Figure 1: A screenshot of the RuleVis interface, depicting a user in the process of building a rule, consisting of two patterns that describe the 'before' and 'after' states of the system (separated by an arrow). The editor panel (left) enables users to add and delete agents, sites, and links in the visualization in the display panel (right). The text and visualization are mirrored, and changes made to one representation are immediately reflected in the other.
ABSTRACTWe introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and other complex systems. Rule-based models involve emergent effects based on the interactions between rules, which can vary considerably with regard to the scale of a model, requiring the user to inspect and edit individual rules. RuleVis bridges the graph rewriting and systems biology research communities by providing an external visual representation of salient patterns that experts can use to determine the appropriate level of detail for a particular modeling context. We describe the visualization and interaction features available in RuleVis and provide a detailed example demonstrating how RuleVis can be used to reason about intracellular interactions.