Rule-based Modeling with BioNetGen

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Rule-based Modeling with BioNetGen
James R. Faeder

Abstract: 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 allows systematic incorporation of site-specific details about protein-protein interactions into a model for the dynamics of a signal-transduction system, as well as other applications. 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 analysis of comprehensive models for signal transduction pathways and similarly large-scale models for other biochemical systems.

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