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 multigraphs 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.

• Type: Conference
• Year: 2007
• Where: SYNASC
• Authors: Oana Andrei, Hélène Kirchner
• Keywords: Biochemical Reaction Rules, Level Transformation Rules, Molecular Complexes, SYNASC 2007