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

Andreas Hoppe, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann-Georg Holzhütter
2011 BMC Bioinformatics  
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
more » ... t 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.
doi:10.1186/1471-2105-12-28 pmid:21255455 pmcid:PMC3038154 fatcat:3rkqpmzf2rgcza7xmoo27fkqnq