Team:Virginia Tech/Notebook

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!align="center"|[[Team:Virginia_Tech|<span style="color:orange;">Home</span>]]
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!align="center"|[[Team:Virginia_Tech/Team|<span style="color:orange;">Team</span>]]
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!align="center"|[https://igem.org/Team.cgi?year=2011&team_name=Virginia_Tech <span style="color:orange;">Official Team Profile</span>]
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!align="center"|[[Team:Virginia_Tech/Project|<span style="color:orange;">Project</span>]]
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!align="center"|[[Team:Virginia_Tech/Parts|<span style="color:orange;">Parts Submitted to the Registry</span>]]
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!align="center"|[[Team:Virginia_Tech/Notebook|<span style="color:orange;">Notebook</span>]]
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!align="center"|[[Team:Virginia_Tech/Safety|<span style="color:orange;">Safety</span>]]
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!align="center"|[[Team:Virginia_Tech/Attributions|<span style="color:orange;">Attributions</span>]]
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=Students=
 
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{{:Team:Cambridge/Templates/Nolineheader|header=Anja Hohmann}}
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__NOTOC__
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:Anja is a biochemist. She likes singing along to 'Fireflies', is extremely efficient and makes sure our lab book is always kept up to date.
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=Notebook=
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<html><img src="https://static.igem.org/mediawiki/2010/3/3c/CambridgeTeamBen.jpg" style="float:left; padding-right:10px" /></html>
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==Week of 5/23/2011==
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<p><big><b> Design Team: </b></big> Started collecting sequences of relevant fluorescent proteins and entering them into GenoCAD. Learned about attribute grammars.  
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</p>
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<p><big><b> Fabrication Team: </b></big> Lab Training.  
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</p>
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<p><big><b> Characterization Team: </b></big> Started looking at model, ways of analyzing data that we'll eventually get, and fitting model to it.  Started training on microscope, cell culture.  Started learning Matlab for GenoSIGHT changes.
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</p>
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{{:Team:Cambridge/Templates/Nolineheader|header=Ben Reeve}}
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==Week of 5/30/2011==
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:Ben is a molecular biologist. He is the Hacky Sack-master, loves the word 'epic' and brought the beats to the Gibson Assembly song.   
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<p><big><b> Design Team: </b></big> 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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.  
 +
</p>
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<p><big><b> Characterization Team: </b></big> Started looking at parameter estimation - methods of getting maturation and degradation rates from fluorescence over time data.  More Matlab training.  More microscope training, in preparation for real experiments once fab team finishes transforming some cells.
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</p>
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==Week of 6/6/2011==
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<p><big><b> Design Team: </b></big> 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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.
 +
</p>
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<p><big><b> Characterization Team: </b></big> More work on parameter estimation, common algorithms for doing this.  More Matlab training, started to modify GenoSIGHT by adding Time Calculator to GUI. 
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</p>
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<html><img src="https://static.igem.org/mediawiki/2010/9/93/CambridgeTeamBill.jpg" style="float:left; padding-right:10px" /></html>
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==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). 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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.  
 +
</p>
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<p><big><b> Characterization Team: </b></big> Started imaging actual cells.  More work on parameter estimation problem and comparing algorithms.  Started looking for new parts in Registry.  More changes to GenoSIGHT GUI.
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</p>
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{{:Team:Cambridge/Templates/Nolineheader|header=Bill Collins}}
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==Week of 6/20/2011==
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:Bill is a control engineer. He is the creator of Gibthon and always happy to assist with helpful advice: 'Get a Mac!'.                                  
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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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We compared the differences in protocol between the Yeast pYES2 vector and E. coli pDsRed vector and updates on Codon Optimization. 
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</p>
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<p><big><b> Characterization Team: </b></big> More imaging of cells from fab team.  More work on parameter estimation.  Started looking at adaptive imaging and timing.  Troubleshooting with Design Team.
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</p>
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==Week of 6/27/2011==
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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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We worked on mCherry and mCitrine from pRSETb into pYES2 for yeast expression, and Biobrick ECFP (BBa_E0020) is being used as a test protein to validate our chosen backbone vector (pSB1AK3 with part J04500). We also worked on converting our existing fluorescent proteins into Biobrick parts in order to further test pSB1AK3.
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</p>
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<p><big><b> Characterization Team: </b></big> More imaging and updates to GenoSIGHT GUI.  Starting to test parameter estimation against simulated data.
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</p>
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<html><img src="https://static.igem.org/mediawiki/2010/7/7e/CambridgeTeamEmily.jpg" style="float:left; padding-right:10px" /></html>
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==Week of 7/4/2011==
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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.
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</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 and Plasmid Prep 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>
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<p><big><b> Characterization Team: </b></big> More imaging and updates to GenoSIGHT GUI.  Testing parameter estimation against simulated data.  Photobleaching issues.  Work on adaptive imaging and timing.
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</p>
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{{:Team:Cambridge/Templates/Nolineheader|header=Emily Knott}}
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==Week of 7/11/2011==
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:Emily is a mechanical engineer. She will happily sing to you about Gibson Assembly. Alternatively, she might teach you the dance moves to 'Blame it on the Boogie'.  
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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>
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<p><big><b> Fabrication Team: </b></big> Loran completed mCherry-pYES2 and started cloning non-Biobrick AcGFP-pYES2 and Biobrick AcGFP-pSB1AK3. Swetha completed mCitrine-pYES2 and started cloning Biobrick CFP-pYES2 and Biobrick GFPmut3b-pYES2. Mandy completed CFP-pSB1AK3 and mCherry-pYES2 and started cloning Biobrick mCherry-pYES2, Biobrick mCherry-pSB1AK3, and Biobrick GFPmut3b-pSB1AK3. Hayley completed mCitrine-pYES2 and started cloning Biobrick mCherry-pSB1AK3 and non-Biobrick mCitrine-pSB1AK3. Martha started cloning Biobrick GFPmut3b-pSB1AK3.
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</p>
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<p><big><b> Characterization Team: </b></big> Lots of imaging - lots of constructs coming from fab team now.  More work on getting parameter estimation to work efficiently and as expected. Adaptive imaging for GenoSIGHT.
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</p>
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==Week of 7/18/2011==
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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.
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</p>
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<p><big><b> Fabrication Team: </b></big> We worked on the mCitrine-J04500, AcGFP-pYES2, GFPmut3b-pYES2, and CFP-pYES2 constructs.
 +
</p>
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<p><big><b> Characterization Team: </b></big> Lots more imaging.  More photobleaching troubleshooting.  More work on getting parameter estimation to work efficiently and as expected.  Adaptive imaging for GenoSIGHT.
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</p>
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<html><img src="https://static.igem.org/mediawiki/2010/7/70/56q23864732.jpg" style="float:left; padding-right:10px" /></html>
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==Week of 7/25/2011==
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<p><big><b> Design Team: </b></big> 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.
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{{:Team:Cambridge/Templates/Nolineheader|header=Hannah Copley}}
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</p>
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:Hannah is a medic. She initated the 'wiki morning turns into afternoon turns into day turns into weekend' and was the only one to remember dress-up friday.
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<p><big><b> Fabrication Team: </b></big> We have designed new primers for constructs with tags, which need to be tested over a range of PCR temperatures to find the optimum. The mCitrine insert with Sul20C tag in J04500  backbone, mCitrine insert with LVA tag in J04500 Backbone, acGFP insert with LVA tag in J04500 backbone, adn GFPmut3B (E0040) with PEST Tag in pYES2 Backbone have been completed.  
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</p>
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<p><big><b> Characterization Team: </b></big> Lots of imaging, more troubleshooting of equipment failures. Parameter estimation working pretty nicely now.  Adaptive imaging working successfully on microscope.
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</p>
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{{:Team:Cambridge/Templates/Nolineheader|header=Paul Masset}}
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:Paul is a systems engineer. He is in charge of characterising our BioBricks, but generally found rowing on the river.  
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<html><img src="https://static.igem.org/mediawiki/2010/e/e1/CambridgeTeamPeter.jpg" style="float:left; padding-right:10px" /></html>
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{{:Team:Cambridge/Templates/Nolineheader|header=Peter Emmrich}}
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:Peter is a plant scientist. He is the team's personal photographer, an instigator of party games and likes plastering the lab with motivational posters.
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{{:Team:Cambridge/Templates/Nolineheader|header=Theo Sanderson}}
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:Theo is a geneticist. He makes good videos, funny faces and wins every fast walk competition.                                                                               
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{{:Team:Cambridge/Templates/Nolineheader|header=Will Handley}}
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:Will is a physicist. He is our expert in oligo design, but can regularly be found juggling with all sorts of laboratory equipment.
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=Mission Statement=
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:As a team of scientists and engineers from very diverse backgrounds we aim to create an environment in which every member is able to apply his or her unique talents and knowledge to the fullest. We will document our literature research as well as our experimental work on the wiki and the online labbook making new content available as soon as possible. To make our work more relevant and transparent we will clearly distinguish between theoretical designs, mathematical simulations and physically designed biological systems, and include measurements where appropriate.
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==Share and Enjoy==
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:In the Open Source spirit of iGEM, we will try to make our ideas, the progress of our work and our results as open as possible. This requires honesty about which parts of our project succeeded, which ones yielded ambiguous results and which ideas had to be abandoned. We believe that such transparency will make our project more useful for future iGEM teams and researchers.
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:Although iGEM takes the form of a competition, all our work is ultimately a collaboration to create a registry that will act as a firm foundation supporting the scientists and engineers of the future.
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:Therefore, we would love to collaborate with other current iGEM teams working on related projects. If you think parts of our work could be useful to you, please get in contact and we will see how we can help. Conversely, if you have any resources or knowledge that you believe could help us, please let us know!
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==Attribution==
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Unless otherwise indicated, all work presented on this wiki is the sole work of the iGEM team members listed above. We are also extremely grateful for the help of the following advisors and instructors.
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=Advisors=
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{{:Team:Cambridge/Templates/Nolineheader2|header=Jim Haseloff}}
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Dr Haseloff is a lecturer and group leader in the Department of Plant Sciences investigating biological engineering of plant systems.
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[http://www.plantsci.cam.ac.uk/Haseloff/ http://www.plantsci.cam.ac.uk/Haseloff/]
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{{:Team:Cambridge/Templates/Nolineheader2|header=Jim Ajioka}}
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Dr Ajioka is a senior lecturer and group leader in the Department of Pathology working on host-parasite interactions during the infection of warm-blooded animals with the intracellular pathogen Toxoplasma gondii.
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http://www.path.cam.ac.uk/research/investigators/ajioka/
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{{:Team:Cambridge/Templates/Nolineheader2|header=Duncan Rowe}}
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Dr Rowe is a laboratory manager and teaching technician in the Department of Genetics with research and development experience in recombinant and synthetic DNA technology, cloning, drug target identification and therapeutic protein expression in bacteria.
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http://www.gen.cam.ac.uk/research/personal/rowe/rowe.html
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{{:Team:Cambridge/Templates/Nolineheader2|header=Gos Micklem}}
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Dr Micklem is director of the Cambridge Computational Biology Institute as well as a group leader in the Department of Genetics interested in bioinformatics and the analysis of small RNAs.
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http://www.gen.cam.ac.uk/research/micklem.html
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{{:Team:Cambridge/Templates/Nolineheader2|header=Fernan Federici, PJ Steiner, James Brown, Shuna Gould}}
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We are very grateful to these people who were working in Dr. Haseloff's lab and were an invaluable source of advice.
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==Contact us==
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You can reach the team by [mailto:info@cambridgeigem.org email]. We will get back to you as soon as we can.
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!align="center"|[[Team:Virginia_Tech|Home]]
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!align="center"|[[Team:Virginia_Tech/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Virginia_Tech Official Team Profile]
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!align="center"|[[Team:Virginia_Tech/Project|Project]]
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!align="center"|[[Team:Virginia_Tech/Modeling|Modeling]]
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!align="center"|[[Team:Virginia_Tech/Notebook|Notebook]]
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==Notebook==
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==Week of 8/1/2011==
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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.  Mark had to leave for the summer because of health issues :(
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</p>
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<p><big><b> Fabrication Team: </b></big> Helped with presentation, poster, and wiki.
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</p>
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<p><big><b> Characterization Team: </b></big> Helped with presentation, lots and lots of imaging - trying to finish imaging everything fab team has made.  Getting actual parameters for data we collected!
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</p>
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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. -->
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==Week of 8/8/2011==
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<p><big><b> Design Team: </b></big> Lots and lots of work on presentation.  Final wrap-up, careful documentation of what we did all summer, etc.
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</p>
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<p><big><b> Fabrication Team: </b></big> Helped with presentation, poster, and wiki.
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</p>
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<p><big><b> Characterization Team: </b></big> Continued helping with presentation.  Got some more parameters for our fluorescent proteins. Lots of imaging to finish getting data on all the constructs we made.
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</p>

Latest revision as of 03:56, 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


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: Lab Training.

Characterization Team: Started looking at model, ways of analyzing data that we'll eventually get, and fitting model to it. Started training on microscope, cell culture. Started learning Matlab for GenoSIGHT changes.

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: We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.

Characterization Team: Started looking at parameter estimation - methods of getting maturation and degradation rates from fluorescence over time data. More Matlab training. More microscope training, in preparation for real experiments once fab team finishes transforming some cells.

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: We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.

Characterization Team: More work on parameter estimation, common algorithms for doing this. More Matlab training, started to modify GenoSIGHT by adding Time Calculator to GUI.

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: We were split into two teams to work autonomously on Miniprep procedure for plasmid DNA extraction and SalI and EcoRI restriction digests of mCherry and pDSRed.

Characterization Team: Started imaging actual cells. More work on parameter estimation problem and comparing algorithms. Started looking for new parts in Registry. More changes to GenoSIGHT GUI.

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: We compared the differences in protocol between the Yeast pYES2 vector and E. coli pDsRed vector and updates on Codon Optimization.

Characterization Team: More imaging of cells from fab team. More work on parameter estimation. Started looking at adaptive imaging and timing. Troubleshooting with Design Team.

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: We worked on mCherry and mCitrine from pRSETb into pYES2 for yeast expression, and Biobrick ECFP (BBa_E0020) is being used as a test protein to validate our chosen backbone vector (pSB1AK3 with part J04500). We also worked on converting our existing fluorescent proteins into Biobrick parts in order to further test pSB1AK3.

Characterization Team: More imaging and updates to GenoSIGHT GUI. Starting to test parameter estimation against simulated data.

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: 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 and Plasmid Prep 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.

Characterization Team: More imaging and updates to GenoSIGHT GUI. Testing parameter estimation against simulated data. Photobleaching issues. Work on adaptive imaging and timing.

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: Loran completed mCherry-pYES2 and started cloning non-Biobrick AcGFP-pYES2 and Biobrick AcGFP-pSB1AK3. Swetha completed mCitrine-pYES2 and started cloning Biobrick CFP-pYES2 and Biobrick GFPmut3b-pYES2. Mandy completed CFP-pSB1AK3 and mCherry-pYES2 and started cloning Biobrick mCherry-pYES2, Biobrick mCherry-pSB1AK3, and Biobrick GFPmut3b-pSB1AK3. Hayley completed mCitrine-pYES2 and started cloning Biobrick mCherry-pSB1AK3 and non-Biobrick mCitrine-pSB1AK3. Martha started cloning Biobrick GFPmut3b-pSB1AK3.

Characterization Team: Lots of imaging - lots of constructs coming from fab team now. More work on getting parameter estimation to work efficiently and as expected. Adaptive imaging for GenoSIGHT.

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: We worked on the mCitrine-J04500, AcGFP-pYES2, GFPmut3b-pYES2, and CFP-pYES2 constructs.

Characterization Team: Lots more imaging. More photobleaching troubleshooting. More work on getting parameter estimation to work efficiently and as expected. Adaptive imaging for GenoSIGHT.

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: We have designed new primers for constructs with tags, which need to be tested over a range of PCR temperatures to find the optimum. The mCitrine insert with Sul20C tag in J04500 backbone, mCitrine insert with LVA tag in J04500 Backbone, acGFP insert with LVA tag in J04500 backbone, adn GFPmut3B (E0040) with PEST Tag in pYES2 Backbone have been completed.

Characterization Team: Lots of imaging, more troubleshooting of equipment failures. Parameter estimation working pretty nicely now. Adaptive imaging working successfully on microscope.

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: Helped with presentation, poster, and wiki.

Characterization Team: Helped with presentation, lots and lots of imaging - trying to finish imaging everything fab team has made. Getting actual parameters for data we collected!

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: Helped with presentation, poster, and wiki.

Characterization Team: Continued helping with presentation. Got some more parameters for our fluorescent proteins. Lots of imaging to finish getting data on all the constructs we made.

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