Agent-based modeling workshop
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.