Rule-based modeling of biochemical networks: Research Articles

  • Authors:

  • James R. Faeder;Michael L. Blinov;Byron Goldstein;William S. Hlavacek

  • Affiliations:

  • Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545;Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545;Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545;Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545

  • Venue:
  • Complexity - Understanding Complex Systems: Part II
  • Year:
  • 2005

Quantified Score

Hi-index 0.01

Visualization

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. © 2005 Wiley Periodicals, Inc. Complexity 10: 22–41, 2005