Modelling biological pathway dynamics with Timed Automata

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

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 tool is based on the formalism of 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 signalling 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
Pages447-453
DOIs
StatePublished - 11 Nov 2012

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Crosstalk
Reaction kinetics
User interfaces
Semantics
Engines
Molecules
Experiments

Keywords

  • METIS-292711

Cite this

Schivo, S., Scholma, J., Urquidi Camacho, R. A., Wanders, B., van der Vet, P. E., Karperien, H. B. J., ... Post, J. N. (2012). Modelling biological pathway dynamics with Timed Automata. 447-453. DOI: 10.1109/BIBE.2012.6399719

Schivo, Stefano; Scholma, Jetse; Urquidi Camacho, R.A.; Wanders, B.; 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. 447-453.

Research output: Other research outputAbstract

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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 tool is based on the formalism of 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 signalling 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 = "METIS-292711",
author = "Stefano Schivo and Jetse Scholma and {Urquidi Camacho}, R.A. and B. Wanders 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",
doi = "10.1109/BIBE.2012.6399719",
pages = "447--453",

}

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

2012. 447-453.

Research output: Other research outputAbstract

TY - CONF

T1 - Modelling biological pathway dynamics with Timed Automata

AU - Schivo,Stefano

AU - Scholma,Jetse

AU - Urquidi Camacho,R.A.

AU - Wanders,B.

AU - van der Vet,P.E.

AU - Karperien,Hermanus Bernardus Johannes

AU - Langerak,Romanus

AU - van de Pol,Jan Cornelis

AU - Post,Janine Nicole

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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 tool is based on the formalism of 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 signalling 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 tool is based on the formalism of 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 signalling 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.

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Schivo S, Scholma J, Urquidi Camacho RA, Wanders B, van der Vet PE, Karperien HBJ et al. Modelling biological pathway dynamics with Timed Automata. 2012. Available from, DOI: 10.1109/BIBE.2012.6399719