Rule-based modelling of biological systems using regulated rewriting

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.

Automated summary

In systems biology, models are essential in understanding systems being studied. Among various modelling approaches, rewriting systems offer a framework for mechanistic level system description. Describing biochemical processes often involves incorporating abstract knowledge to simplify the system or compensate for missing details. To address this, we propose regulation mechanisms as an extension of this formalism, introducing additional controls on the rewriting process. We demonstrate the application of these mechanisms in a rule-based language suitable for modeling biological phenomena and present case studies from the biochemical domain.