SOS Rules for Equivalences of Reaction Systems

08/29/2020
by   Linda Brodo, et al.
0

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. RS semantics is defined in terms of an (unlabelled) rewrite system: given the current set of entities, a rewrite step consists of the application of all and only the enabled reactions. In this paper we define, for the first time, a labelled transition system for RSs in the structural operational semantics (SOS) style. This is achieved by distilling a signature whose operators directly correspond to the ingredients of RSs and by defining some simple SOS inference rules for any such operator to define the behaviour of the RS in a compositional way. The rich information recorded in the labels allows us to define an assertion language to tailor behavioural equivalences on some specific properties or entities. The SOS approach is suited to drive additional enhancements of RSs along features such as quantitative measurements of entities and communication between RSs. The SOS rules have been also exploited to design a prototype implementation in logic programming.

READ FULL TEXT
POST COMMENT

Comments

There are no comments yet.

Authors

page 1

page 2

page 3

page 4

12/03/2020

Graph Surfing in Reaction Systems from a Categorial Perspective

Graph-based reaction systems were recently introduced as a generalizatio...
06/20/2009

Hybrid Rules with Well-Founded Semantics

A general framework is proposed for integration of rules and external fi...
07/29/2021

Proof-Theoretic Semantics, a Problem with Negation and Prospects for Modality

This paper discusses proof-theoretic semantics, the project of specifyin...
03/02/2021

Neural Production Systems

Visual environments are structured, consisting of distinct objects or en...
04/02/2021

Fairness and Observed Communication Semantics for Session-Typed Languages

Observed communication semantics provide an intuitive notion of equivale...
04/30/2018

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Declarative modeling uses symbolic expressions to represent models. With...
01/12/2022

Biochemical Space Language in Relation to Multiset Rewriting Systems

This technical report relates Biochemical Space Language (BCSL) to Multi...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.