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 18 – July 24
Colin - This week we made a major step in the project. We ordered a server! Honestly, it felt like Christmas here in the IGB. We spent the last few days of the week installing basic software such as the operating system onto the server. In a final decision we unanimously decided to run Ubuntu: server edition, since we are all familiar with it. A major setback occurred this week, however. Due to computer malfunctions on a team mate's computer, we have been set back considerably in our project.
Jeremy - This week is an echo of the week of 6/21. I'm rewriting the same code, but more efficiently and cleaner. The difficulty is limiting the number of times the code goes through all the reactions in the database, which currently limits the tool to delivering your results by email, instead of in real-time.
Anna - This week I read up more about COBRA and started to look into MATLAB tutorials to be able to work with the COBRA and design a project that will work well. I also tried running samples of the program. This involved looking at the dynamic Flux Balance Analysis, which I believe will be the core of the project. I emailed and discussed specific questions I came up with during the week to Caroline and Matt. We looked into Circos, among other ways to be able to visualize the plasmid design. We looked into the server as well; it would be nice to run multiple servers for the graphs and other projects that go on so the whole program can go a lot quicker.
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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