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FlexFlux specifications

Information


Unique identifier OMICS_20296
Name FlexFlux
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some metabolic networks, components, initial values and update rules, objective function for the FBA and may contain additional constraints.
Input format SBML
Operating system Unix/Linux, Windows
Programming languages C, Java, Javascript, Shell (Bash), TeX
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Ludovic Cottret

Additional information


http://lipm-bioinfo.toulouse.inra.fr/flexflux/

Publication for FlexFlux

FlexFlux citations

 (4)
library_books

Methanol essential growth of Escherichia coli

2018
Nat Commun
PMCID: 5904121
PMID: 29666370
DOI: 10.1038/s41467-018-03937-y

[…] as co-substrates in addition to methanol: acetate, gluconate, glucose, glycerol, pyruvate, ribose, xylose, and succinate. reaction knockout (ko) analysis was performed using the open-source software flexflux and the uptake rate for all carbon sources was set to 7 mmol gcdw−1 h−1 as an approximation (corresponding to glucose uptake rates under shake flask condition). applying an iterative […]

library_books

Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen

2018
Nat Commun
PMCID: 5788922
PMID: 29379078
DOI: 10.1038/s41467-017-02660-4

[…] vrn reconstruction and was therefore well-suited to test the prediction capacity of the vrn module. the prediction of gene expression was performed through a discrete logical modeling method using flexflux under various environmental conditions, including in vitro and in planta conditions (see supplementary data ; supplementary note ). experimental gene expression values were discretized using […]

library_books

Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum

2016
PLoS Pathog
PMCID: 5135139
PMID: 27911943
DOI: 10.1371/journal.ppat.1006044

[…] of bacterial phenotypes were performed by flux balance analysis [] using the genome-scale metabolic network model of r. solanacearum gmi1000 []. simulations were conducted using the software flexflux []. predictions of the phenotypes feasibility were done by optimizing the metabolic fluxes corresponding to each phenotype using the degs as constraint. two sets of degs constraints […]

library_books

A Resource Allocation Trade Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum

2016
PLoS Pathog
PMCID: 5061431
PMID: 27732672
DOI: 10.1371/journal.ppat.1005939

[…] metabolic network module plus the macromolecule network module was performed using constraint based modeling []. flux distributions were simulated by flux balance analysis using the software flexflux []. various constraints were applied on simulation. environmental conditions were defined by constraining lower and/or upper bound of exchange fluxes depending of the availability […]


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FlexFlux institution(s)
INRA, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR2594, Castanet-Tolosan, France
FlexFlux funding source(s)
Supported by the Institut National de la Recherche Agronomique (grant 31000363) and the Région Midi-Pyrénées (grant 13050322) as well as by the French Laboratory of Excellence project “TULIP” (ANR-10-LABX-41; ANR-11-IDEX-0002-02); the EMBO (Long-Term Fellowship ALTF 1627-2011) and Marie Curie Actions (EMBOCOFUND2010, GA-2010-267146).

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