Improving the Timed Automata Approach to Biological Pathway Dynamics

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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
Number of pages16
ISBN (Electronic)978-3-319-63121-9
ISBN (Print)978-3-319-63120-2
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

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Nature


Abbreviated titleKimFest
Internet address


  • Systems Biology
  • Timed Automata
  • Signalling pathway


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