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@article{2253358,
author = {Troják, Matej and Šafránek, David and Pastva, Samuel and Brim, Luboš},
article_number = {104843},
doi = {http://dx.doi.org/10.1016/j.biosystems.2023.104843},
keywords = {systems biology; rule-based modelling; regulations; multiset rewriting},
language = {eng},
issn = {0303-2647},
journal = {Biosystems},
title = {Rule-based Modelling of Biological Systems Using Regulated Rewriting},
url = {https://www.sciencedirect.com/science/article/pii/S0303264723000187},
volume = {225},
year = {2023}
}
TY - JOUR
ID - 2253358
AU - Troják, Matej - Šafránek, David - Pastva, Samuel - Brim, Luboš
PY - 2023
TI - Rule-based Modelling of Biological Systems Using Regulated Rewriting
JF - Biosystems
VL - 225
IS - 104843
SP - 1-15
EP - 1-15
PB - Elsevier
SN - 03032647
KW - systems biology
KW - rule-based modelling
KW - regulations
KW - multiset rewriting
UR - https://www.sciencedirect.com/science/article/pii/S0303264723000187
N2 - 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.
ER -
TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA and Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. \textit{Biosystems}. Elsevier, 2023, vol.~225, No~104843, p.~1-15. ISSN~0303-2647. Available from: https://dx.doi.org/10.1016/j.biosystems.2023.104843.
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