OptFlux

OptFlux is a tool for metabolic modeling, simulations, and analysis. The OptFlux algorithm includes functions for Evolutionary Algorithms, Simulated Annealing metaheuristics, OptKnock method, stoichiometric metabolic modeling of phenotypes, Metabolic Flux Analysis, pathway analysis, and method for model simplification.

Topic

Systems biology;Molecular interactions, pathways and networks;Genotype and phenotype;Genetics;Microbiology

Detail

  • Operation: Metabolic network modelling

  • Software interface: Graphical user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: 3.4.0

  • Credit: The Luso-American Development Foundation.

  • Input: The Systems Biology Markup Language, SBML, standard

  • Output: The Systems Biology Markup Language, SBML, standard

  • Contact: support@optflux.org

  • Collection: -

  • Maturity: Mature

Publications

  • Evolutionary programming as a platform for in silico metabolic engineering
  • Patil KR, Rocha I, Förster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics. 2005 Dec 23;6:308. doi: 10.1186/1471-2105-6-308. PMID: 16375763; PMCID: PMC1327682.
  • https://doi.org/10.1186/1471-2105-6-308
  • PMID: 16375763
  • PMC: PMC1327682
  • Natural computation meta-heuristics for the in silico optimization of microbial strains
  • Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics. 2008 Nov 27;9:499. doi: 10.1186/1471-2105-9-499. PMID: 19038030; PMCID: PMC2612012.
  • https://doi.org/10.1186/1471-2105-9-499
  • PMID: 19038030
  • PMC: PMC2612012
  • OptFlux: an open-source software platform for in silico metabolic engineering.
  • Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M. OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol. 2010 Apr 19;4:45. doi: 10.1186/1752-0509-4-45. PMID: 20403172; PMCID: PMC2864236.
  • https://doi.org/10.1186/1752-0509-4-45
  • PMID: 20403172
  • PMC: PMC2864236

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