Improving the Timed Automata Approach to Biological Pathway Dynamics

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
StatePublished - 19 Aug 2017
EventKimFest - Aalborg, Denmark

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Nature
Volume10460

Workshop

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

Fingerprint

Computer science
Model checking
Biological systems
User interfaces
Genes

Keywords

  • Systems Biology
  • Timed Automata
  • ANIMO
  • Signalling pathway

Cite this

Langerak, R., Pol, J. V. D., 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. DOI: 10.1007/978-3-319-63121-9_5

Langerak, R.; Pol, Jaco van de; Post, Janine N.; Schivo, Stefano / Improving the Timed Automata Approach to Biological Pathway Dynamics.

Models, Algorithms, Logics and Tools: Essays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday. ed. / Luca Aceto; Giorgio Bacci; Giovanni Bacci; Anna Ingólfsdóttir; Axel Legay; Radu Mardare. Springer, 2017. p. 96-111 (Lecture Notes in Computer Science; Vol. 10460).

Research output: Scientific - peer-reviewConference contribution

@inbook{f4d0afa37e604acfa0135dd454f6ea76,
title = "Improving the Timed Automata Approach to Biological Pathway Dynamics",
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.",
keywords = "Systems Biology, Timed Automata, ANIMO, Signalling pathway",
author = "R. Langerak and Pol, {Jaco van de} and Post, {Janine N.} and Stefano Schivo",
year = "2017",
month = "8",
doi = "10.1007/978-3-319-63121-9_5",
isbn = "978-3-319-63120-2",
series = "Lecture Notes in Computer Science",
publisher = "Springer",
pages = "96--111",
editor = "Luca Aceto and Giorgio Bacci and Giovanni Bacci and Anna Ingólfsdóttir and Axel Legay and Radu Mardare",
booktitle = "Models, Algorithms, Logics and Tools",

}

Langerak, R, Pol, JVD, Post, JN & 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. Lecture Notes in Computer Science, vol. 10460, Springer, pp. 96-111, KimFest, Aalborg, Denmark, 19-20 August. DOI: 10.1007/978-3-319-63121-9_5

Improving the Timed Automata Approach to Biological Pathway Dynamics. / Langerak, R.; Pol, Jaco van de; Post, Janine N.; Schivo, Stefano.

Models, Algorithms, Logics and Tools: Essays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday. ed. / Luca Aceto; Giorgio Bacci; Giovanni Bacci; Anna Ingólfsdóttir; Axel Legay; Radu Mardare. Springer, 2017. p. 96-111 (Lecture Notes in Computer Science; Vol. 10460).

Research output: Scientific - peer-reviewConference contribution

TY - CHAP

T1 - Improving the Timed Automata Approach to Biological Pathway Dynamics

AU - Langerak,R.

AU - Pol,Jaco van de

AU - Post,Janine N.

AU - Schivo,Stefano

PY - 2017/8/19

Y1 - 2017/8/19

N2 - 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.

AB - 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.

KW - Systems Biology

KW - Timed Automata

KW - ANIMO

KW - Signalling pathway

U2 - 10.1007/978-3-319-63121-9_5

DO - 10.1007/978-3-319-63121-9_5

M3 - Conference contribution

SN - 978-3-319-63120-2

T3 - Lecture Notes in Computer Science

SP - 96

EP - 111

BT - Models, Algorithms, Logics and Tools

PB - Springer

ER -

Langerak R, Pol JVD, Post JN, Schivo S. Improving the Timed Automata Approach to Biological Pathway Dynamics. In Aceto L, Bacci G, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, editors, Models, Algorithms, Logics and Tools: Essays Dedicated to Kim Guldstrand Larsen on the Occasion of His 60th Birthday. Springer. 2017. p. 96-111. (Lecture Notes in Computer Science). Available from, DOI: 10.1007/978-3-319-63121-9_5