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 a...

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Vydané v:BMC bioinformatics Ročník 12; číslo 1; s. 28
Hlavní autori: Hoppe, Andreas, Hoffmann, Sabrina, Gerasch, Andreas, Gille, Christoph, Holzhütter, Hermann-Georg
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 22.01.2011
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Batch processing
Bioinformatics
Biomedical and Life Sciences
Cell metabolism
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer applications
Computer programs
Computer science
Computer Simulation
Data processing
Enzymes
Expectation-maximization algorithm
Fitness
Fluctuations
Freeware
Life Sciences
Metabolic engineering
metabolic networks
Metabolic Networks and Pathways
Metabolites
Microarrays
Models, Biological
Networks analysis
Objectives
Operating systems
Programming languages
Science
Simulation
Software
Structural analysis
Studies
Thermodynamics
User interface
Description File
Commercial Solver
Flux Distribution
Flux Variability Analysis
Open Source Program
ISSN:1471-2105, 1471-2105
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Shrnutí: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-12-28