IGEM:Illinois Tools Team/2009/Notebook/Biofuels Software/Entry Base

iGEM Project name 1

Main project page

Meeting 1 Tools Team Meeting 5/28/07 2:00 PM Possible Ideas — Have the initial inputs be pollutants (such as CFCs or CO) ◦ This is a good Idea based on how the KEGG Database is arranged — Make the initial outputs be biofuels — Incorporate biobricks as an addition to the program ◦ Program will be able to deal with both the biobrick registry and KEGG ◦ Ultimately, we should be able to integrate the two ◦ This would be a final step — Link inputs to price and determine the best one ◦ This would be a final step Program Output — Pathway ◦ List the reactions and enzymes necessary — Suggest a Host ◦ Eliminate this—takes a very long time to determine the actual host it will work in — Gene Sequence for each reaction ◦ does this exist? — Other parts necessary for this pathway(activators, etc.) Steps — Download database in usable form — Select Input/Output — Form a tree with several paths — Use COBRA to select the best path — Determine other parts necessary Results — Output a work flow model of the pathway — COBRA analysis —  % of sequence that exists in the host — List of biobricks that can be used Further Discussion: Following the iGEM guidelines · Use the KEGG Database to determine reactions and then use the biobricks from the registry to determine the promoters, activators, etc. that are necessary Creating the Program · Time consuming step will be optimization · Agreed to write the program in Python