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Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. | Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. | ||
[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering]. | [http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering]. | ||
− | + | ''BMC Bioinformatics'' 2005, ""6"":308 | |
Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. | Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. | ||
[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains]. | [http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains]. | ||
− | + | ''BMC Bioinformatics'' 2008, ""9"":499 | |
[[Image:1258649492 label new red.png]] | [[Image:1258649492 label new red.png]] |
Revision as of 15:48, 10 May 2010
OptFlux is now published. Please cite using:
Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha. OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology 2010, 4:45
Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, ""6"":308
Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 2008, ""9"":499
OptFlux 2.1 is now available! Check the downloads section and the new documentation.
Problems with SBML? Validate your sbml model here!
Introduction
The OptFlux 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, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes) 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.
The OptFlux 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 2009
CCTC - Computer Science and Technology Center
IBB-CEB - Institute for Biotechnology and Bioengineering - Centre of Biological Engineering
University of Minho
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 http://www.gnu.org/licenses/
Created inside the SysBio Research Group (http://sysbio.di.uminho.pt)