A Minimal OO Calculus for Modelling Biological Systems

TL;DR

This paper introduces a minimal object-oriented calculus tailored for modeling biological systems, enabling formal representation of biological types and inheritance within term rewriting frameworks.

Contribution

It presents a novel minimal OO calculus that captures biological ontologies and can be integrated into existing term rewriting formalisms for biological modeling.

Findings

Supports encapsulation, method invocation, subtyping, and inheritance.

Applicable to various term-rewriting formalisms.

Facilitates reuse of class models across different biological models.

Abstract

In this paper we present a minimal object oriented core calculus for modelling the biological notion of type that arises from biological ontologies in formalisms based on term rewriting. This calculus implements encapsulation, method invocation, subtyping and a simple formof overriding inheritance, and it is applicable to models designed in the most popular term-rewriting formalisms. The classes implemented in a formalism can be used in several models, like programming libraries.