Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
+ | |||
+ | [[Image:1258649492 label new red.png]] | ||
+ | '''OptFlux is now published''' [ Check here | http://www.biomedcentral.com/1752-0509/4/45] | ||
+ | Check the [[Downloads|downloads section]] and the [[HowTos|new documentation]]. | ||
[[Image:1258649492 label new red.png]] | [[Image:1258649492 label new red.png]] |
Revision as of 21:16, 9 May 2010
OptFlux is now published [ Check here | http://www.biomedcentral.com/1752-0509/4/45]
Check the downloads section and the new documentation.
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
Powered By
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)