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


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
Number of pages7
ISBN (Print)978-1-4673-4358-9
Publication statusPublished - 1 Nov 2012
Externally publishedYes
Event12th IEEE International Conference on Bioinformatics & Bioengineering - Larnaca, Cyprus
Duration: 11 Nov 201213 Nov 2012


Conference12th IEEE International Conference on Bioinformatics & Bioengineering
Abbreviated titleBIBE
Internet address


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


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