Towards Scalable Modeling of Biology in Event-B

TL;DR

This paper presents a scalable, function-based modeling approach using Event-B to accurately represent complex biological systems, demonstrated by constructing the largest known Event-B model of the ErbB signaling pathway with 1320 reactions.

Contribution

Introduces a novel, concise Event-B modeling method for biology, enabling automated consistency checks and demonstrating it with the largest ErbB pathway model to date.

Findings

Successfully modeled 1320 reactions in the ErbB pathway

Demonstrated scalability and conciseness of the approach

Enabled automated model consistency verification

Abstract

Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to check for model consistency step-by-step in an automated way. Our approach based on functions leads to an elegant and concise modeling method. We demonstrate this approach by constructing what is, to our knowledge, the largest ever built Event-B model, describing the ErbB signaling pathway, a key evolutionary pathway with a significant role in development and in many types of cancer. The Event-B model for the ErbB pathway describes 1320 molecular reactions through 242 events.