Design issues for qualitative modelling of biological cells with Petri nets

Abstract

Petri nets are a widely used formalism to qualitatively model concurrent systems such as a biological cell. We present techniques for modelling biological processes as Petri nets for further analyses and in-silico experiments. Instead of extending the formalism with ,colours" or rates, as is most often done, we focus on preserving the simplicity of the formalism and developing an execution semantics which resembles biology - we apply a principle of maximal parallelism and introduce the novel concept of bounded execution with overshooting. A number of modelling solutions are demonstrated using the example of the well-studied C. elegans vulval development process. To date our model is still under development, but first results, based on Monte Carlo simulations, are promising. © 2008 Springer-Verlag Berlin Heidelberg.