IllinoisTools/1 August 2009

7/26-8/1
Donny

I attempted to use RPAIR data as another potential weight (with the help of Kanishka's research). One helpful thing was to read about other similar applications to determine their weighting scheme. I rearranged our class models to incorporate stoichiometry with Palak and modified the database accordingly.

Riyad

Wrote a program to identify possible trivial compounds by seeing how many compounds go into and come out of a given compound and then going through the top 100 compounds and deciding which seemed trivial or not.

Palak

This week I spent time getting stoichiometry information about the into our database. We decided to incorporate a stoichiometric matrix as part of our program output. I also rearranged some of our models so in order to incorporate the stoichiometric information properly.

Kanishka

I read articles to find a weighing system and found how to incorporate weights with different point values. I also spent time thinking about ideas for the webpage.

Nate

In the beginning of the week, I worked on examining certain reactions that required multiple enzymes to facilitate them. One reaction had as many as 66 different types of enzymes needed!! This is a little ambiguous point about KEGG and/or the naming of enzymes. It is hard to discern if the types of enzymes listed for a reaction are either all needed (they are all subunits), or some of them are interchangeable (the organism makes two different enzymes that facilitate the same reaction). After reporting my findings to Donny, I set work on writing code that would ideally export the data obtained with IMPtools in a xgmml file format. Xgmml is a coding language that specifies a graph of nodes and edges. This type of code is recognized by Cytoscape, a program that we had looked at in the beginning of the summer. We have recently decided to use cytoscape for graphically representing the outputs of IMPtools. I was very successful with my program, as it makes a nice, easy to see graph of any reaction pathway. I sent this code to Donny, so that he may work it into our website. This has been a super fun summer!