Mechanistic analysis of reaction network models

— Chemical reaction networks have been used for a long time to model biochemical systems. Rule-based modeling is a newer graph-based approach that allows explicit consideration of molecular structures and reaction configurations. We have previously developed a tool called Atomizer that infers molecular structures and interactions from reaction network models to gen-erate rule-based representations. Here, we have atomized reaction network models in the BioModels database and performed a statistical analysis of their composition in terms of the five basic graph operations that can occur in reactions.