RuleVis: Constructing Patterns and Rules for Rule-Based Models

TL;DR

RuleVis is a web-based tool that helps biologists and systems researchers create, visualize, and edit executable rules for modeling complex biochemical and protein interaction networks, enhancing understanding and model accuracy.

Contribution

It introduces a novel visualization and editing platform that bridges graph rewriting and systems biology, enabling better rule-based modeling of complex biological systems.

Findings

Facilitates inspection and editing of individual rules

Provides visual patterns for understanding emergent effects

Supports reasoning about intracellular interactions

Abstract

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.