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== Institutions == | == Institutions == | ||
| − | === University of Minho === | + | *=== University of Minho === |
| − | '''[http://www.uminho.pt University of Minho]''' | + | | |
| + | |'''[http://www.uminho.pt University of Minho]''' | ||
| + | | | ||
| + | |[[Image:Uminho.gif]] | ||
| − | [[Image: | + | *=== IBB-CEB === |
| + | | | ||
| + | |'''[http://www.ibb.pt/ IBB - Institute for Biotechnology and Bioengineering]''' | ||
| + | | | ||
| + | |'''[http://ceb.uminho.pt/ Centre of Biological Engineering]''' | ||
| + | | | ||
| + | |[[Image:Logo_ibb.png]] | ||
| − | + | *=== CCTC === | |
| − | + | | | |
| − | + | |'''[http://cctc.di.uminho.pt CCTC - Computer Science and Technology Center]''' | |
| − | + | | | |
| − | + | |[[Image:Logo_cctc.png]] | |
| − | |||
| − | |||
| − | |||
| − | === CCTC === | ||
| − | |||
| − | '''[http://cctc.di.uminho.pt CCTC - Computer Science and Technology Center]''' | ||
| − | |||
| − | [[Image:Logo_cctc.png]] | ||
Revision as of 00:01, 11 February 2009
Contents
Introduction
The OptGene application includes a number of tools to support in silico metabolic engineering. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the wild type and mutants (original strain with a set of selected gene deletions).
The simulation of these strains will be conducted using a number of approaches (e.g. Flux-Balance Analysis or Minimization of Metabolic Adjustment) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. Evolutionary Algorithms or Simulated Annealing) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.
A more complete description can be found in the manual, linked bellow. The OptGene application is being developed taking as a basis the AIBench framework. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.
Institutions
- === University of Minho ===
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|University of Minho
|
|
- === IBB-CEB ===
|
|IBB - Institute for Biotechnology and Bioengineering
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|Centre of Biological Engineering
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|
- === CCTC ===
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|CCTC - Computer Science and Technology Center
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|
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