes are molecular interactions between membrane proteins, structural dynamics of membrane bound protein helices, membrane protein/lipid interactions and structure/function relationships of integral membrane protein complexes.<br />
<br />
''During the planning phase of our project we asked Prof. Langosch for advice concerning the design of the transmembrane domain of our constructs.''<br />
<br />
==== Laboratory of Prof. Dr. Rost ====<br />
Prof. Rost works in the field of '''bioinformatics''' and computer-based biology, focusing on the '''prediction of structure and function of proteins''' and genes. His team's specialty is the use of artificial intelligence and machine learning algorithms to predict structure and function of proteins.<br />
<br />
''After developing an early version of our [https://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator AutoAnnotator], we presented our work to Prof. Rost and his group. He gave us some very helpful advice on features we could add and provided us with access to his [http://www.predictprotein.org/ PredictProtein] server. A special "thank you" goes to Manfred Roos for tailoring the access point of the server to our needs.''<br />
<br />
==== Laboratory of Prof. Dr. Schneitz ====<br />
The [http://plantdev.bio.wzw.tum.de/index.php?id=36 Chair for Plant Developmental Biology] is interested in the genetic and molecular basis of the '''regulatory pathways controlling organ development and tissue morphogenesis''' in plants. <br />
<br />
''The chair gave us great access to their '''microscopes''' and excellent support in how to use them. Many thanks for that, especially to Prasad Vaddepalli for his introduction into fluorescence microscopy.''<br />
<br />
==== Laboratory of Prof. Dr. Schwechheimer ====<br />
The [http://www.sysbiol.wzw.tum.de Chair for Systems Biology of Plants] investigates a range of '''queries''' concerning the '''ubiquitin proteasome''' system of plants applying a combination of genetics, molecular biology and cell biology with both '''genomic''' and '''proteomic''' approaches. <br />
<br />
''Together with Prof. Schwechheimer we discussed several different signal transduction pathways that could be utilised for our '''[https://2013.igem.org/Team:TU-Munich/Project/Killswitch kill-switch]'''. Moreover he kindly granted us access to a '''fluorescence microscope'''.''<br />
<br />
==== Laboratory of Prof. Dr. Scherer ====<br />
The [http://www.micbio.wzw.tum.de/index.php Chair for microbial ecology] conducts basic research in the field of '''molecular genetics and ecology of pathogenic microorganisms'''. Projects include the microbial characterization of food and microbial diagnostics and consulting in the food industry for prevention and clearance of contaminations.<br />
<br />
''The team kindly provided us with a culture of ''Micrococcus luteus'' for the '''[https://2013.igem.org/wiki/index.php?title=Team:TU-Munich/Results/Recombinant#Kirby-Bauer_Assay:_Measuring_remaining_erythromycin_on_a_pertri_dish Kirby-Bauer assay]''' and also helped out with a tube of restriction enzyme during an unexpected shortage.''<br />
<br />
== Other Universities ==<br />
The team also obtained help from other universities in order to complete the project. As nobody at our university works with ''Physcomitrella patens'' which the team chose to work with we had to find an advisor who could support us with the '''transformation procedure''' which is not really simple for plants. Additionally researches from other universities helped us by '''providing plasmids'''. <br />
<br />
==== Laboratory of [https://2013.igem.org/Team:TU-Munich/Team/Members#Prof._Dr._Ralf_Reski Prof. Dr. Reski] at Freiburg University (Germany) ====<br />
The team at the [http://www.plant-biotech.net/ Chair for Plant Biotechnology] is working on '''gene expression''' in the bryophyte model plant ''Physcomitrella patens'' (Hedw.) B.S.G. at different levels in correlation with phenotype analysis and additionally employs comparative genomic approaches.<br />
<br />
''The Reski team kindly supported us by supervising [https://2013.igem.org/Team:TU-Munich/Results/GM-Moss our moss transformations at their lab] and by allowing us to use some of their equipment and materials for the process. Our special thanks go to [https://2013.igem.org/Team:TU-Munich/Team/Members#Dr._Gertrud_Wiedemann Dr. Gertrud Wiedemann].''<br />
<br />
==== Laboratory of Prof. Dr. Fussenegger at ETH Zurich (Switzerland)====<br />
The research group at the [http://www.bsse.ethz.ch/groups/group_fussenegger/index/ Chair for Biotechnology and Bioengineering] is implementing a progress in basic research to achieve generic and prototypic advances in '''human therapy''' by focusing on '''mammalian cells''' and capitalizing on an integrated interdisciplinary systems approach. Their current research initiatives include several programs interfacing with '''biopharmaceutical manufacturing''', '''gene therapy''' and '''tissue engineering'''.<br />
<br />
''They kindly provided us with the pSH21 plasmid which was used as template for the Polioviral Internal Ribosome Entry Site (<partinfo>BBa_K1159300</partinfo>).''<br />
<br />
==== Laboratory of Dr. G.D. Wright at McMaster University (Canada) ====<br />
<br />
The [http://www.thewrightlab.com Wright Lab] is trying to understand fundamental aspects of '''how antibiotics work''', their sources and '''how bacteria become resistant''' to them.<br />
<br />
''They kindly provided us with the plasmids pDEST14_ereA and pDEST14_ereB which was used as a template for the Erythromycin Esterase Type II (<partinfo>BBa_K1159000</partinfo>).''<br />
<br />
==== Laboratory of Prof. Dr. Arndt at Potsdam University (Germany)====<br />
The team at the [http://www.uni-potsdam.de/index.php?id=13895 Chair for Molecular Biotechnology] investigates the '''factors that mediate interactions in coiled-coil proteins''' in order to target coiled-coil domains of proteins e.g. involved in tumorigenesis, tumor proliferation and metastasis.<br />
<br />
''Sven Hagen who had participated several times in iGEM in the past kindly provided us with the pBad-mVenus (<nowiki>RFC 25</nowiki>) expression plasmid. This plasmid was used for the production of recombinant protein in '''E. coli'''. ''<br />
<br />
== Webdesign ==<br />
The webdesign was entirely done by Florian Albrecht who has programmed different websites before. He also wrote the [https://2013.igem.org/Team:TU-Munich/Results/How_To webdesign tutorial] we put online to explain other teams how to use the code, developed by our team. The graphic elements used on the website were created by several different student members (such as Ingmar Polte, Katrin Fischer, Jeffery Truong, Rosario Ciccone and others) using the open source vector software Inkscape. The only component that was bought are the two direction signs used in the header (obtained from [http://vector-images.de/clipart/clp217632/ http://vector-images.de/clipart/clp217632]).<br />
<br />
==== normalize.css ====<br />
<br />
[http://necolas.github.io/normalize.css/ Normalize.css] was used to reset the wiki style (version used: 2.1.3).<br />
<br />
==== jQuery ====<br />
<br />
[http://jquery.com/ jQuery] is a powerful JavaScript extension used by many Webdesigners (version used: 1.10.2).<br />
<br />
==== jQuery UI ====<br />
<br />
[http://jqueryui.com/ jQuery UI] is a GUI extension of jQuery and was used for the datepicker on the Arduino data page (version used: 1.10.3).<br />
<br />
==== Slimbox 2 ====<br />
<br />
[http://code.google.com/p/slimbox/ Slimbox 2] was used as a picture viewer (version used: 2.05). The code had to be adapted to work with the wiki and bxSlider and we added a feature that fits the viewer to the browser size.<br />
<br />
==== bxSlider ====<br />
<br />
[http://bxslider.com/ bxSlider] is a JavaScript content slider and powers the slideshows and picture galleries on our wiki (version used: 4.1.1). The code was modified so all the images are scaled to the same height in gallery mode.<br />
<br />
==== NVD3 ====<br />
<br />
[http://nvd3.org/ NVD3] is a JavaScript chart library and was used for the interactive chart of the Arduino data (version used: 1.1.13).<br />
<br />
== Software - The AutoAnnotator ==<br />
The software tool we have written to '''facilitate and improve the annotation''' of protein coding BioBricks (the [https://2013.igem.org/Team:TU-Munich/Results/Software AutoAnnotator]) was developed and programmed by the student member [https://2013.igem.org/Team:TU-Munich/Team/Members Christopher Wolf]. He developed this idea himself to import, translate sequences and to compute important parameters. After this was completed he contacted the bioinformatics group of Prof. Rost and presented his idea and the program in a group seminar. In the seminar, ideas for further improvements were generated. The group advised Chrostopher to implement a bioinformatic module that does alignments to several databases and bioinformatic servers. The research group of Prof. Rost has a server that concentrates bioinformatic information and they enabled Christopher to use this tool. He implemented these information into the AutoAnnotator himself. It was also Chrostopher Wolf who has written the [http://dspace.mit.edu/handle/1721.1/81330 RFC 96] to describe the usage of the AutoAnnotator and who created the [http://vimeo.com/75965599 introduction video].<br><br />
For further information please see our [https://2013.igem.org/Team:TU-Munich/Results/Software Software page].<br />
<br />
====jQuery====<br />
Powerful extension of JavaScript<br />
<br />
====James Padolsey====<br />
''We used [http://james.padolsey.com James Padolsey´s] jQuery extension for [http://james.padolsey.com/javascript/cross-domain-requests-with-jquery/ Cross-domain AJAX requests] in the AutoAnnotator.''<br />
<br />
====Flot.js====<br />
Plotting Charts (see flotchart.org)<br />
<br />
<br />
====Flot-AxisLabels====<br />
Adds axis labels to Flot.js<br />
https://github.com/markrcote/flot-axislabels<br />
<br />
====Excanvas====<br />
Extend <canvas>-tag to IE 8.0 and earlier.<br />
<br />
====Paul Johnston====<br />
MD5 generator<br />
<br />
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