Fig. 1

General architecture of FlexFlux. FlexFlux takes as an input two SBML files and a constraint file : one SBML file for the description of the metabolic network, and the Qualitative extension for the regulatory network. The constraint file specifies the objective function and can contain constraints. From the metabolic network definition, FlexFlux creates mass balance constraints that will be used for the flux balance analysis (FBA). The regulatory network is analysed by a regulatory steady-state analysis (RSA). The starting point of the RSA comes from both SBML-qual and constraint files. Then the qualitative states are translated into constraints for the FBA. FBA and RSA can also be run independently