Melding Boolean networks and reaction systems under synchronous, asynchronous and most permissive semantics
Year: 2024
Type: article
Abstract: This paper forges a strong connection between two well known computational frameworks for representing biological systems, in order to facilitate the seamless transfer of techniques between them. Boolean networks are a well established formalism employed from biologists. They have been studied under different (synchronous and asynchronous) update semantics, enabling the observation and characterisation of distinct facets of system behaviour. Recently, a new semantics for Boolean networks has been proposed, called most permissive semantics, that enables a more faithful representation of biological phenomena. Reaction systems offer a streamlined formalism inspired by biochemical reactions in living cells. Reaction systems support a full range of analysis techniques that can help for gaining deeper insights into the underlying biological phenomena. Our goal is to leverage the available toolkit for predicting and comprehending the behaviour of reaction systems within the realm of Boolean networks. In this paper, we first extend the behaviour of reaction systems to several asynchronous semantics, including the most permissive one, and then we demonstrate that Boolean networks and reaction systems exhibit isomorphic behaviours under the synchronous, general/fully asynchronous and most permissive semantics.
Source: Natural Computing
Institutions: University of Pisa, Université Paris-Saclay
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,090
Funder: Università di Pisa
OpenAlex ID: W4400725385