Improving the Timed Automata Approach to Biological Pathway Dynamics

R. Langerak; Jaco van de Pol; Janine N. Post; Stefano Schivo

doi:10.1007/978-3-319-63121-9_5

Improving the Timed Automata Approach to Biological Pathway Dynamics

R. Langerak, Jaco van de Pol, Janine N. Post, Stefano Schivo

Developmental BioEngineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

1 Citation (Scopus)

284 Downloads (Pure)

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 language	English
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	https://doi.org/10.1007/978-3-319-63121-9_5
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
Publisher	Springer Nature
Volume	10460

Workshop

Workshop	KimFest
Abbreviated title	KimFest
Country/Territory	Denmark
City	Aalborg
Period	19/08/17 → 20/08/17
Internet address	http://kimfest.cs.aau.dk

Keywords

Systems Biology
Timed Automata
ANIMO
Signalling pathway

Access to Document

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

KimFest_finalversionAccepted author version, 593 KB

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

Langerak, R. ; van de Pol, Jaco ; Post, Janine N. et al. / 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. editor / Luca Aceto ; Giorgio Bacci ; Giovanni Bacci ; Anna Ingólfsdóttir ; Axel Legay ; Radu Mardare. Springer, 2017. pp. 96-111 (Lecture Notes in Computer Science).

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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{\textquoteright}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 {van de Pol}, Jaco and Post, {Janine N.} and Stefano Schivo",

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Langerak, R , van de Pol, J , 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, 19/08/17. https://doi.org/10.1007/978-3-319-63121-9_5

Improving the Timed Automata Approach to Biological Pathway Dynamics. / Langerak, R.; van de Pol, Jaco ; Post, Janine N. et al.
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: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

TY - GEN

T1 - Improving the Timed Automata Approach to Biological Pathway Dynamics

AU - Langerak, R.

AU - van de Pol, Jaco

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

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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

A2 - Aceto, Luca

A2 - Bacci, Giorgio

A2 - Bacci, Giovanni

A2 - Ingólfsdóttir, Anna

A2 - Legay, Axel

A2 - Mardare, Radu

PB - Springer

T2 - KimFest

Y2 - 19 August 2017 through 20 August 2017

ER -

Langerak R , van de Pol J , 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). doi: 10.1007/978-3-319-63121-9_5

Improving the Timed Automata Approach to Biological Pathway Dynamics

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