In order to perform a dynamic simulation with such a network it is necessary to construct an ordinary differential equation
system that describes the rates of change in each metabolite's concentration or amount. To this end, a rate law, i.e., a kinetic equation that determines the rate of reaction based on the concentrations of all reactants is required for each reaction. Software packages that include numerical integrators, such as COPASI or [http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator SBMLsimulator], are then able to simulate the system dynamics given an initial condition. Often these rate laws contain kinetic parameters with uncertain values. In many cases it is desired to estimate these parameter values with respect to given time-series data of metabolite concentrations. The system is then supposed to reproduce the given data. For this purpose the distance between the given data set and the result of the simulation, i.e., the numerically or in few cases analytically obtained solution of the differential equation system is computed. The values of the parameters are then estimated to minimize this distance. One step further, it may be desired to estimate the mathematical structure of the differential equation system because the real rate laws are not known for the reactions within the system under study. To this end, the program [http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer SBMLsqueezer] allows automatic creation of appropriate rate laws for all reactions with the network.