Figure 1

Construction of large-scale kinetic models using commonly available information and data. The method starts with the automatic translation of a metabolic network reconstruction into a generic kinetic model, which is parameterized using the metabolic profile for a reference condition (ref). The kinetic model is parameterized to simulate other conditions using gene expression profiles and tuned using the metabolic profiles for the conditions of interest (cnd). The tuned model can be used to perform different model-based analyses. C denotes a diagonal matrix with elements equal to the absolute metabolite concentrations, c represents the vector of normalized metabolite concentrations and ċ denotes its time derivative, S denotes the stoichiometric matrix of the metabolic network reconstruction, r represents the vector of reaction rates, v denotes the flux distribution, g represents the vector of gene expression ratios, and p represents a vector of other condition-specific model parameters.