Rule-Based Modeling of Biochemical Systems with BioNetGen

  • James R. Faeder
  • Michael L. Blinov
  • William S. Hlavacek
Part of the Methods in Molecular Biology book series (MIMB, volume 500)

Summary

Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects. The approach is notable in that it allows one to systematically incorporate site-specific details about protein—protein interactions into a model for the dynamics of a signal-transduction system, but the method has other applications as well, such as following the fates of individual carbon atoms in metabolic reactions. The consequences of protein—protein interactions are difficult to specify and track with a conventional modeling approach because of the large number of protein phosphoforms and protein complexes that these interactions potentially generate. Here, we focus on how a rule-based model is specified in the BioNetGen language (BNGL) and how a model specification is analyzed using the BioNetGen software tool. We also discuss new developments in rule-based modeling that should enable the construction and analyses of comprehensive models for signal transduction pathways and similarly large-scale models for other biochemical systems.

Keywords

Computational systems biology Mathematical modeling Combinatorial complexity Software Formal languages Stochastic simulation Ordinary differential equations protein—protein interactions Signal transduction Metabolic networks 

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Copyright information

© Humana Press 2009

Authors and Affiliations

  • James R. Faeder
    • 1
  • Michael L. Blinov
  • William S. Hlavacek
  1. 1.Department of Computational BiologyUniversity of Pittsburgh School of MedicinePittsburgh

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