Construction of ODEs from network topology. Schematic representation of the conversion of a GRN topology to an ODE model. In the diagram to the left, A, B, C and X denote genes. In the Boolean formula in the center, the variables represent the gene products, translation and transcription are combined to one step. In the differential equation to the right, X indicates concentration of mRNA of gene X, while A, B and C are protein concentrations, small letters are kinetic parameters. The topology is used to derive a Boolean formulation of the regulatory inputs to a gene. This Boolean formulation is automatically translated to an ODE model. For details, see section Methods.