Team:TU-Eindhoven/Notebook

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Revision as of 01:37, 5 October 2013 by Pascalaldo (Talk | contribs)

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 Team:TU-Eindhoven/LabJournal 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

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