title: FlexFlux: combining metabolic flux and regulatory network analyses.
abstract: BACKGROUND
  Expression of cell phenotypes highly depends on metabolism that supplies matter and energy. To achieve proper utilisation of the different metabolic pathways, metabolism is tightly regulated by a complex regulatory network composed of diverse biological entities (genes, transcripts, proteins, signalling molecules…). The integrated analysis of both regulatory and metabolic networks appears very insightful but is not straightforward because of the distinct characteristics of both networks. The classical method used for metabolic flux analysis is Flux Balance Analysis (FBA), which is constraint-based and relies on the assumption of steady-state metabolite concentrations throughout the network. Regarding regulatory networks, a broad spectrum of methods are dedicated to their analysis although logical modelling remains the major method to take charge of large-scale networks.
  
  
  RESULTS
  We present FlexFlux, an application implementing a new way to combine the analysis of both metabolic and regulatory networks, based on simulations that do not require kinetic parameters and can be applied to genome-scale networks. FlexFlux is based on seeking regulatory network steady-states by performing synchronous updates of multi-state qualitative initial values. FlexFlux is then able to use the calculated steady-state values as constraints for metabolic flux analyses using FBA. As input, FlexFlux uses the standards Systems Biology Markup Language (SBML) and SBML Qualitative Models Package ("qual") extension (SBML-qual) file formats and provides a set of FBA based functions.
  
  
  CONCLUSIONS
  FlexFlux is an open-source java software with executables and full documentation available online at http://lipm-bioinfo.toulouse.inra.fr/flexflux/. It can be defined as a research tool that enables a better understanding of both regulatory and metabolic networks based on steady-state simulations. FlexFlux integrates well in the flux analysis ecosystem thanks to the support of standard file formats and can thus be used as a complementary tool to existing software featuring other types of analyses.
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR441, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. lucas.marmiesse@toulouse.inra.fr.|CNRS, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR2594, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. lucas.marmiesse@toulouse.inra.fr.
authors.forename: Lucas
authors.initials: L
authors.lastname: Marmiesse
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR441, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. remi.peyraud@toulouse.inra.fr.|CNRS, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR2594, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. remi.peyraud@toulouse.inra.fr.
authors.forename: Rémi
authors.initials: R
authors.lastname: Peyraud
authors.affiliation: INRA, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR441, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. ludovic.cottret@toulouse.inra.fr.|CNRS, Laboratoire des Interactions Plantes-Microrganismes (LIPM), UMR2594, 24 chemin de Borde Rouge - Auzeville, CS52627, Castanet-Tolosan Cedex, F31326, France. ludovic.cottret@toulouse.inra.fr.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Cottret
mesh_terms: D055785:Gene Knockdown Techniques; D053263:Gene Regulatory Networks; D023281:Genomics; D064688:Metabolic Flux Analysis; D010641:Phenotype; D012984:Software; D049490:Systems Biology / Q000379:methods*