FASIMU (Flux-balance Analysis based SIMUlations)is a command line oriented software implementing the most frequently applied FBA(Flux-balance Analysis) algorithms. Moreover, it offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins.
- CPLEX and BiNA
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FASIMU: flexible software for flux-balance computation series in large metabolic networks
Andreas Hoppe , Sabrina Hoffmann , Andreas Gerasch , Christoph Gille and Hermann-Georg Holzhütter
BMC Bioinformatics 2011, 12:28