Automated Visualization of Rule-based Models

Rule-based modeling frameworks provide a specification format in which kinetic interactions are modeled as \"reaction rules\". These rules are specified on phosphorylation motifs, domains, binding sites and other sub-molecular structures, and have proved useful for modeling signal transduction. Visual representations are necessary to understand individual rules as well as analyze interactions of hundreds of rules, which motivates the need for automated diagramming tools for rule-based models. Here, we present a theoretical framework that unifies the layers of information in a rule-based model and enables automated visualization of (i) the mechanism encoded in a rule, (ii) the regulatory inte