Difference between revisions of "Agent-based modeling workshop"

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(New page: Rule-based Modeling with BioNetGen Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes o...)
 
 
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Rule-based Modeling with BioNetGen
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Rule-based modeling with [http://bionetgen.org/ BioNetGen] 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 cellular regulatory 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.
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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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Latest revision as of 16:16, 26 February 2010

Rule-based modeling with BioNetGen 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 cellular regulatory 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.

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