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.
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 language | English |
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Title of host publication | Models, Algorithms, Logics and Tools |
Subtitle of host publication | Essays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday |
Editors | Luca Aceto, Giorgio Bacci, Giovanni Bacci, Anna Ingólfsdóttir, Axel Legay, Radu Mardare |
Publisher | Springer |
Pages | 96-111 |
Number of pages | 16 |
ISBN (Electronic) | 978-3-319-63121-9 |
ISBN (Print) | 978-3-319-63120-2 |
DOIs | |
Publication status | Published - 19 Aug 2017 |
Event | KimFest: Conference in honour of Kim G. Larsen on the occasion of his 60th birthday - Aalborg University, Aalborg, Denmark Duration: 19 Aug 2017 → 20 Aug 2017 http://kimfest.cs.aau.dk |
Publication series
Name | Lecture Notes in Computer Science |
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Publisher | Springer Nature |
Volume | 10460 |
Workshop
Workshop | KimFest |
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Abbreviated title | KimFest |
Country/Territory | Denmark |
City | Aalborg |
Period | 19/08/17 → 20/08/17 |
Internet address |
Keywords
- Systems Biology
- Timed Automata
- ANIMO
- Signalling pathway