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

Oana Andrei (1) , Maribel Fernández (2) , Hélène Kirchner (3) , Bruno Pinaud (4, 5)

1 University of Glasgow
2 King‘s College London
3 Inria Siège
4 LaBRI - Laboratoire Bordelais de Recherche en Informatique
5 UB - Université de Bordeaux

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.

Mots clés: Computational systems biology; Rule-based modelling; Graph transformations; Visual Analytics Software; Strategic rewriting; Biochemical networks

Domaines: Informatique [cs]; Modélisation et simulation

Oana Andrei, Maribel Fernández, Hélène Kirchner, Bruno Pinaud. Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy. Bill Hlavacek. Modeling Biomolecular Site Dynamics, 1945, Springer, pp 43-70, 2019, Methods in Molecular Biology, 978-1-4939-9100-6. ⟨10.1007/978-1-4939-9102-0_3⟩. ⟨hal-01429890⟩