Types for BioAmbients

The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in which the ambient can stay. The type system ensures that, in a well-typed process, ambients cannot be nested in a way that violates the type hierarchy. Exploiting the information given by the group types, we also extend the operational semantics of BioAmbients with rules signalling errors that may derive from undesired ambients' moves (i.e. merging incompatible tissues). Thus, the signal of errors can help the modeller to detect and locate unwanted situations that may arise in a biological system, and give practical hints on how to avoid the undesired behaviour

A Minimal OO Calculus for Modelling Biological Systems

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.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Type Directed Semantics for the Calculus of Looping Sequences

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. Here we enrich this calculus with a type discipline which preserves some biological properties deriving from the requirement of certain elements, and the repellency of others. In particular, the type system guarantees the soundness of the application of reduction rules with respect to the elements which are required (all requirements must be satisfied) and to the elements which are excluded (two elements which repel each other cannot occur in the same compartment). As an example, we model the possible interactions (and compatibility) of different blood types with different antigens. The type system does not allow transfusion with incompatible blood types

Generic process shape types and the Poly* system

Shape types are a general concept of process types which allows verification of various properties of processes from various calculi. The key property is that shape types “look like processes”, that is, they resemble process structure and content. PolyV, originally designed by Makholm and Wells, is a type system scheme which can be instantiated to a shape type system for many calculi. Every PolyV instantiation has desirable properties including subject reduction, polymorphism, the existence of principal typings, and a type inference algorithm. In the first part of this thesis, we fix and describe inconsistencies found in the original PolyV system, we extend the system to support name restriction, and we provide a detailed proof of the correctness of the system. In the second part, we present a description of the type inference algorithm which we use to constructively prove the existence of principal typings. In the third part, we present various applications of shape types which demonstrate their advantages. Furthermore we prove that shape types can provide the same expressive power as and also strictly superior expressive power than predicates of three quite dissimilar analysis systems from the literature, namely, (1) an implicitly typed π-calculus, (2) an explicitly typed Mobile Ambients, (3) and a flow analysis system for BioAmbients.Engineering and Physical Sciences Research Council (EPSRC) EP/C013573/