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
University of Minho
IBB-CEB
IBB - Institute for Biotechnology and Bioengineering Centre of Biological Engineering
CCTC
CCTC - Computer Science and Technology Center
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License
Copyright 2008
<a href="http://cctc.di.uminho.pt/">CCTC - Computer Science and Technology Center</a>
<a href="http://www.ceb.uminho.pt/">IBB-CEB - Institute for Biotechnology and Bioengineering - Centre of Biological Engineering</a>
<a href="http://www.uminho.pt/">University of Minho</a>
This is free software: you can redistribute it and/or modify
it under the terms of the GNU Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This code is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Public License for more details.
You should have received a copy of the GNU Public License
along with this code. If not, see <a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/></a>
Created inside the SysBio Research Group <a href="http://sysbio.di.uminho.pt/">(http://sysbio.di.uminho.pt)</a>
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