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

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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.)


— 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