We've updated our Privacy Policy to make it clearer how we use your personal data.

We use cookies to provide you with a better experience. You can read our Cookie Policy here.

Advertisement
FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks
News

FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks

FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks
News

FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks

Read time:
 

Want a FREE PDF version of This News Story?

Complete the form below and we will email you a PDF version of "FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks"

First Name*
Last Name*
Email Address*
Country*
Company Type*
Job Function*
Would you like to receive further email communication from Technology Networks?

Technology Networks Ltd. needs the contact information you provide to us to contact you about our products and services. You may unsubscribe from these communications at any time. For information on how to unsubscribe, as well as our privacy practices and commitment to protecting your privacy, check out our Privacy Policy

The paper, entitled 'FASIMU: Flexible Software for Flux-balance Computation Series in Large Metabolic Networks' can be read in full online in BioMed Centrals: Bioinformatics.

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.

Advertisement