Scalable Reaction Network Modeling with Automatic Validation of Consistency in Event-B

Abstract

Constructing a large biological model is a difficult, error-prone process. Small errors in writing a part of the model cascade to the system level and their sources are difficult to trace back. In this paper we extend a recent approach based on Event-B, a state-based formal method with refinement as its central ingredient, allowing us to validate for model consistency step-by-step in an automated way. We demonstrate this approach on a model of the heat shock response and its scalability on a model of the ErbB signaling pathway, a key evolutionary pathway with a significant role in development and in many types of cancer. All consistency properties of the model were proved automatically with computer support.