View source for Agent-based modeling workshop

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.