Diffusable and non-diffusable gene products play a major role in body plan formation. A quantitative understanding of the spatio-temporal patterns formed in body plan formation, by using simulation models is an important addition to experimental observation. The inverse modelling approach consists of describing the body plan formation by a rule-based model, and fitting the model parameters to real observed data. In body plan formation, the data are usually obtained from fluorescent immunohistochemistry or in situ hybridizations. Inferring model parameters by comparing such data to those from simulation is a major computational bottleneck. An important aspect in this process is the choice of method used for parameter estimation. When no information on parameters is available, parameter estimation is mostly done by means of heuristic algorithms.