Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy

Abstract

This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.