A Formal Framework for Composing Qualitative Models of Biological Systems

Alkhudhayr, H; Steggles, J

doi:10.1007/978-3-319-71069-3_2

A Formal Framework for Composing Qualitative Models of Biological Systems

Lookup NU author(s): Hanadi Alkhudhayr, Dr Jason Steggles

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Abstract

Boolean networks are a widely used qualitative modelling approach which allows the abstract description of a biological system. One issue with the application of Boolean networks is the state space explosion problem which limits the applicability of the approach to large realistic systems. In this paper we investigate developing a compositional framework for Boolean networks to facilitate the construction and analysis of large scale models. The compositional approach we present is based on merging entities between Boolean networks using conjunction and we introduce the notion of compatibility which formalises the preservation of behaviour under composition. We investigate characterising compatibility and develop a notion of trace alignment which is sufficient to ensure compatibility. The compositional framework developed is supported by a prototype tool that automates composition and analysis.