Rule-based Modelling of Biological Systems Using Regulated
Rewriting

J 2023

Rule-based Modelling of Biological Systems Using Regulated Rewriting

TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA a Luboš BRIM

Základní údaje

Originální název

Rule-based Modelling of Biological Systems Using Regulated Rewriting

Autoři

TROJÁK, Matej (703 Slovensko, domácí), David ŠAFRÁNEK (203 Česká republika, domácí), Samuel PASTVA (703 Slovensko, domácí) a Luboš BRIM (203 Česká republika, domácí)

Vydání

Biosystems, Elsevier, 2023, 0303-2647

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.600 v roce 2022

Kód RIV

RIV/00216224:14330/23:00134056

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1016/j.biosystems.2023.104843

UT WoS

000933884300001

Klíčová slova anglicky

systems biology; rule-based modelling; regulations; multiset rewriting

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 4. 2024 10:08, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Návaznosti

GA22-10845S, projekt VaV

Název: Studium role polyhydroxyalkanoátů u bakterie Schlegelella thermodepolymerans – slibného bakteriálního kandidáta pro biotechnologie nové generace (Akronym: PHAST)

Investor: Grantová agentura ČR, Studium role polyhydroxyalkanoátů u bakterie Schlegelella thermodepolymerans – slibného bakteriálního kandidáta pro biotechnologie nové generace

MUNI/G/1771/2020, interní kód MU

Název: Computational reconstruction of mechanistic framework underlying receptor tyrosine kinase function in signal transduction (Akronym: FGFSIGMOD)

Investor: Masarykova univerzita, Computational reconstruction of mechanistic framework underlying receptor tyrosine kinase function in signal transduction, INTERDISCIPLINARY - Mezioborové výzkumné projekty

Citovat

TROJÁK, Matej, David ŠAFRÁNEK, Samuel PASTVA a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. Biosystems. Elsevier, 2023, roč. 225, č. 104843, s. 1-15. ISSN 0303-2647. Dostupné z: https://dx.doi.org/10.1016/j.biosystems.2023.104843.

@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 a Luboš BRIM. Rule-based Modelling of Biological Systems Using Regulated Rewriting. \textit{Biosystems}. Elsevier, 2023, roč.~225, č.~104843, s.~1-15. ISSN~0303-2647. Dostupné z: https://dx.doi.org/10.1016/j.biosystems.2023.104843.

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