Team:Illinois-Tools

From 2009.igem.org

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Our tool will utilize the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. We will most likely create a list of toxic pollutants as our input to the pathway and have value added products such as biofuels as the product. The goal is to create a network of reactions that connect our input to output and then to determine an optimal path. We are going to focus this task on one or two hosts (most likely E. Coli or Yeast). Constraint based reconstruction analysis (COBRA) will be used to determine the production rates of our product. The goal is to hopefully link together reactions in such a way that production and biomass growth are working together (thus it is favorable for the host to be producing). Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures.  
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Our tool utilizes the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. Once inputing your desired input and output products, our program searches for the most optimal metabolic path. Our program has the ability to provide different pathways according to user defined weights, for example, ATP or host organism. The end product we give you is a collection of metabolic pathways and their associated gene sequences. We then give you useful infromation necessary to carry out experiments in order to validate our results. Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures.  

Revision as of 15:32, 21 October 2009

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2009 University of Illinois Software Tools Team


This is the first software tools team from Illinois. We are comprised of Biology, Bioengineering, and Chemical Engineering majors. With limited programming and synthetic biology experience we have been learning a lot along the way.


Our tool utilizes the Kegg database of reactions to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. Once inputing your desired input and output products, our program searches for the most optimal metabolic path. Our program has the ability to provide different pathways according to user defined weights, for example, ATP or host organism. The end product we give you is a collection of metabolic pathways and their associated gene sequences. We then give you useful infromation necessary to carry out experiments in order to validate our results. Long-term we hope to then determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for our wetlab team to predict some of their metabolic engineering ventures.



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