RuleVis: Constructing Patterns and Rules for Rule-Based Models
This tool addresses the problem of managing complex rule-based models for experts in graph rewriting and systems biology, but it is incremental as it builds on existing visualization and modeling techniques.
They tackled the challenge of inspecting and editing individual rules in rule-based models for biochemical systems by introducing RuleVis, a web-based application that provides visual representations and interaction features, demonstrated through an example of reasoning about intracellular interactions.
We 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 RuleVisand provide a detailed example demonstrating how RuleVis can be used to reason about intracellular interactions.