Graph Rewriting and Strategies for Modeling Biochemical Networks

Authors:
Oana Andrei;Helene Kirchner
Affiliations:
-;-
Venue:
SYNASC '07 Proceedings of the Ninth International Symposium on Symbolic and Numeric Algorithms for Scientific Computing
Year:
2007

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Abstract

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.