Difference between revisions of "Team:UC San Diego/Notebook"
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<div class="cd-timeline-content"> | <div class="cd-timeline-content"> | ||
<h2>Modeling</h2> | <h2>Modeling</h2> | ||
− | <p> | + | <p>>Literature research |
+ | <br>>Looking for techniques to combine the deterministic model and genome-scale model | ||
+ | <br>>Attended the Q-bio Summer School: Computational Synthetic Biology | ||
+ | <br><br>Learned to code SBML | ||
+ | <br>>added reactions and metabolites manually to version 7 model since the built-in function addReactions was unusable | ||
+ | </p> | ||
<span class="cd-date">WEEK 5</span> | <span class="cd-date">WEEK 5</span> | ||
</div> <!-- cd-timeline-content --> | </div> <!-- cd-timeline-content --> | ||
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<div class="cd-timeline-content"> | <div class="cd-timeline-content"> | ||
<h2>Modeling</h2> | <h2>Modeling</h2> | ||
− | <p> | + | <p>>Searched for genome-scale model parameters |
+ | <br>>Developed core network diagram and found some nominal parameters for ODE model | ||
+ | <br>>Constructed core model for our bioluminescent system | ||
+ | <br>>Compile various literature sources necessary to understand bioluminescent network | ||
+ | <br>>Developed kinetic equations corresponding to network | ||
+ | <br><br>Thinking of making an isolated COBRA model to visualize flux distribution | ||
+ | <br>>installed Cytoscape and CyFluxViz | ||
+ | <br>>investigation on exporting model and fluxes from Matlab structure format | ||
+ | </p> | ||
<span class="cd-date">WEEK 4</span> | <span class="cd-date">WEEK 4</span> | ||
</div> <!-- cd-timeline-content --> | </div> <!-- cd-timeline-content --> | ||
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<br>>made first digitalized diagram of the entire bioluminescent system | <br>>made first digitalized diagram of the entire bioluminescent system | ||
<br><br>Installed MATLAB student copy sponsored by iGEM | <br><br>Installed MATLAB student copy sponsored by iGEM | ||
+ | <br>> Made first script to add igem reactions | ||
<br><br>Installed APE | <br><br>Installed APE | ||
<br>> thinking about incorporating protein synthesis into the COBRA model | <br>> thinking about incorporating protein synthesis into the COBRA model |
Revision as of 22:06, 18 September 2015
TIMELINE
September 24-28
Giant Jamboree!
Giant Jamboree!
Modeling
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WEEK 14Wet Lab
+Final preparations before the wiki freeze.
WEEK 14Modeling
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WEEK 13Wet Lab
+ Mapped out errors in the parts that we assembled
+ Mutagenesis to fix recurring errors in C sequence
Modeling
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WEEK 12Wet Lab
+ Attempted Gibson Assembly with CDE with AB
+ Designed sequence primers
+ Miniprepped full size clones
Modeling
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WEEK 11Wet Lab
+ Attempted full gibson assembly of AB fragment
+ Miniprepped CDE fragments
Modeling
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WEEK 10Wet Lab
+ Selected error free clones for CDE fragments from sequencing data
+ Designed primers for PacBio Sequencing
+ Transformed error free clones of CDE
Modeling
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WEEK 9Wet Lab
+ Assembled using Gibson Assembly and sequenced CDE fragments
+ PCR and transformed fragments
Modeling
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WEEK 8Wet Lab
+ Received our DNA fragments from SGI thanks to the BioXP!
+ Attempted to PCR and transform our fragments.
Modeling
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WEEK 7Wet Lab
+ Assembled Interlab Devices. Resuspended and measured them successfully.
+ Prepared YPD plates.
Modeling
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WEEK 6Wet Lab
+ Continued interlab study with miniprep, restriction digests, ligation, gel electrophoresis and gel purification.
WEEK 6Modeling
>Literature research
>Looking for techniques to combine the deterministic model and genome-scale model
>Attended the Q-bio Summer School: Computational Synthetic Biology
Learned to code SBML
>added reactions and metabolites manually to version 7 model since the built-in function addReactions was unusable
Wet Lab
+ Started interlab study with transformation.
WEEK 5Modeling
>Searched for genome-scale model parameters
>Developed core network diagram and found some nominal parameters for ODE model
>Constructed core model for our bioluminescent system
>Compile various literature sources necessary to understand bioluminescent network
>Developed kinetic equations corresponding to network
Thinking of making an isolated COBRA model to visualize flux distribution
>installed Cytoscape and CyFluxViz
>investigation on exporting model and fluxes from Matlab structure format
Wet Lab
+ Sent our genes to SGI and ordered lab supplies. Almost ready to go!
WEEK 4Modeling
>Developed lecture on enzymatic kinetics and gene expression modeling, along with corresponding MATLAB simulations
Continued Investigation of literature on lux system reactions in-detail
>attempted to link pathways to rate-constants found in literature
>made first digitalized diagram of the entire bioluminescent system
Installed MATLAB student copy sponsored by iGEM
> Made first script to add igem reactions
Installed APE
> thinking about incorporating protein synthesis into the COBRA model
Investigation about the CrabTree Effect in s288c
>could affect how much light is made (acetate is a substrate)
Wet Lab
+ Added frp gene sequence from Vibrio Harveyi to our plasmid to stabilize the production of luciferase.
+ Optimized our plasmid sequences.
Modeling
Became familiarized with genome-scale modeling and metabolic control analysis
Literature research: Understanding the different components of the bioluminescent system
>aldehyde synthesis
>light production
Researched Literature on COBRA analysis and methods
>used e.coli as a toy model
>ran stimulations of FBA, robustness analysis, and phenotype phase plane
Wet Lab
+ Created a preliminary design for the plasmids using ApE.
+ Improved them over the week by adding tags, removed illegal restriction sites, and changing repetitive sequences.
Modeling
Developed and finalized Primer to MATLAB Programming
Researched potential modeling avenues
>genome scale analysis of synthetic construct
>analysis of the tradeoffs between different genetic circuit designs and gene dynamics
>analysis of metabolic activity in an isolated network via Metabolic Control Analysis
Browsed recent literature for lux system
>identified its advantages and disadvantages as a reporter system
>differences in luciferase systems of beetles and bacteria
Familiarized ourselves with basics of enzyme kinetics
>Michaelis-Menten equations
Downloaded COBRA Toolbox plugin for Matlab
Wet Lab
+ Found genes coding for fatty acid reductase complex that have been validated in an in vitro synthesis paper.
+ Planned how to assemble our plasmids and determined nucleotide sequences for lux A-E of Photobacterium Phosphoreum.
+ Compared the amino acid sequences to those of other organisms on BLAST to check for significant discrepancies in our sequence.