Team:Illinois-Tools

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2009 University of Illinois Software Tools Team
2009 University of Illinois Software Tools Team
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|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.
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Interactive Metabolic Pathway Tools (IMP Tools) is an open source, web based program that involves model-guided cellular engineering where new metabolic functions can be added to existing microorganisms. This program will assist in the design stage of synthetic biology research. IMP tools is written primarily in python using the Django web framework. It takes a user-defined input compound, output compound, and weighting scheme and determines the ideal pathway from the starting to the ending compound. Our program presents an exciting capability to help transform important processes in the world for applications ranging from bioremediation to biofuels.  
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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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IMPtools utilizes the reactions stored in the Kegg (Kyoto Encyclopedia for Genes and Genomes) database to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. After inputting your desired input and output products, our program searches for the optimal metabolic path connecting the input and output compound. Our program has the ability to provide different pathways according to user defined weights; as an example, least ATP consumption or fewest changes to host organism. The end product we give you is a collection of metabolic pathways and their associated gene sequences. Along with the sequence, we also give you useful information necessary, such as a graphical representation and stoichiometric matrix, to carry out experiments in order to validate our results. Our long-term goals include being able to determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for other teams to predict some of their synthetic biology ventures.
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Go to [http://abe-bhaleraolab.age.uiuc.edu/igem/ IMPtools]
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== '''Sponsors''' ==
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<a href="http://www.igb.uiuc.edu/"><img src="/wiki/images/0/04/Igbsponsor.png" height="85px"></a><br>
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<a href="http://www.tetravitae.com/index.html"><img src="https://static.igem.org/mediawiki/2009/4/42/IllinoistoolsTvitae.jpg" height="85px"></a> Specifically Steven Stodard <br>
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<a href="http://engineering.illinois.edu/"><img src="https://static.igem.org/mediawiki/2009/1/1e/IllinoistoolsEngineering.jpg" height="85px"></a>

Latest revision as of 22:59, 27 June 2010

Homeanimationillinoistools.gif

2009 University of Illinois Software Tools Team

Interactive Metabolic Pathway Tools (IMP Tools) is an open source, web based program that involves model-guided cellular engineering where new metabolic functions can be added to existing microorganisms. This program will assist in the design stage of synthetic biology research. IMP tools is written primarily in python using the Django web framework. It takes a user-defined input compound, output compound, and weighting scheme and determines the ideal pathway from the starting to the ending compound. Our program presents an exciting capability to help transform important processes in the world for applications ranging from bioremediation to biofuels.


IMPtools utilizes the reactions stored in the Kegg (Kyoto Encyclopedia for Genes and Genomes) database to create a metabolic pathway that is in some sense optimized for the production of a desired by-product while consuming some desired input. After inputting your desired input and output products, our program searches for the optimal metabolic path connecting the input and output compound. Our program has the ability to provide different pathways according to user defined weights; as an example, least ATP consumption or fewest changes to host organism. The end product we give you is a collection of metabolic pathways and their associated gene sequences. Along with the sequence, we also give you useful information necessary, such as a graphical representation and stoichiometric matrix, to carry out experiments in order to validate our results. Our long-term goals include being able to determine what intermediate BioBricks would be necessary to activate the required enzymes for production. In future years, this tool may be useful for other teams to predict some of their synthetic biology ventures.


Go to [http://abe-bhaleraolab.age.uiuc.edu/igem/ IMPtools]

Sponsors


Specifically Steven Stodard

Retrieved from "http://2009.igem.org/Team:Illinois-Tools"