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From 2011.igem.org

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Notebook

Week of 5/23/2011

Design Team: Started collecting sequences of relevant fluorescent proteins and entering them into GenoCAD. Learned about attribute grammars.

Fabrication Team: blah

Characterization Team: blah

Week of 5/30/2011

Design Team: Created first draft of attribute grammar. Collected more fluorescent proteins for GenoCAD. Started looking at modeling aspect of project - explored modeling software that can handle SBML (Systems Biology Markup Language) input - Matlb Simbiology looks nice.

Fabrication Team: blah

Characterization Team: blah

Week of 6/6/2011

Design Team: Small changes to grammar (fixing stop codon issues) and big changes to grammar (changing how parts are ordered and thus how GenoCAD constructs the sequence of a construct we make). Looked further into modeling, how our attribute grammar will connect to that. Collected more fluorescent proteins, started to look into degradation tags and linker sequences for fusion proteins.

Fabrication Team: blah

Characterization Team: blah

Week of 6/13/2011

Design Team: Started working on Prolog compiler which will take a construct from GenoCAD and use it to write a Java file, which will in turn write an SBML file for modeling (this is a good way to do it, we promise). Carefully documented gene sequences we've found so far. Looked more into best degradation tags to use. Started learning how to verify sequencing results so we can look at sequencing data from our constructs made by the fab team.

Fabrication Team: blah

Characterization Team: blah

Week of 6/20/2011

Design Team: More work on Prolog compiler (long and frustrating work). Lots of troubleshooting with the fab team picking a better plasmid to use in E. coli Verified that our grammar implementation in GenoCAD is producing accurate DNA sequences for constructs.

Fabrication Team: blah

Characterization Team: blah

Week of 6/27/2011

Design Team: Added linker sequences and degradation tags to GenoCAD, along with plasmids. Got compiler working - we can now make a construct in GenoCAD and generate a valid SBML file, which can be simulated in Matlab, etc. Started writing iGEM safety proposal and project description. Started adapting grammar to make a bigger variety of constructs.

Fabrication Team: blah

Characterization Team: blah

Week of 7/4/2011

Design Team: Finished safety proposal and project description. Looked into software to simulate our SBML files. Major changes to grammar to be able to make more types of constructs. Added N-terminal degradation tags to grammar and GenoCAD.

Fabrication Team: blah

Characterization Team: blah

Week of 7/11/2011

Design Team: Finished safety proposal and project description again. Started verifying sequences of constructs made by fab team.

Fabrication Team: blah

Characterization Team: blah

Week of 7/18/2011

Design Team: Lots of sequence verification. Started writing up details of our procedures and methods (materials used, manufacturers, etc). Started editing wiki. Explored ways of representing our grammar (just a list of rules) graphically, for easier interpetation.

Fabrication Team: blah

Characterization Team: blah

Week of 7/25/2011

Design Team: Started to work on presentation for iGEM, more work on wiki. Continued talking to other teams to write up our methods and procedures. Major changes to database where our grammar and parts are stored to accomodate attributes better.

Fabrication Team: blah

Characterization Team: blah

Week of 8/1/2011

Design Team: Lots of work on presentation for iGEM. Continued talking to other teams, writing up our methods and procedures. Mark had to leave for the summer because of health issues :(

Fabrication Team: blah

Characterization Team: blah

Week of 8/8/2011

Design Team: Lots and lots of work on presentation. Final wrap-up, careful documentation of what we did all summer, etc.

Fabrication Team: blah

Characterization Team: blah