Rule-based Modelling of Biological Systems Using Regulated Rewriting

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Authors

TROJÁK Matej ŠAFRÁNEK David PASTVA Samuel BRIM Luboš

Year of publication 2023
Type Article in Periodical
Magazine / Source Biosystems
MU Faculty or unit

Faculty of Informatics

Citation
Web https://www.sciencedirect.com/science/article/pii/S0303264723000187
Doi http://dx.doi.org/10.1016/j.biosystems.2023.104843
Keywords systems biology; rule-based modelling; regulations; multiset rewriting
Description 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.
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