Title: Rule-based Modeling of Biochemical Networks

Speaker: James R. Faeder, Los Alamos National Laboratory  

Date/Time: Monday, January 19, 2005, 9:00-10:00 am

Location: Building 980, Room 95 (Sandia NM)

Brief Abstract: We present a method for generating a biochemical reaction network from a description of the interactions of components of biomolecules. The interactions are specified in the form of reaction rules, each of which defines a class of reaction associated with a type of interaction. Reactants within a class have shared properties, which are specified in the rule defining the class. A rule also provides a rate law, which governs each reaction in a class, and a template for transforming reactants into products. A set of reaction rules can be applied to a seed set of chemical species and, subsequently, any new species that are found as products of reactions to generate a list of reactions and a list of the chemical species that participate in these reactions, i.e., a reaction network, which can be translated into a mathematical model.