Modelling biological pathway dynamics with Timed Automata

Stefano Schivo, Jetse Scholma, B. Wanders, R.A. Urquidi Camacho, P.E. van der Vet, Hermanus Bernardus Johannes Karperien, Romanus Langerak, Jan Cornelis van de Pol, Janine Nicole Post

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

Abstract

When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The foundations of the tool are based on Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.
Original languageEnglish
Title of host publication2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012)
Place of PublicationUnited States
PublisherIEEE Computer Society
Pages447-453
Number of pages7
ISBN (Print)978-1-4673-4358-9
DOIs
Publication statusPublished - 1 Nov 2012
Externally publishedYes
Event12th IEEE International Conference on Bioinformatics & Bioengineering - Larnaca, Cyprus
Duration: 11 Nov 201213 Nov 2012
https://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6387371

Conference

Conference12th IEEE International Conference on Bioinformatics & Bioengineering
Abbreviated titleBIBE
CountryCyprus
CityLarnaca
Period11/11/1213/11/12
Internet address

Fingerprint

Crosstalk
Reaction kinetics
User interfaces
Semantics
Engines
Molecules
Experiments
Intercellular Signaling Peptides and Proteins

Keywords

  • EWI-22597, Timed Automata, Dynamic behaviour, METIS-297592, Signalling pathway, IR-83516, Modelling

Cite this

Schivo, S., Scholma, J., Wanders, B., Urquidi Camacho, R. A., van der Vet, P. E., Karperien, H. B. J., ... Post, J. N. (2012). Modelling biological pathway dynamics with Timed Automata. In 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012) (pp. 447-453). United States: IEEE Computer Society. https://doi.org/10.1109/BIBE.2012.6399719
Schivo, Stefano ; Scholma, Jetse ; Wanders, B. ; Urquidi Camacho, R.A. ; van der Vet, P.E. ; Karperien, Hermanus Bernardus Johannes ; Langerak, Romanus ; van de Pol, Jan Cornelis ; Post, Janine Nicole. / Modelling biological pathway dynamics with Timed Automata. 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012). United States : IEEE Computer Society, 2012. pp. 447-453
@inproceedings{fc2cea5c35d1498c88a8e9503bac0f3a,
title = "Modelling biological pathway dynamics with Timed Automata",
abstract = "When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The foundations of the tool are based on Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.",
keywords = "EWI-22597, Timed Automata, Dynamic behaviour, METIS-297592, Signalling pathway, IR-83516, Modelling",
author = "Stefano Schivo and Jetse Scholma and B. Wanders and {Urquidi Camacho}, R.A. and {van der Vet}, P.E. and Karperien, {Hermanus Bernardus Johannes} and Romanus Langerak and {van de Pol}, {Jan Cornelis} and Post, {Janine Nicole}",
year = "2012",
month = "11",
day = "1",
doi = "10.1109/BIBE.2012.6399719",
language = "English",
isbn = "978-1-4673-4358-9",
pages = "447--453",
booktitle = "2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012)",
publisher = "IEEE Computer Society",
address = "United States",

}

Schivo, S, Scholma, J, Wanders, B, Urquidi Camacho, RA, van der Vet, PE, Karperien, HBJ, Langerak, R, van de Pol, JC & Post, JN 2012, Modelling biological pathway dynamics with Timed Automata. in 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012). IEEE Computer Society, United States, pp. 447-453, 12th IEEE International Conference on Bioinformatics & Bioengineering , Larnaca, Cyprus, 11/11/12. https://doi.org/10.1109/BIBE.2012.6399719

Modelling biological pathway dynamics with Timed Automata. / Schivo, Stefano; Scholma, Jetse; Wanders, B.; Urquidi Camacho, R.A.; van der Vet, P.E.; Karperien, Hermanus Bernardus Johannes; Langerak, Romanus; van de Pol, Jan Cornelis; Post, Janine Nicole.

2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012). United States : IEEE Computer Society, 2012. p. 447-453.

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingAcademicpeer-review

TY - GEN

T1 - Modelling biological pathway dynamics with Timed Automata

AU - Schivo, Stefano

AU - Scholma, Jetse

AU - Wanders, B.

AU - Urquidi Camacho, R.A.

AU - van der Vet, P.E.

AU - Karperien, Hermanus Bernardus Johannes

AU - Langerak, Romanus

AU - van de Pol, Jan Cornelis

AU - Post, Janine Nicole

PY - 2012/11/1

Y1 - 2012/11/1

N2 - When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The foundations of the tool are based on Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.

AB - When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The foundations of the tool are based on Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.

KW - EWI-22597, Timed Automata, Dynamic behaviour, METIS-297592, Signalling pathway, IR-83516, Modelling

U2 - 10.1109/BIBE.2012.6399719

DO - 10.1109/BIBE.2012.6399719

M3 - Conference article in proceeding

SN - 978-1-4673-4358-9

SP - 447

EP - 453

BT - 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012)

PB - IEEE Computer Society

CY - United States

ER -

Schivo S, Scholma J, Wanders B, Urquidi Camacho RA, van der Vet PE, Karperien HBJ et al. Modelling biological pathway dynamics with Timed Automata. In 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012). United States: IEEE Computer Society. 2012. p. 447-453 https://doi.org/10.1109/BIBE.2012.6399719