FASIMU: flexible software for flux-balance computation series in large metabolic networks.
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.
Institute of Biochemistry, University Medicine Charité Berlin, Seestr, 73, 13347 Berlin, Germany. hoppe@bioinformatics.org
Andreas
A
Hoppe
Sabrina
S
Hoffmann
Andreas
A
Gerasch
Christoph
C
Gille
Hermann-Georg
HG
Holzhütter
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software
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