IllinoisTools/30 May 2009

5/24-5/30
The team developed a better idea of how we are to make this software thanks to the advice and guidance from Professor Bhalerao.

Donny

I spent the week brainstorming possible ideas and applications of our project as well as researching some of the considerations we might need to account for. I also looked into what software tools have been made in the past to ensure originality of our design. We made a list of "Donny's Crazy Ideas" for the project. After a lot of brainstorming, we decided to stick with our original idea after all, but the planning process was very beneficial because it gave some direction on how to get started.

Im not sure what Nate thinks he will get by sucking up to me, but I don't trust him for a second.

Nate

Nate learned some fun basic stuff about Python. Also, he looked into graphical options that we hope to use in the future in conjunction with our program with help from Kanishka. Graphviz was the main application investigated, as well as the modules that would be needed to run it via Python, such as Pydot, Pygraphviz, and Networkx. Not sure what Donny is talking about, given that the software has yet to be written. However, he is very thankful to have Donny "The Ultimate Programmer" Amfahr on the team for his infinite knowledge and wisdom about programming and such.

Palak

I read papers by Dr. Price about constraint based modeling and the factors that need to be taken into account when genome-scale models are created. I also read another paper by a group from San Diego that described a program called COBRA that is used for constraint based modeling. COBRA is a Matlab software that gives various outputs based on a metabolic pathway and host organism as an input. I began learning how to program in python using tutorials from python.org. This week we also made our first template of what we thought our final product would look like. We debated adding and removing various functions till we came up with a list of the functions we wanted to try to implement first.