Team:Virginia Tech/Notebook

From 2011.igem.org

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==Week of 6/13/2011==
==Week of 6/13/2011==
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<p><big><b> Design Team: </b></big> 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).   
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<p><big><b> Design Team: </b></big> 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.
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  
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==Week of 6/20/2011==
==Week of 6/20/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> More work on Prolog compiler (long and frustrating work).  Lots of troubleshooting with the fab team picking a better plasmid to use in <i> E. coli </i>  Verified that our grammar implementation in GenoCAD is producing accurate DNA sequences for constructs.
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  
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==Week of 6/27/2011==
==Week of 6/27/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> 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.
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  
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==Week of 7/4/2011==
==Week of 7/4/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> 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.
</p>
</p>
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<p><big><b> Fabrication Team: </b></big> Hayley worked on mCitrine insert in pYES2 backbone and mCherry (E2060) insert in pSB1AK3 backbone with Lac promotor and RBS binding site (J04500). Loran worked on mCherry insert in pYES2 backbone, Plasmid Prep of BioBrick mCherry, and CFP (E0020) inserts. Mandy worked on CFP insert in pSB1AK3 backbone and mCherry insert in PYES2 backbone. Martha worked on GFPmut3b in pSB1AK3 backbone. Swetha worked on mCitrine insert in pYES2 backbone and Degradation Tags Primer Design.
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<p><big><b> Fabrication Team: </b></big> blah
</p>
</p>
<p><big><b> Characterization Team: </b></big> blah
<p><big><b> Characterization Team: </b></big> blah
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===Week of 7/11/2011===
===Week of 7/11/2011===
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<p><big><b> Design Team: </b></big> Finished safety proposal and project description again.  Started verifying sequences of constructs made by fab team.
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<p><big><b> Design Team: </b></big> blah blah blah
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</p>
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<p><big><b> Fabrication Team: </b></big> Loran worked on mCherry-pYES2, non-Biobrick AcGFP-pYES2, and Biobrick AcGFP-pSB1AK3. Swetha worked on mCitrine-pYES2,Biobrick CFP-pYES2, and Biobrick GFPmut3b-pYES2. Mandy worked on CFP-pSB1AK3, mCherry-pYES2,Biobrick mCherry-pYES2, Biobrick mCherry-pSB1AK3, and Biobrick GFPmut3b-pSB1AK3. Hayley worked on mCitrine-pYES2, Biobrick mCherry-pSB1AK3, and non-Biobrick mCitrine-pSB1AK3. Martha worked on Biobrick GFPmut3b-pSB1AK3.
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<p><big><b> Fabrication Team: </b></big> blah
</p>
</p>
<p><big><b> Characterization Team: </b></big> blah
<p><big><b> Characterization Team: </b></big> blah
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==Week of 7/18/2011==
==Week of 7/18/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> 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.
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  
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==Week of 8/1/2011==
==Week of 8/1/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> Lots of work on presentation for iGEM.  Continued talking to other teams, writing up our methods and procedures.
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  
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==Week of 8/8/2011==
==Week of 8/8/2011==
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<p><big><b> Design Team: </b></big> blah blah blah
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<p><big><b> Design Team: </b></big> Lots and lots of work on presentation and poster (along with Swetha, from the Fabrication Team
</p>
</p>
<p><big><b> Fabrication Team: </b></big> blah  
<p><big><b> Fabrication Team: </b></big> blah  

Revision as of 03:29, 29 September 2011

Division.png Virginia Tech logo.png Diatoms.png

Home Team Official Team Profile Project Parts Submitted to the Registry Notebook Safety Attributions


Contents

Notebook

You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.

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: blah blah blah

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.

Fabrication Team: blah

Characterization Team: blah

Week of 8/8/2011

Design Team: Lots and lots of work on presentation and poster (along with Swetha, from the Fabrication Team

Fabrication Team: blah

Characterization Team: blah

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