From 2010.igem.org
- The notebook is organized into weeks. Click on the Saturday of each week to view that week's notebook entry
Weekly Lab Notebook
June 27 – July 3
Colin - This week, I began brainstorming to come up with a logo for BioMORTAR. Also, I spent a lot of time looking into social media to spread the word about our project. Anna and I created our own twitter page, and made a lot of connections with other iGEM teams from around the world. I am really liking this, if only we can update our twitter.
Jeremy - I was away this week.
Anna - implemented Twitter and set up an official team email address, this will allow us to keep in contact with the public about our project. I looked more at the APE designer and the biobricks registry. If we need help on the plasmid design, Dr. Bhalerao knows people that could help us out. Is there a way to play back with IMPTools to yield the most ideal host organism for the specific pathway of interest? Once a host organism is chosen, we could perform metabolic simulations that would show how the additional proteins change the organism. What this requires is us to Take network, stoichiometry of the netowrk and then study new pathway - number of algorithms (opt-knock strategy) - what knockouts will benefit growth of organism - simulate it. Is the change worth it - show engineer pathway (30% increase in ethanol production) - simulates growth based on additions. This can be done with COBRA through MATLAB. Genes for some cases and some enzymes - cases wher eit finds the gene in selected organsim - some don't have gene information - some enzymes have no link with database in KEGG. Is there an easy solution? Can you give more information - no gene sequence but here is the reference. Can we incorporate Biobricks also by applying a simpler table for the Biobricks parts registry.
Bobak - Ironing out bugs from entrez format changes
Researching COBRA toolbox, matlab-python interface
Implementing and iterating on views in BioMORTAR: imptools and strain designer
Performance improvements to enzyme -> gene sequence Entrez lookup
Implementing organism enzyme -> gene search and 'closest' organism
Implementing PNG -> SVG conversion for plasmid display on server
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