Graph Rewriting and Strategies for Modeling Biochemical Networks

In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of molecular complexes as a particular type of multi- graphs with ports called molecular graphs. The advantage of this approach is to obtain for free a rewriting calculus which allows defining at the same level transformation rules and strategies for modeling rule selection and application, in order to prototype network generation.