Automated visualization of rule-based models
Fig 3
(A) Atoms, which are elementary structural features, shown in BioNetGen syntax and graphic. (B) Atom-rule graphs derived from the individual rules in Fig 2B. (C) The full atom-rule graph of the model, merged from individual graphs in panel B. AR graphs have three edge types: reactant (dark color, pointed towards rule), product (dark color, pointed away from rule), and context (light color, pointed towards rule), which indicate whether an instance of an atom is present in the rule’s reaction center (reactant/product) or reaction context.