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Rule-based modeling of biochemical networks: Research Articles

Published: 01 March 2005 Publication History

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

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  1. Rule-based modeling of biochemical networks: Research Articles

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    Published In

    cover image Complexity
    Complexity  Volume 10, Issue 4
    Understanding Complex Systems: Part II
    March 2005
    84 pages

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    John Wiley & Sons, Inc.

    United States

    Publication History

    Published: 01 March 2005

    Author Tags

    1. automatic model generation
    2. combinatorial complexity
    3. local rules
    4. networks
    5. signal transduction
    6. systems biology

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