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
July 11 – July 17
Colin – At the beginning of the week, I began to learn the basics of Inkscape and how to graphically design. This will help in creating the logo, since it allows for meticulous graphical editing. I have an idea for the logo, and it includes a trowel, some DNA, then bricks, representing the process from metabolic pathway to a series of BioBricks. The only problem with the logo is that it is very tedious to create and I feel like I am getting no where.
Jeremy – I begin to rewrite the branching code, starting from a fresh checkout of the code that has been running on the server the whole time. A valuable lesson about the importance of backups was learned by all.
Anna – The cell modeling is based on Genome-scale metabolic reconstructions of an organism using the BIGG database. From genome annotation to biochemical data to physiological data to inferred reactions and finally to model development which is an interative process. Computaiton biochemical investation is needed and is a complex mathematical representation of a biochemical network. The network is represented as a stoichiometrix matrix with reactions as columns and rows as metabolites with specific boundaries. It requires element balancing in a chemical reaction as well. The current state of the art project is the UCSD COBRA project which takes MAPS and GPR associations as well as reaction and metabolite lists and supplementary information such as reaction rates and designs a cellular growth model. It involves taking a Flux Balance Analysis as well as a constraint base approach. Solution point requires complete knowledge - we don’t have -- we want a solution space -- exclude impossible solutions and we will be left with range of solutions - apply constraints and there iw illbe a range - go as far as experimental data willa llow you but not further. Take stoichiometric matrix and think about it differently. In physics and chemistry - we solve for solution point. The basic premise - imposing the governing physico-chemical and system-specific.
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
"
