Team:TU-Eindhoven/Notebook

From 2013.igem.org

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* Editing the newly arrived revised "facts"
* Editing the newly arrived revised "facts"
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* Making sure all the goodies for the Jamboree are good to go
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''General Activities''
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* Get ready for the European Jamboree!
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* Have fun at the European Jamboree.
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''General Activities''
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* Regular team meetings
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* Looking for more sponsors
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* Contacting the media for outreach purposes
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* Improving the poster, presentation and wiki
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''Wetlab''
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* Doing a few more experiments.
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''Human Practices''
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* Analyzing and adding to the wiki the results from the poll we did during the European Jamboree.
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''General Activities''
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* Regular team meetings
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* Looking for more sponsors
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* Contacting the media for outreach purposes
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* Adding final touches to the poster, presentation and wiki
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''Wetlab''
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* Doing a few more experiments.
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Revision as of 21:09, 17 October 2013

In this section you can find a small description of all the work we have done so far organized by the category it belongs to. For the journal of the wet lab, see our Lab Journal page.

Feb-Apr

Feb-Mar

  • Background research


Mar-Apr

  • Selection of topic
  • Further research
  • Selection of project

Apr-May

  • Further research


May

1-5 May
General Activities

  • Regular team meeting
  • Looking for sponsors
  • Month planning


Wetlab

  • Researching about the promoters
  • Researching about the possible proteins for CEST imaging


Drylab

  • Defining what needs to be modeled and what type of model is the most appropriate for it

6-12 May
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Researching and defining the killing mechanism


Drylab

  • Starting the Molecular Dynamics model for the proteins selection.

13-19 May
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Defining the needed materials
  • Defining the needed equipment


Drylab

  • Continuing the Molecular Dynamics model for the proteins selection.

20-26 May
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Locating, booking and learning how to use the necessary equipment


Drylab

  • Analyzing the results from the Molecular Dynamics model for the proteins selection and identifying the most useful proteins for CEST imaging
  • Researching and defining the needed parameters for the analysis of the decoy sites through a stochastic simulations model


Human Practices

  • Selecting a main project

27-31 May
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Locating, booking and learning how to use the necessary equipment


Drylab

  • Starting the stochastic simulations for the analysis of the decoy sites


Human Practices

  • Selecting a main project

June

3-9 June
General Activities

  • Regular team meeting
  • Looking for sponsors
  • Collaborating with Purdue iGEM team
  • Planning month activities


Wetlab

  • General construct design


Drylab

  • Continuing the stochastic simulations for the analysis of the decoy sites


Human Practices

  • Defining the structure of the fact checker project

10-16 June
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Protein design


Drylab

  • Continuing the stochastic simulations for the analysis of the decoy sites


Human Practices

  • Redacting the preliminary description and survey for collaborators of the fact checker project

17-23 June
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Final design of the constructs


Drylab

  • Continuing the stochastic simulations for the analysis of the decoy sites


Human Practices

  • Revising the preliminary description and survey for collaborators of the fact checker project

24-30 June
General Activities

  • Regular team meeting
  • Looking for sponsors


Wetlab

  • Ordering the constructs
  • Working on the protocols


Drylab

  • Analyzing the results from the stochastic simulations for the analysis of the decoy sites

Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked

July

1-7 July
General Activities

  • Regular team meeting
  • Looking for sponsors
  • Planning month activities


Wetlab

  • Finalizing the protocols
  • Planning lab schedule


Drylab

  • Starting the ODE model for the analysis of the FNR promoter


Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked

8-14 July
General Activities

  • Regular team meeting
  • Looking for sponsors
  • Collaborating with Purdue iGEM team


Drylab

  • Continuing the ODE model for the analysis of the FNR promoter


Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked

15-21 July

22-28 July
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Collaborating with Purdue iGEM team


Wetlab

  • Creating agar plates
  • Transforming DNA
  • Plating bacteria
  • Making LB medium
  • Creating small cultures
  • DNA retention from cultures
  • Nano-drop tests


Drylab

  • Analyzing the results from the ODE model for the analysis of the FNR promoter


Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked
  • Sending the survey to collaborators

29-31 July
General Activities

  • Regular team meetings
  • Looking for sponsors


Wetlab

  • Creating agar plates
  • Transforming DNA
  • Plating bacteria
  • Making LB medium
  • Creating small cultures
  • DNA retention from cultures
  • Nano-drop tests


Drylab

  • Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter


Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked

August

1-4 August
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Working on outreach ideas


Wetlab

  • Creating the Cultures
  • Retaining the DNA
  • Nanodrop Test


Drylab

  • Merging the stochastic simulations model for the decoy sites with the ODE model for the FNR promoter
  • Working on the pharmacokynetics model


Human Practices

  • Researching for facts and myths related to Synthetic Biology to be checked
  • Working on the fact checker web platform
  • Redacting the first facts to be added on our fact checker platform

5-11 August
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Working on outreach ideas


Wetlab

  • Creating the cultures
  • Retaining the DNA
  • Nanodrop test


Drylab

  • Improving the merged model
  • Making an ODE model of the decoy sites
  • Working on the pharmacokynetics model


Human Practices

  • Working on the fact checker web platform
  • Preparing the instructions and example files for collaborating teams

12-18 August
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Working on outreach ideas
  • Sharing our project with colleagues and faculty members


Wetlab

  • Digestion
  • Construct digestion
  • Vector digestion
  • PCR purification for the constructs
  • PCR puricfication for the vectors
  • Nanodrop results
  • Continuing with the purification
  • Vector purification
  • Construct purification
  • Ligation
  • Preparing agar plates
  • Transformation
  • Plating
  • Colony picking and PCR
  • Culturing the ligation products


Drylab

  • Sensitivity analysis of the merged model
  • Estimating promotor rates
  • Working on the pharmacokynetics model


Human Practices

  • Working on the fact checker web platform

19-25 August
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Working on outreach ideas


Wetlab

  • Colony picking and PCR
  • Small cultures and preparation for protein expression
  • Miniprepping new constructs
  • Sequencing
  • Trnasformation and plating
  • Expressing samples
  • Protein purification
  • Determining protein concentration
  • SDS analysis
  • Performing the protein expression in an anaerobic environment
  • MRI experiments


Drylab

  • Working on the pharmacokynetics model


Human Practices

  • Fact checker platform is up and running

26-31 August
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Contacting the media for outreach purposes
  • Editing and sending our Brick of knowledge to the Copenhagen iGEM team for our collaboration with them.


Wetlab

  • Expression cultures
  • Anaerobic expression
  • Protein expression
  • Making the BioBricks
  • SDS analysis
  • BugBuster protocol
  • SDS PAGE gel


Drylab

  • Working on the pharmacokynetics model


Human Practices

  • Editing the newly arrived revised "facts"

September

2-8 Sept
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Contacting the media for outreach purposes
  • Designing our team t-shirts


Wetlab

  • Digesting samples
  • Gel extraction purification
  • PCR purification
  • Nanodrop test
  • Ligation
  • Transformation
  • Plating
  • Colony picking and PCR
  • Gel analysis


Drylab

  • Working on the pharmacokynetics model last details


Human Practices

  • Editing the newly arrived revised "facts"
  • Designing promotional goodies for the Synthetic Facts website


9-15 Sept
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Contacting the media for outreach purposes


Wetlab

  • Preparation for protein expression
  • Preparation of LB medium
  • Protein expression
  • Making more BioBricks
  • Preparation for CEST measurements
  • Miniprepping
  • PCR and PCR purification
  • Gel extraction
  • Re-digesting 1G70
  • Ligation


Drylab

  • Working on the update of the models on the wiki


Human Practices

  • Editing the newly arrived revised "facts"
  • Getting promotional goodies for the Synthetic Facts website

16-22 Sept
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Contacting the media for outreach purposes
  • Designing the poster and the presentation


Wetlab

  • Transformation and plating
  • Colony picking and PCR
  • Small cultures
  • Miniprepping
  • Preparing the BioBricks for shippment to Boston
  • Making of samples for sequencing


Drylab

  • Working on the update of the models on the wiki


Human Practices

  • Editing the newly arrived revised "facts"


23-30 Sept
General Activities

  • Regular team meetings
  • Looking for sponsors
  • Contacting the media for outreach purposes
  • Designing the poster and the presentation


Wetlab

  • Preparing the BioBricks for shipment once more due to an external issue with the shipment of the BioBricks
  • Culturing bacteria
  • Prepare bacteria for electroporation and electroporation
  • Creating small samples
  • Preparing LB medium


Drylab

  • Working on the update of the models on the wiki


Human Practices

  • Editing the newly arrived revised "facts"

October

1-4 Sept-Oct
General Activities

  • Regular team meetings
  • Contacting the media for outreach purposes
  • Adding the final touches to the poster and the presentation
  • Adding final details to the wiki
  • Adding last details on the judging form


Wetlab

  • Protein purification
  • SDS analysis
  • Fluorescence analysis
  • Filling in the characterization forms from our BioBricks on the registry


Drylab

  • Double checking modeling content on the wiki


Human Practices

  • Editing the newly arrived revised "facts"
  • Making sure all the goodies for the Jamboree are good to go



7-13 Oct
General Activities

  • Get ready for the European Jamboree!
  • Have fun at the European Jamboree.


14-20 Oct
General Activities

  • Regular team meetings
  • Looking for more sponsors
  • Contacting the media for outreach purposes
  • Improving the poster, presentation and wiki


Wetlab

  • Doing a few more experiments.


Human Practices

  • Analyzing and adding to the wiki the results from the poll we did during the European Jamboree.

<!-

21-27 Oct
General Activities

  • Regular team meetings
  • Looking for more sponsors
  • Contacting the media for outreach purposes
  • Adding final touches to the poster, presentation and wiki


Wetlab

  • Doing a few more experiments.


->

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