Team:Illinois-Tools/Project

Overall project

Synthetic biology is the creation of new functions using existing existing biological systems. In order to assist synthetic biologists, the 2009 Illinois tools team is trying to create a web-based open source program that outputs a theoretical pathway to synthesize a desired chemical product given an input and an output compound. This network will meet several constraints such as maximal reaction rates and mass balance. The ideal network will consist of known reactions taken from the Kyoto Encyclopedia of Genes and Genomes (KEGG)database, which consists of well-studied organisms. The capabilites of our program will be exemplified by establishing a network for the synthesis of biofuels from various input compounds.

Our program is modular and has 4 major components. The first aspect is obtaining reactions from the KEGG database via KEGG API and determining the shortest paths from the starting compound to the ending compound. The second is putting in an input and output for which you want a theoretical pathway. From then on you use our program to add weights in the pathway and customize it as you would like. We then give you the top three results as well as a stoichmetric matrix and a graphical representation. We also show how it would look like in Biobrick format and check it for compatablity with the registry. Now that you have your theoretical pathways you can proceed to the lab to test it.

Project Details

Part 2

The Experiments

Part 3

Results