Wed Tech Talk: Rule-Based Modeling of Biochemical Systems

LANL researcher Bill Hlavacek hosts a WedTech talk on rule-based modeling of biomechanical systems. This approach involves representing molecules as structured objects (graphs) and molecular interactions as (graph-rewriting) 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. In this tutorial talk, I will 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 framework.