Table 1

Overview of model features
Model 1 Model 2
Levels Metabolic Metabolic, transcriptional
Parameters 918 178
States 115 47
Observables 115 47
Measures 1150 7614
Static / Dynamic Static Dynamic

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 file 2.

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 [18]. For simulation purposes it is assumed that all of the states are measured. More information about the model is included in the Additional file 3.

Villaverde et al.

Villaverde et al. BMC Systems Biology 2012 6:75   doi:10.1186/1752-0509-6-75

Open Data