Fully Automated Attractor Analysis of Cyanobacteria Models

D 2018

Fully Automated Attractor Analysis of Cyanobacteria Models

BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK et. al.

Basic information

Original name

Fully Automated Attractor Analysis of Cyanobacteria Models

Name in Czech

Plne Automatizovaná Analýza Atraktorů Modelů Cyanobaktérií

Authors

BENEŠ, Nikola (203 Czech Republic, belonging to the institution), Luboš BRIM (203 Czech Republic, belonging to the institution), Jan ČERVENÝ (203 Czech Republic), Samuel PASTVA (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, belonging to the institution), Jakub ŠALAGOVIČ (703 Slovakia) and Matej TROJÁK (703 Slovakia, belonging to the institution)

Edition

Neuveden, 22nd International Conference on System Theory, Control and Computing, p. 354-359, 6 pp. 2018

Publisher

IEEE

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14330/18:00101265

Organization unit

Faculty of Informatics

ISBN

978-1-5386-4444-7

DOI

http://dx.doi.org/10.1109/ICSTCC.2018.8540762

UT WoS

000465109800058

Keywords (in Czech)

atraktory; parametrizovaný graf; koncové silne souvislé komponenty; cyanobaktérie

Keywords in English

attractors; parametrised graph; terminal strongly connected components; cyanobacteria

Abstract

V originále

Complex dynamics arising in biological systems can be characterised by various kinds of attractors. To that end, the task of determining attractors becomes important in modern systems analysis. Biological systems are typically formalised as highly parametrised continuous-time ODE models. Such models can be abstracted in the form of parametrised graphs. In such abstractions, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we demon- strate a novel method for detecting tSCCs in parametrised graphs on several models of cyanobacteria taken from the domain- specific online platform e-cyanobacterium.org.

Links

GA18-00178S, research and development project

Name: Diskrétní bifurkační analýza reaktivních systémů

Investor: Czech Science Foundation

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/0854/2017, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace VII.

Investor: Masaryk University, Category A

Citovat

BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIČ and Matej TROJÁK. Fully Automated Attractor Analysis of Cyanobacteria Models. In Marian Barbu, Răzvan Şolea, Adrian Filipescu. 22nd International Conference on System Theory, Control and Computing. Neuveden: IEEE, 2018, p. 354-359. ISBN 978-1-5386-4444-7. Available from: https://dx.doi.org/10.1109/ICSTCC.2018.8540762.

@inproceedings{1450516,
   author = {Beneš, Nikola and Brim, Luboš and Červený, Jan and Pastva, Samuel and Šafránek, David and Šalagovič, Jakub and Troják, Matej},
   address = {Neuveden},
   booktitle = {22nd International Conference on System Theory, Control and Computing},
   doi = {http://dx.doi.org/10.1109/ICSTCC.2018.8540762},
   editor = {Marian Barbu, Răzvan Şolea, Adrian Filipescu},
   keywords = {attractors; parametrised graph; terminal strongly connected components; cyanobacteria},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Neuveden},
   isbn = {978-1-5386-4444-7},
   pages = {354-359},
   publisher = {IEEE},
   title = {Fully Automated Attractor Analysis of Cyanobacteria Models},
   url = {https://ieeexplore.ieee.org/document/8540762},
   year = {2018}
}

TY  - JOUR
ID  - 1450516
AU  - Beneš, Nikola - Brim, Luboš - Červený, Jan - Pastva, Samuel - Šafránek, David - Šalagovič, Jakub - Troják, Matej
PY  - 2018
TI  - Fully Automated Attractor Analysis of Cyanobacteria Models
PB  - IEEE
CY  - Neuveden
SN  - 9781538644447
KW  - attractors
KW  - parametrised graph
KW  - terminal strongly connected components
KW  - cyanobacteria
UR  - https://ieeexplore.ieee.org/document/8540762
N2  - Complex dynamics arising in biological systems can be characterised by various kinds of attractors. To that end, the task of determining attractors becomes important in modern systems analysis. Biological systems are typically formalised as highly parametrised continuous-time ODE models. Such models can be abstracted in the form of parametrised graphs. In such abstractions, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we demon- strate a novel method for detecting tSCCs in parametrised graphs on several models of cyanobacteria taken from the domain- specific online platform e-cyanobacterium.org.
ER  -

BENEŠ, Nikola, Luboš BRIM, Jan ČERVENÝ, Samuel PASTVA, David ŠAFRÁNEK, Jakub ŠALAGOVIČ and Matej TROJÁK. Fully Automated Attractor Analysis of Cyanobacteria Models. In Marian Barbu, R\u azvan \c Solea, Adrian Filipescu. \textit{22nd International Conference on System Theory, Control and Computing}. Neuveden: IEEE, 2018, p.~354-359. ISBN~978-1-5386-4444-7. Available from: https://dx.doi.org/10.1109/ICSTCC.2018.8540762.

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