Modeling and Analyzing Reaction Systems in Maude

Author:

Ballis Demis1ORCID,Brodo Linda2ORCID,Falaschi Moreno3ORCID

Affiliation:

1. Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Università degli Studi di Udine, 33100 Udine, Italy

2. Dipartimento di Scienze Economiche e Aziendali, Università di Sassari, 07100 Sassari, Italy

3. Dipartimento di Ingegneria dell’Informazione e Scienze Matematiche, Università di Siena, 53100 Siena, Italy

Abstract

Reaction Systems (RSs) are a successful computational framework for modeling systems inspired by biochemistry. An RS defines a set of rules (reactions) over a finite set of entities (e.g., molecules, proteins, genes, etc.). A computation in this system is performed by rewriting a finite set of entities (a computation state) using all the enabled reactions in the RS, thereby producing a new set of entities (a new computation state). The number of entities in the reactions and in the computation states can be large, making the analysis of RS behavior difficult without a proper automated support. In this paper, we use the Maude language—a programming language based on rewriting logic—to define a formal executable semantics for RSs, which can be used to precisely simulate the system behavior as well as to perform reachability analysis over the system computation space. Then, by enriching the proposed semantics, we formalize a forward slicer algorithm for RSs that allows us to observe the evolution of the system on both the initial input and a fragment of it (the slicing criterion), thus facilitating the detection of forward causality and influence relations due to the absence/presence of some entities in the slicing criterion. The pursued approach is illustrated by a biological reaction system that models a gene regulation network for controlling the process of differentiation of T helper lymphocytes.

Funder

Ministero dell'Università e della Ricerca

EU - The Next Generation EU Programme

University of Udine

Publisher

MDPI AG

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