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FASIMU: flexible software for flux-balance computation series in large metabolic networks

Abstract:

ABSTRACT: 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.

21255455

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.4: Linking signalling to metabolic functions

BMC Bioinformatics
BMC Bioinformatics 12: 28
22nd Oct 2010

Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann-Georg Holzhütter

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[Andreas Hoppe] [Hermann-Georg Holzhütter]

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Views: 2334
  • Created: 7th Feb 2011 at 12:27
  • Last updated: 24th Oct 2013 at 16:19

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