Model 1: states are initial concentrations of internal metabolites and initial values of metabolic fluxes. Data corresponds to 10 different simulated experiments. For each experiment, the enzyme levels and external metabolite levels are randomly chosen. Then the metabolic fluxes and internal metabolite levels can be obtained solving for the steady state. The optimization goal is to minimise the residuals for the fluxes and internal metabolite levels, which are assumed to be measurable. More information about the model is included in the Additional file2.
Model 2: states are the species concentrations; data corresponds to extended diauxic shift scenario consisting of 3 consecutive environments: first the carbon source is glucose, then acetate, and finally a mixture of both. The scenario is described in the simulation files included as supplementary material in. For simulation purposes it is assumed that all of the states are measured. More information about the model is included in the Additional file3.