Team:Illinois-Tools

From 2009.igem.org

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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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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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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. Along with the sequence, we also give you useful infromation necessary, such as a graphical representation and stoichmetric matrix, 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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== '''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