A logical and graphical framework for reaction systems

Abstract

Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by reactions. Entities can also be provided by an external context sequence to simulate in silico biological experiments. In this paper we define an extension of RSs considering nondeterministic and recursive context operators, and give an original labelled transition system (LTS) for extended RSs in the structural operational semantics (SOS) style. Thanks to extended contexts, a single LTS can now account for several biological experiments. The rich information recorded in transition labels is useful to guarantee the compositionality of SOS inference rules as well as to define an assertion language to tailor behavioural and logical equivalences on some specific properties or entities. The SOS rules have been also exploited to design a flexible prototype implementation in logic programming that allows to inspect the LTS and to extract useful information when performing experiments on a RS. Our implementation provides a rapid prototyping tool for (extensions of) RSs, with a user friendly online interface to our interpreter. A parser allows to introduce the logical formulas and the contexts using the usual comfortable concrete syntax. The user can visualise and inspect the LTS for a RS and make some analysis of its underlying computation patterns, can check if the main RS satisfies a given property and if it is equivalent to a second adversarial RS. Finally, the SOS approach is suited to drive additional enhancements of RSs.