BACKGROUND: Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a computational tool flexible enough to realize a wide variety of FBA algorithms and able to handle batch series of flux-balance optimizations is of great benefit. RESULTS: We present FASIMU, a command line oriented software for the computation of flux distributions using a variety of the most common FBA algorithms, including the first available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) of the concentration-based thermodynamic feasibility constraint. It allows batch computation with varying objectives and constraints suited for network pruning, leak analysis, flux-variability analysis, and systematic probing of metabolic objectives for network curation. Input and output supports SBML. FASIMU can work with free (lp_solve and GLPK) or commercial solvers (CPLEX, LINDO). A new plugin (faBiNA) for BiNA allows to conveniently visualize calculated flux distributions. The platform-independent program is an open-source project, freely available under GNU public license at http://www.bioinformatics.org/fasimu including manual, tutorial, and plugins. CONCLUSIONS: We present a flux-balance optimization program whose main merits are the implementation of thermodynamics as a constraint, batch series of computations, free availability of sources, choice on various external solvers, and the flexibility on metabolic objectives and constraints.
BACKGROUND: Flux-balance analysis based on linear optimization is widely used to compute metabolic fluxes in large metabolic networks and gains increasingly importance in network curation and structural analysis. Thus, a computational tool flexible enough to realize a wide variety of FBA algorithms and able to handle batch series of flux-balance optimizations is of great benefit. RESULTS: We present FASIMU, a command line oriented software for the computation of flux distributions using a variety of the most common FBA algorithms, including the first available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) of the concentration-based thermodynamic feasibility constraint. It allows batch computation with varying objectives and constraints suited for network pruning, leak analysis, flux-variability analysis, and systematic probing of metabolic objectives for network curation. Input and output supports SBML. FASIMU can work with free (lp_solve and GLPK) or commercial solvers (CPLEX, LINDO). A new plugin (faBiNA) for BiNA allows to conveniently visualize calculated flux distributions. The platform-independent program is an open-source project, freely available under GNU public license at http://www.bioinformatics.org/fasimu including manual, tutorial, and plugins. CONCLUSIONS: We present a flux-balance optimization program whose main merits are the implementation of thermodynamics as a constraint, batch series of computations, free availability of sources, choice on various external solvers, and the flexibility on metabolic objectives and constraints.
Authors: Scott A Becker; Adam M Feist; Monica L Mo; Gregory Hannum; Bernhard Ø Palsson; Markus J Herrgard Journal: Nat Protoc Date: 2007 Impact factor: 13.491
Authors: Wilbert B Copeland; Bryan A Bartley; Deepak Chandran; Michal Galdzicki; Kyung H Kim; Sean C Sleight; Costas D Maranas; Herbert M Sauro Journal: Metab Eng Date: 2012-05 Impact factor: 9.783
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Authors: Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N Mendoza; Anne Richelle; Almut Heinken; Hulda S Haraldsdóttir; Jacek Wachowiak; Sarah M Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H J Chan; Maike K Aurich; Catherine M Clancy; Jennifer Modamio; John T Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C El Assal; Luis V Valcarcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M Le; Ding Ma; Yuekai Sun; Lin Wang; James T Yurkovich; Miguel A P Oliveira; Phan T Vuong; Lemmer P El Assal; Inna Kuperstein; Andrei Zinovyev; H Scott Hinton; William A Bryant; Francisco J Aragón Artacho; Francisco J Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A Saunders; Costas D Maranas; Nathan E Lewis; Thomas Sauter; Bernhard Ø Palsson; Ines Thiele; Ronan M T Fleming Journal: Nat Protoc Date: 2019-03 Impact factor: 13.491