IllinoisTools/18 July 2009

• • • Note: Our notebook is organized in a weekly fashion. Click on the Saturday of every week to view the notes from the previous week.

7/12-7/18

Donny

I modified the graph library to add room for additional weights. I also added search fields rather than drop down menus for selecting the desired compound.

Nate

This was also a very productive week. I was able to get a slew of programs written that I ended up combining to collect and organize data from the KEGG in ways that are most beneficial to our goals. Using this master program, I have assembled a few dictionaries that we can use for our web-tool. Here are the types of dictionaries I have made using my master program:

-Organism Enzymes to Genes (specify organism and enzyme, and it returns the gene)

-Enzymes to Organisms (specify enzyme, and it returns the organisms that the enzyme has genes in)

-Reactions to Enzymes (specify reaction, and it returns the enzymes that facilitate that reaction)

-Enzymes to Genes (specify enzyme, and it returns all genes that can encode that enzyme that are listed on KEGG)

The great thing about this master program is that it is super fast! Hurray for python! Also, I changed the colors for our wiki, and fixed it up a bit. Now it looks a lot better than before (as everybody liked the colors better this time around...).

Palak

This week I continued to populate the database with information from KEGG such as reaction reversibility, reactants, products, etc. I worked particularly long on creating a script to update reversibility because I ran into problem being able to check if it had been changed on the KEGG database.

Riyad

Finished up writing the program to blast a gene sequence against a file of BioBrick sequences

Kanishka

Worked with Ruyad to figure out the python code that allowed us to blast through the Biobrick database