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

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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


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