IllinoisTools/27 June 2009

6/21-6/27
Donny

During this week I put a lot of focus into writing code to update our database. Eventually, we will be able to re-use some of this code in an automated process that keeps our network up to date with the Kegg database.

Kanishka

worked on Biobricks

Riyad

worked on BioBricks as well with Kanishka

Palak

This week I worked through the Django tutorials and learned how to make databases using Django and SQLite. I began creating models for the categories of databases that we would need. We went through many of the KEGG files to determine the way that we are going to organize our databases. We used the KEGG API to write scripts to create some of the databases and the FTP server to create the rest.

Nate

This week was not as exciting as last week. I at first started looking over the FTP files on the KEGG database, and tried to better understand how they organize their data. One thing that is really confusing about KEGG is the topic of cofactors. They have an odd way of organizing this data. In the FTP file for enzyme data, there is a section specific for listing relevant cofactors for the enzyme. However, there are some enzymes that list cofactors in the comment section of each enzyme as well. This makes things somewhat more frustrating when trying to organize cofactor data. I also brainstormed some on how I could organize information that is relevant to us in a way that we could use it. I didn't come up with any good way in the end. We ended meeting with the professors again this week. After the meeting, I decided to look more into graphical ways to represent our outputs of program once it is completed. I mostly investigated Networkx, but I also investigated other libraries that python can work with to see how else I can make a graph using python. I learned some new things, but I am not sure if they will be useful to us in the future.