IllinoisTools/13 June 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.

6/7-6/13

Donny

We have considered using toxic chemicals as inputs to our program to suggest a pathway that would convert harmful pollutants into valuable chemicals. I wrote a script that scans a list of harmful chemicals from the EPA and then forms a dictionary pairing the chemical name to its KEGG_ID. The script doesn't quite work perfectly and not all chemicals are found on Kegg. This will be improved throughout the week. Also, I am looking into the possibility of using django to host our application on the web.

I was finally able to figure out who that girl is that I saw in the gatehouse and at work. Potential suspects were Lucy from the other team or Jacinda the secretary. After extensive facebook searches, the unlikely candidate of Julie Richards turned out to be the culprit. I look forward to meeting her or something so I feel less strange about all the stalking

Riyad

Read articles related to metabolic pathways and biological networks to better understand how fluxes work. Also messed around with the Flux Balance Analysis in the COBRA toolbox.

Kanishka

Worked on learning the python language through tutorials and textbooks.

Nate

Explored the world that is wiki. I learned some useful things about wikis(such as templates), and investigated ways to create and edit our wiki page. Looked into some programs, such as dreamweaver, but I am not sure if that will really be of any help with the wiki. I also learned some fun stuff about Linux, and learned some linux commands via Cygwin, a linux emulator for windows. Lots of fun indeed! Towards the end of the week, I learned a great deal about Python programming. In particular, I learned about for and while statements, classes, def statements, regular and global variables, lists and strings. This will be very useful in the future. I was also able to write some small programs. These included a number guesser program(user gives input of what to add and subtract to get to the goal) and a prime number generator. These very basic programs are not very useful of course, but they allowed me to better understand the programming language. Can't wait to start writing some useful code. Also, watching Donny stalk people on facebook has been very entertaining.

Palak

I determined that one of the necessary elements in finding the ideal pathway from a starting to an ending compound is flux balance analysis. I spent sometime looking into what the flux of a reaction is as well as how it is calculated. I read a many papers on metabolic engineering. It turns out that the function in COBRA that finds the flux balance analysis uses a linear solver. I experimented with various linear solvers that are compatible with python interpreters. I found the NUMpy and SCIpy were the most useful modules. I also continued to learn how to program in python using several tutorials.