Rule-based modelling of biological systems using regulated rewriting. (March 2023)

• Record Type: Journal Article
• Authors: Troják, Matej; Šafránek, David; Pastva, Samuel; Brim, Luboš
• Is Part Of: Bio systems. Volume 225(2023)
• Publication Date: 2023-03
• Subjects: Systems biology -- Rule-based modelling -- Regulations -- Multiset rewriting; Biological systems -- Periodicals; Biology -- Periodicals; Biology -- Periodicals; Evolution -- Periodicals; Biologie -- Périodiques; Évolution -- Périodiques; 570
• DOI: 10.1016/j.biosystems.2023.104843
• Languages: English
• ISSNs: 0303-2647

Abstract

Abstract: In systems biology, models play a crucial role in understanding studied systems. There are many modelling approaches, among which rewriting systems provide a framework for describing systems on a mechanistic level. Describing biochemical processes often requires incorporating knowledge on an abstract level to simplify the system description or substitute the missing details. For this purpose, we present regulation mechanisms, an extension of this formalism with additional controls on the rewriting process. We introduce several regulation mechanisms and apply them to a rule-based language, a notation suitable for modelling biological phenomena. Finally, we demonstrate the usage of such regulations on several case studies from the biochemical domain.