FASIMU - flexible software for flux-balance computation series in large metabolic networks
In large metabolic networks, methods based on flux-balance optimization have been recognized as acceptable quantitative predictors for metabolic fluxes. Their validity depends on the adequacy of the chosen optimization criteria and constraints. Systematic application of these methods gains more and more importance in network curation and structural analysis. Thus, a flexible, and easy-to-use computational tool able to handle batch series of flux-balance optimizations is required.
Here, we present FASIMU, a command line oriented software implementing the most frequently applied FBA 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.
The platform-independent program is an open-source project, freely available under GNU public license, including manual, tutorial, BiNA and Cytoscape plugin and respective manuals.
The following picture shows the main outline of the software including files and function calls: