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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
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:

Problems with SBML? Validate your sbml model here!


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.


University of Minho

University of Minho



Centre of Biological Engineering




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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
GNU Public License for more details.

You should have received a copy of the GNU Public License
along with this code. If not, see

Created inside the SysBio Research Group (
Supported by SilicoLife Lda. (