Section: New Results
Petri Net Representation of Biological Networks
In  , we present a way to compute the minimal semi-positive invariants of a Petri net representing a biological reaction system, as a Constraint Satisfaction Problem. The use of Petri-nets to manipulate reaction models,and make available a variety of tools is quite old, and recently analyses based on invariant computation for biological models have become more and more frequent, especially in the context of module decomposition. In our case, this analysis brings both qualitative and quantitative information on the models, in the form of conservation laws and consistency checking, thanks to finite domain constraint programming. It is noticeable that some of the most recent optimizations of standard invariant computation techniques in Petri-nets correspond to well-known techniques in CSPs, like symmetry-breaking. A simple prototype based on GNU-Prolog's FD solver, and including symmetry detection and breaking, was incorporated into the BIOCHAM modelling environment.
In  , we show how the Petri Net approach to modelling can be extended to gene regulatory networks.