Rule-based Modelling of Biological Systems Using Regulated Rewriting

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TROJÁK Matej ŠAFRÁNEK David PASTVA Samuel BRIM Luboš

Rok publikování 2023
Druh Článek v odborném periodiku
Časopis / Zdroj Biosystems
Fakulta / Pracoviště MU

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Citace
www https://www.sciencedirect.com/science/article/pii/S0303264723000187
Doi http://dx.doi.org/10.1016/j.biosystems.2023.104843
Klíčová slova systems biology; rule-based modelling; regulations; multiset rewriting
Popis 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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