Team:TU-Eindhoven/Notebook

From 2013.igem.org

(Difference between revisions)
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''Wetlab''
''Wetlab''
-
* Creating the Cultures
+
* Creating the cultures
* Retaining the DNA
* Retaining the DNA
-
* Nanodrop Test
+
* Nanodrop test
''Drylab''
''Drylab''
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''Wetlab''
''Wetlab''
* Digestion
* Digestion
-
* Construct Digestion
+
* Construct digestion
-
* Vector Digestion
+
* Vector digestion
-
* PCR Purification for the Constructs
+
* PCR purification for the constructs
-
* PCR Puricfication for the Vectors
+
* PCR puricfication for the vectors
-
* Nanodrop Results
+
* Nanodrop results
-
* Continuing with the Purification
+
* Continuing with the purification
-
* Vector Purification
+
* Vector purification
-
* Construct Purification
+
* Construct purification
* Ligation
* Ligation
-
* Preparing Agar Plates
+
* Preparing agar plates
* Transformation
* Transformation
* Plating
* Plating
-
* Colony Picking and PCR
+
* Colony picking and PCR
-
* Culturing the Ligation Products
+
* Culturing the ligation products
''Drylab''
''Drylab''
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''Wetlab''
''Wetlab''
-
* Colony Picking and PCR
+
* Colony picking and PCR
-
* Small Cultures and Preparation for Protein Expression
+
* Small cultures and preparation for protein expression
-
* Miniprepping New Constructs
+
* Miniprepping new constructs
* Sequencing
* Sequencing
-
* Trnasformation and Plating
+
* Trnasformation and plating
-
* Expressing Samples
+
* Expressing samples
-
* Protein Purification
+
* Protein purification
-
* Determining Protein Concentration
+
* Determining protein concentration
-
* SDS Analysis
+
* SDS analysis
-
* Performing the Protein Expression in an Anaerobic Environment
+
* Performing the protein expression in an anaerobic environment
-
* MRI Experiments
+
* MRI experiments
''Drylab''
''Drylab''
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{{:Team:TU-Eindhoven/Template:TimelineEnd}}
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{{:Team:TU-Eindhoven/Template:Timeline | day=26-31 | month=August | year= }}
{{:Team:TU-Eindhoven/Template:Timeline | day=26-31 | month=August | year= }}
-
*...
+
''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"
 +
 
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineBottom}}
{{:Team:TU-Eindhoven/Template:TimelineBottom}}
{{:Team:TU-Eindhoven/Template:TimelineTop | unit=September | nr=}}
{{:Team:TU-Eindhoven/Template:TimelineTop | unit=September | nr=}}
{{:Team:TU-Eindhoven/Template:Timeline | day=2-8 | month=Sept | year= }}
{{:Team:TU-Eindhoven/Template:Timeline | day=2-8 | month=Sept | year= }}
-
*...
+
''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
 +
 
 +
 
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:Timeline | day=9-15 | month=Sept | year= }}
{{:Team:TU-Eindhoven/Template:Timeline | day=9-15 | month=Sept | year= }}
-
*...
+
''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
 +
 
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:Timeline | day=16-22 | month=Sept | year= }}
{{:Team:TU-Eindhoven/Template:Timeline | day=16-22 | month=Sept | year= }}
-
*...
+
''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"
 +
 
 +
 
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:Timeline | day=23-29 | month=Sept | year= }}
{{:Team:TU-Eindhoven/Template:Timeline | day=23-29 | month=Sept | year= }}
-
*...
+
''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"
 +
 
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineEnd}}
{{:Team:TU-Eindhoven/Template:TimelineBottom}}
{{:Team:TU-Eindhoven/Template:TimelineBottom}}

Revision as of 10:00, 26 September 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.

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"


23-29 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"

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Retrieved from "http://2013.igem.org/Team:TU-Eindhoven/Notebook"