ArticleBMC bioinformatics2011
FASIMU: flexible software for flux-balance computation series in large metabolic networks.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.Metabolites · 2021Article
- EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models.Metabolites · 2020Article
- Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer.BMC genomics · 2019Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells.PLoS computational biology · 2018Article
- Article
- PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.BMC systems biology · 2016Article
- From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model.Frontiers in microbiology · 2016Article
- FlexFlux: combining metabolic flux and regulatory network analyses.BMC systems biology · 2015Article
- An integrated network visualization framework towards metabolic engineering applications.BMC bioinformatics · 2014Article
- Computational strategies for a system-level understanding of metabolism.Metabolites · 2014Review
- Improving collaboration by standardization efforts in systems biology.Frontiers in bioengineering and biotechnology · 2014Review
- Sybil--efficient constraint-based modelling in R.BMC systems biology · 2013Article
- COBRApy: COnstraints-Based Reconstruction and Analysis for Python.BMC systems biology · 2013Article
- A community-driven global reconstruction of human metabolism.Nature biotechnology · 2013Article
- Precise generation of systems biology models from KEGG pathways.BMC systems biology · 2013Article
- Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.PLoS computational biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFlux-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.
resultsWe 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.
conclusionsWe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.