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A major new release of OptFlux is now available, with several important improvements and new features.
Please visit also the new OptFlux website at www.optflux.org.
A new tutorial is available in the section BeginnersTutorial.

SOURCEFORGE NOW AVAILABLE: - All the code is now available at sourceforge.


OptFlux is 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

  • 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

  • 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

Older versions:

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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

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CEB

Centre of Biological Engineering

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SilicoLife

SilicoLife

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License


Copyright 2009-2014
CEB - Centre of Biological Engineering
University of Minho
SilicoLife Lda.

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)
Supported by SilicoLife Lda. (http://www.silicolife.com)


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