Improving the Timed Automata Approach to Biological Pathway Dynamics

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Abstract

Biological systems such as regulatory or gene networks can be seen as a particular type of distributed systems, and for this reason they can be modeled within the Timed Automata paradigm, which was developed in the computer science context. However, tools designed to model distributed systems often require a computer science background, making their use less attractive for biologists. ANIMO (Analysis of Networks with Interactive MOdeling) was built with the aim to provide biologists with access to the powerful modeling formalism of Timed Automata in a user friendly way. Continuous dynamics is handled by discrete approximations.
In this paper we introduce an improved modeling approach that allows us to considerably increase ANIMO’s performances, opening the way for the analysis of bigger models. Moreover, this improvement makes the introduction of model checking in ANIMO a realistic feature, allowing for reduced computation times. The user interface of ANIMO allows to rapidly build non-trivial models and check them against properties formulated in a human-readable language, making modeling a powerful support for biological research.
Original languageEnglish
Title of host publicationModels, Algorithms, Logics and Tools
Subtitle of host publicationEssays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday
EditorsLuca Aceto, Giorgio Bacci, Giovanni Bacci, Anna Ingólfsdóttir, Axel Legay, Radu Mardare
PublisherSpringer
Pages96-111
Number of pages16
ISBN (Electronic)978-3-319-63121-9
ISBN (Print)978-3-319-63120-2
DOIs
Publication statusPublished - 19 Aug 2017
EventKimFest: Conference in honour of Kim G. Larsen on the occasion of his 60th birthday - Aalborg University, Aalborg, Denmark
Duration: 19 Aug 201720 Aug 2017
http://kimfest.cs.aau.dk

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Nature
Volume10460

Workshop

WorkshopKimFest
Abbreviated titleKimFest
CountryDenmark
CityAalborg
Period19/08/1720/08/17
Internet address

Keywords

  • Systems Biology
  • Timed Automata
  • ANIMO
  • Signalling pathway

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  • Cite this

    Langerak, R., van de Pol, J., Post, J. N., & Schivo, S. (2017). Improving the Timed Automata Approach to Biological Pathway Dynamics. In L. Aceto, G. Bacci, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools: Essays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday (pp. 96-111). (Lecture Notes in Computer Science; Vol. 10460). Springer. https://doi.org/10.1007/978-3-319-63121-9_5