The implementation of the dynamic flux balance simulation of the E. coli mono-culture illustrates how the developed code can be used. We consider the metabolic network model of the E. coli K-12 bacterium, iJR904 [1], which is available online [2]. This study is based on the study presented in [3]. The model structure is based on the Dynamic Multispecies Metabolic Modeling (DMMM) framework but allows the modeler to extend the structure beyond the capabilities of the DMMM framework. The current implementation is based on the model format used by DSL48LPR. Specifically, the dFBA framework is realized in the three FORTRAN files:

  • The simulation (main.f), in which the FBA models, the external metabolites, simulation time, initial conditions and other simulation parameter such as numerical tolerances can be set.
  • The environment (res0.f), which contains the ordinary differential equations describing the volume of the bioreactor, the microbial community and the accumulation of the external metabolites. The format of the differential equations is based on the DMMM framework.
  • The uptake kinetics (uptakekinetics subroutine in lprhs.f), which determines the exchange fluxes as functions of the external metabolite concentrations.