FASIMU: FBA simulation software for metabolomics, fluxomics, and biotechnology

FASIMU is a

• free (GPL),
• customizable (e.g. many parameters of FBA and the simulations), and
• very flexible (functions can be modified)

software that allows batch computation of flux distributions.

Cellular objectives include

• Flux minimization (Holzhütter 2004)
• Fitness maximization (Holzhütter 2006)
• Biomass maximization (Edwards et al. 2001)
• Network prediction based on expression profiles (Shlomi et al. 2008, GIMME)
• Combined flux optimization and expression profile match (Huthmacher et al. 2010)
• Distance to a reference solution (MOMA) (Segrè et al. 2002)
• Threshold-based distance to a refence solution (ROOM) (Shlomi et al. 2005)

Constraints include

• Concentration-based thermodynamic constraint (Hoppe et al. 2007)
• Constraining individual fluxes (Holzhütter 2006)
• MFA (predict flux distribution by setting measured fluxes) (Lee et a. 1999)
• Knock-outs (e.g. Oh et al. 2007)

The following implemented methods comprise series of flux predictions:

• Flux-variability analysis (Burgard and Maranas 2001, see also Reed and Palsson 2004, Llaneras and Picó 2007)
• Flux control analysis (Burgard et al. 2004)
• MinModes (Hoffmann et al. 2006)
• Network pruning (Hoffmann et al. 2007)
• Leak analysis (similar to Gevorgyan et al. 2008)
• Scoring flux distributions with expression profiles
• Heterogenous simulations for the curation of large networks

The computed solutions may be prepared for visualisation in BiNA, Cytoscape, and CellNetAnalyzer.