Team:TU-Munich/Results/Implementation

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Latest revision as of 03:56, 29 October 2013

Implementation of a Plant Biofilter

How does a biofilter look like? To face this question we considered the requirements for a moss filter and took a look at existing solutions.
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 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.
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.

Closed tube reactor

Figure 9: tube reactor

File:TUM13 moss tube turning.gif

Figure 10: moss turning

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.

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.

Open filter on felt base

Figure 11: open pond

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.

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.

Our swimming remediation raft

Figure 12: Rendering of our remediation rafts in front of the MIT

Figure 13: 3D-print of our remediation raft

At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. 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. 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.

Slightly we return to the question how a biofilter could look like. 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.

Figure 14: Blueprint for our remediation raft

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.

Our answer to that is the remediation raft.
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. 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.

Shopping for the remediation raft

**Table 1**: Shopping list for our Arduino-Project
Component	Quantity	Source	Price in € (per piece)	Price in € (sum)
PVC-tubes 1,5 m, ⌀ 75mm	3	Hardware Store	4,69	14,07
One-eight bend (45°)	3	Hardware Store	1,09	3,27
Bend (67°)	3	Hardware Store	1,09	3,27
Fleece	1,3 m²	Hardware Store	3,99 (per m²)	5,19
Clamps	3	Hardware Store	2,30	6,90
Carbon rod	1 (1,25 m)	Hardware Store	4,75	4,75
Round eyelets	3	Hardware Store	0,34	1,01
Total				38,44

Images from our trip to the construction center

Monitoring by an Arduino Microcontroller

Introduction

Figure 21: Arduino Uno, released in September 2010

One advantage of our raft is that it works quite autonomic. Once the moss is installed it filters until it's "saturated", assumed that the environmental parameters fit and a proper living space is provided. The main goal of our measurement device is to monitor these environmental parameters in real time. Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited. 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. So our aim was to engineer a low cost and low energy solution, that maintain the filters autonomy.

Figure 22: Idea for a measuring device

This is where Arduino comes into play. Arduino is a platform that is based on one microcontroller which is attached to a circuit board. Its convenient handling and easy programming, the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for multidisciplinary applications. Among its many fans it already enjoys cult status. We first used the Arduino Uno. It is the most commonly used board. The first revision was released in September 2010. Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers. Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. But the Arduino Uno came to it's limits, when we tried to get a display, WiFi and several sensors working.

Therefore we ordered the Arduino Due, which is the most powerful Arduino board at the moment. 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. 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$).

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. 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.

File:TUM13 How It Works Flowmodel.gif

Figure 23: How it works

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.

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 tutorial how to set up an Arduino Due with some basic functions.

Figure 24: components

**Table 2**: Shopping list for our Arduino-Project
Component	Quantity	Source	Price	Figure
Arduino Due microcontroller	1	[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]	46.41 €	Fig. 1 A
Arduino WIFI Shield	1	sparkfun	63.58 €	Fig. 1 B
Watterott mega msd-shield	1	[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]	19.49 €	Fig. 1 C
Display MI0283QT-9	1	[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]	36.00 €	Fig. 1 D
Light sensor TSL2561	1	[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]	7.74 €	Fig. 1 E
Temperature sensor DS18B20	1	[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]	8.80 €	Fig. 1 G
Water sensor	1	[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]	2.90 €	Fig. 1 H
Lithium-Battery	1	[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]	16.35 €
Stackable Headers	3	[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]	5.37 €
Linking wires and resistors			1.00 €
Photo-diodes	3
			207.64 €	280.77 $

Server site

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 save.php stores them in a MySQL database. The data can be viewed by visiting index.php, which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time 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.

How could it look installed in a river?

New York PARALLEL NETWORKS

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. 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". 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.

Commercially available rafts called "Kampen"

Figure 30: Commercially available rafts

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.

Swimming remediation raft in action

References:

http://bvt.blt.kit.edu/ KIT Homepage about Institute of bioprocess Engineering

http://op-n.net/filter/work/PARALLEL-NETWORKS Op.N Op.N Homepage

http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ www.bustler.net, Thursday, August 04, 2011 Article: ONE PRIZE: Water as the 6th Borough - Winners Announced;

http://www.bestmann-green-systems.de/ BGS Ingenieurbiologie und -ökologie GmbH BGS Homepage

@@ Line 7: / Line 7: @@
 ==Implementation of a Plant Biofilter==
-<div class="box-center">Text</div>
+How does a '''biofilter''' look like?
+To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<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>
+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>
+<div class="box-center">
+<ul class="bxgallery">
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg"  alt="Figure 4"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg"  alt="Figure 5"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg"  alt="Figure 6"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg"  alt="Figure 7"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg"  alt="Figure 8"/></li>
+</ul>
+</div>
+</html>
+<div class="box-left" style="height: 1650px;">
+===Closed tube reactor===
+[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]
+[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]
+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.
+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.
-==Our Physco-Filter Prototype==
+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><br>
+</div>
-<div class="box-center">Text</div>
-<br><br>
+<div class="box-right" style="height: 1650px;">
+===Open filter on felt base===
+[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]
+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.
+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.
+</div>
+==Our swimming remediation raft==
+[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]
+[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]
+At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense.
+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.
+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.
+Slightly we return to the question how a '''biofilter''' could look like.
+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.
+[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]
+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.
+Our answer to that is the '''remediation raft'''. <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.
+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.
+===Shopping for the remediation raft===
+{|cellspacing="0" border="1"
+|+ '''Table 1''': Shopping list for our Arduino-Project
+!Component
+!Quantity
+!Source
+!Price in € (per piece)
+!Price in € (sum)
+|-
+|PVC-tubes 1,5 m, ⌀ 75mm
+| align=right | 3
+|Hardware Store
+| align=right | 4,69
+| align=right | 14,07
+|-
+|One-eight bend (45°)
+| align=right | 3
+|Hardware Store
+| align=right | 1,09
+| align=right | 3,27
+|-
+|Bend (67°)
+| align=right | 3
+|Hardware Store
+| align=right | 1,09
+| align=right | 3,27
+|-
+|Fleece
+| align=right | 1,3 m<sup>2</sup>
+|Hardware Store
+| align=right | 3,99 (per m<sup>2</sup>)
+| align=right | 5,19
+|-
+|Clamps
+| align=right | 3
+|Hardware Store
+| align=right | 2,30
+| align=right | 6,90
+|-
+|Carbon rod
+| align=right | 1 (1,25 m)
+|Hardware Store
+| align=right | 4,75
+| align=right | 4,75
+|-
+|Round eyelets
+| align=right | 3
+|Hardware Store
+| align=right | 0,34
+| align=right | 1,01
+|-
+|'''Total'''
+|
+|
+|
+| align=right | '''38,44'''
+|-
+|}
-==Arduino Microcontroller==
+===Images from our trip to the construction center===
+<html>
 <div class="box-center">
-===Introduction===
+<ul class="bxgallery">
+    <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>
+    <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>
+    <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>
+    <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>
+    <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>
+    <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>
+</ul>
+</div>
+</html>
-One advantage of a moss filter is that it works quite autonomic. Once the moss is installed it filters until it's "saturated", assumed that
+==Monitoring by an Arduino Microcontroller==
-the environmental parameters fit and a proper living space is provided.
-The main goal of our measurenment device is to monitor these environmental parameters in real time.
-Since the filter's autonomy has to be obtained and the costs should be kept as low as possible, the usage of ordinary lab measurenment tools is limited.
-Looking one step ahead it's suggesting to use the moss for cleaning waters like ponds or streams. Places that are not continuously supervised by humans.
-So the aim was to use a low cost and low energy solution, that maintain the filters autonomy.
-This is where Arduino comes into play.
+===Introduction===
-Arduino is a platform that is based on one microcontroller wich is attached to a circuit board. Its convenient handling and easy programming,
+[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]
-the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, espacially for
+One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that
-multidisciplinary applications. Among its many fans it already enjoys cult status.
+the environmental parameters fit and a proper living space is provided.
-We first used the Arduino Uno. It is the most commonly used board and the first revision was released in September 2010.
+The main goal of our measurement device is to '''monitor''' these environmental parameters in real time.
-Designed for beginners, it gave us an easy start into the handling, since no one of us had any experience working with microcontrollers. ABBILDUNG_UNO
+Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.
+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.
+So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.
+[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]
+This is where '''Arduino''' comes into play.
+Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming,
+the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for
+multidisciplinary applications. Among its many fans it already enjoys '''cult status'''.
+We first used the '''Arduino Uno'''. It is the most commonly used board. The first revision was released in September 2010.
+Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers.
 Most libraries already worked out of the box and all shields and sensors we ordered came with an example code.
-But the Arduino Uno came to it's limits, when we tried to get a display, wifi and several sensors working.
+But the Arduino Uno '''came to it's limits''', when we tried to get a display, WiFi and several sensors working.
-Therefore we ordered the Arduino Due, wich is the most powerful Arduino board.
+Therefore we ordered the '''Arduino Due''', which is the '''most powerful''' Arduino board at the moment.
 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.
 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$).
-[[File:xx.jpg|thumb|right|350px|Gruppenfoto]]
+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.
+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.
+[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]
+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'''.
+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.
+[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]
 {|cellspacing="0" border="1"
-|colspan="5"| Table 1:
+|+ '''Table 2''': Shopping list for our Arduino-Project
-====Shopping list for our Arduino-Project====
+!Component
-|-
+!Quantity
-|Component
+!Source
-|Quantity
+!Price
-|Source
+!Figure
-|Price
-|Figure
 |-
 |Arduino Due microcontroller
 |1
-|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 Source]
+|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]
 |46.41 €
 |Fig. 1 A
@@ Line 65: / Line 190: @@
 |Arduino WIFI Shield
 |1
-|[https://www.sparkfun.com/products/11287 Source]
+|[https://www.sparkfun.com/products/11287 sparkfun]
 |63.58 €
 |Fig. 1 B
@@ Line 71: / Line 196: @@
 |Watterott mega msd-shield
 |1
-|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield Source]
+|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]
 |19.49 €
 |Fig. 1 C
@@ Line 77: / Line 202: @@
 |Display MI0283QT-9
 |1
-|[http://www.watterott.com/de/MI0283QT-2-Adapter Source]
+|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]
 |36.00 €
 |Fig. 1 D
@@ Line 83: / Line 208: @@
 |Light sensor TSL2561
 |1
-|[http://www.watterott.com/de/TSL2561-Lichtsensor Source]
+|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]
 |7.74 €
 |Fig. 1 E
@@ Line 89: / Line 214: @@
 |Temperature sensor DS18B20
 |1
-|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html Source]
+|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]
 |8.80 €
-|Fig. 1 F
+|Fig. 1 G
 |-
 |Water sensor
 |1
-|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html Source]
+|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]
 |2.90 €
-|Fig. 1 G
+|Fig. 1 H
 |-
 |Lithium-Battery
 |1
-|[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 Source]
+|[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]
 |16.35 €
 |
@@ Line 107: / Line 232: @@
 |Stackable Headers
 |3
-|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html Source]
+|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]
 |5.37 €
 |
@@ Line 117: / Line 242: @@
 |
 |-
-|Photodiodes
+|Photo-diodes
 |3
 |
@@ Line 127: / Line 252: @@
 |
 |207.64 €
-|
+|280.77 $
-|}<br>
+|}
-===part description===
+=== Server site ===
-====Arduino Due====
+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.
-[[File:Arduino_Due.jpg|thumb|right|250px|Fig 1 A: Arduino Due, released in October 2012]]
-The Arduino Due is the most powerful Arduino board. It's underlying 32bit-processor is the Atmel SAM3X8E.
-Contrary to the other boards that run at 5V the Due works with 3.3V.
-Data:
+==How could it look installed in a river?==
-Mhz	CPU Clock
+===New York PARALLEL NETWORKS===
-	KBytes of SRAM.
+<html>
-	KBytes of Flash memory.
+<div class="box-center">
-	Digital I/O Pins
+<ul class="bxgallery">
-	Analog Input Pins
+    <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>
-	(DAC)Analog Outputs Pins
+    <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>
+    <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>
-====Arduino WiFi Shield====
+    <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>
-[[File:Arduino_WiFi.png|thumb|right|250px|Fig 1 B: Arduino WiFi, released in August 2012]]
+    <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>
-The Arduino WiFi Shield is an attachable shield that provides Wireless LAN 802.11b/g to the Arduino.
+</ul>
-It can scan for networks, connect to networks and open and transfer data through TCP and UDP sockets. It also supports WEP and WPA2 encryption.
+</div>
-The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi-library.
+</html>
-There is also an SD-card socket onboard to store received data.
-As the SD-card is accessable seperatly, it can also be used as a storage for any data generated by the Arduino.
-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.
-'''Pin usage:'''
-	SS for SD card (Slave Select)
-	Handshake between Arduino and WiFi Shield
-	SS for WiFi
-	SPI MISO (Master in, Slave out)
-	SPI MOSI (Master out, Slave in)
-	SPI SCK  (Serial clock)
-  gnd
-.3V
-V
-====Watterott mega msd-shield====
-[[File:Arduino_Mega_MSD.JPG|thumb|right|250px|Fig 1 C: Watterott mega msd-shield]]
-The mega msd-shield was designed by Watterott and consists of a couple of components.
-The components are one real time clock, one SD-card socket we won't use, a small battery, a socket for a touch display.
-To get it ready to run, the shield must be assembled. The stackable headers and the quartz must be soldered to the board and you must insert the battery.
-Unluckiely the mega msd-shield and therefore also the MI0283QT-9 touch display only come with a working library for older Arduinos such as the Uno.
-The Due is not yet supported and all libraries have to be rewritten.
-The touch display and the SD-card-slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmit its data via I²C.
-'''Pin usage:'''
-	SS for SD card
-	SS for the touch of the touch display
-(25)SS for the LCD (Workarround of the double usage of pin 7 by the WIFI Shield)
-	reset LCD
-	LCD LED
-	RTC (real time clock) 	I²C	SDA (Serial Data Line)
-	RTC  			I²C	SCL (Serial Clock)
-	SPI MISO
-	SPI MOSI
-	SPI SCK
-  gnd
-.3V
-====Display MI0283QT-9====
-[[File:Arduino_MI0283.jpg|thumb|right|250px|Fig 1 D: MI0283QT-9]]
-The MI0283QT-9 is a multicolor touch display. It comes already attached to a board, where only the pin headers are still to be soldered.
-Once assembled it can easiely be plugged into the mega msd-shield. It has an onboard touch controller (TI ADS7846).
-The display size is 2.83"(43.2 x 57.6mm) with a resolution of 240x320. It supports 262k colors.
-The pin usage is already considered in the mega msd-shield description.
-====Light sensor TSL2561====
-The light sensor is a small, so called beakout board. It is usually not directly plugged to the Arduino board or into a shield but connected by wires.
-The light sensor has two photodiodes onboard that measure visible and infrared light. Similar to the RTC, the TSL2561 is adressed via I²C.
-Once you get the I²C library working on your Arduino Due working it takes only little effort to integrate additional I²C devices.
-Just very few lines of the library have to be rewritten.
-The photodiodes can be adressed seperately or both at one. Their output is already converted to Lux. ABBILDUNG_TSL2561+KURVE
-'''pin usage:'''
-	TSL2561		 	I²C	SDA (Serial Data Line)
-	TSL2561			I²C	SCL (Serial Clock)
-  gnd
-.3V
-====Temperature sensor DS18B20====
-[[File:Arduino_Tempsen.jpg|thumb|right|250px|Fig 1 F: DS18B20 ]]
-The temperature sensor is embedd into a water proof cable. It is adressed via One-Wire.
-The provided data are digital raw data, which need to be converted into degrees celsius. Information about the conversion are given by the manufacturer.
-Similar to the I²C (TwoWire) bus, you only have to get the One-Wire interface working once. After that you can easiely set up One-Wire more devices.
-Again, just very few lines of the library have to be rewritten.
-'''pin usage:'''
-	One-Wire DS18B20 (pin was randomly chosen)
-  gnd
-.3V
-====Water sensor====
+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.
-[[File:Arduino_Watersensor.jpg|thumb|right|250px|Water sensor Fig 1 G]]
+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"'''.
-The water sensor is very easy to set up. If and how much water the sensor registered can be measured via an analog pin.
+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.
-ABBILDUNG_WATERSENSOR
-'''pin usage:'''
+===Commercially available rafts called "Kampen"===
+[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]
- A7	Water sensor
+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.
-  gnd
-.3V
-====Photodiodes====
-We disassembled a broken "Biorad 550"-photometer and recovered a halogen lamp, a small number of wavelength filters,
-three of eight Photodiodes and fitting Resistors.
-===Tools===
-*Breadboard
-*Soldering bolt
-*Solder
-===Assembly===
-[[File:Arduino_Pinout.png|right|x400px|Arduino Due pinout diagram ]]
-Try to keep everything clear during the assembly. If you have different colors for linking cables. Try to always use the same color code.
-For example: brown cable for 3.3V etc. Troubleshooting can get nasty.
+==Swimming remediation raft in action==
+<html>
+<div class="box-center">
+<ul class="bxgallery">
+    <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>
+    <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>
+    <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>
+    <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>
+    <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>
+    <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>
+<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>
+<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>
+</ul>
 </div>
+</html>
-<br><br>
 ==References:==
-<div class="box-center">
-<!-- Kopiervorlagen -->
-[[http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984]]
-#[[http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984]] Edens, L., Bom, I., Ledeboer, A. M., Maat, J., Toonen, M. Y., Visser, C., and Verrips, C. T. (1984). Synthesis and processing of the plant protein thaumatin in yeast. ''Cell'', 37(2):629–33.
 <!-- Ab hier richtige Referenzen einfügen -->
-#
-</div>
+[[http://bvt.blt.kit.edu/ KIT]] Homepage about Institute of bioprocess Engineering
+[[http://op-n.net/filter/work/PARALLEL-NETWORKS Op.N]] Op.N Homepage
+[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ www.bustler.net, Thursday, August 04, 2011]] Article: ONE PRIZE: Water as the 6th Borough - Winners Announced;
+[[http://www.bestmann-green-systems.de/ BGS Ingenieurbiologie und -ökologie GmbH]] BGS Homepage
 <!-- Ende des Inhalts -->