On verifying Bio-PEPA models

Allan Clark; Stephen Gilmore; Maria Luisa Guerriero; Peter Kemper

doi:10.1145/1839764.1839769

On verifying Bio-PEPA models

Allan Clark, Stephen Gilmore, Maria Luisa Guerriero, Peter Kemper

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Verifying that a computational model implements the conceptual model of some dynamic biological phenomena is an important yet non-trivial task. In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA process algebra as a modelling language and describing the verification steps that are supported by the Bio-PEPA tool. In particular, we elaborate on both static analysis based on the structure of models and dynamic analysis of generated stochastic simulation traces performed using the Traviando trace analyser. We illustrate the approach with a model of a JAK/STAT signalling pathway.

Original language	English
Title of host publication	Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Place of Publication	New York, NY, USA
Publisher	ACM
Pages	23-32
Number of pages	10
ISBN (Print)	978-1-4503-0068-1
DOIs	https://doi.org/10.1145/1839764.1839769
Publication status	Published - 2010

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10.1145/1839764.1839769

Clark Gilmore ET AL 2010 On Verifying Bio PEPA ModelsSubmitted manuscript, 634 KB

http://dl.acm.org/citation.cfm?doid=1839764.1839769

SIGNAL: SIGNAL -Stochastic process algebra for biochemical signaling pathway analysis
Gilmore, S. (Principal Investigator) & Hillston, J. (Co-investigator)
EPSRC
1/09/07 → 31/01/11
Project: Research

Cite this

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title = "On verifying Bio-PEPA models",

abstract = "Verifying that a computational model implements the conceptual model of some dynamic biological phenomena is an important yet non-trivial task. In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA process algebra as a modelling language and describing the verification steps that are supported by the Bio-PEPA tool. In particular, we elaborate on both static analysis based on the structure of models and dynamic analysis of generated stochastic simulation traces performed using the Traviando trace analyser. We illustrate the approach with a model of a JAK/STAT signalling pathway.",

author = "Allan Clark and Stephen Gilmore and Guerriero, \{Maria Luisa\} and Peter Kemper",

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AU - Gilmore, Stephen

AU - Guerriero, Maria Luisa

AU - Kemper, Peter

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AB - Verifying that a computational model implements the conceptual model of some dynamic biological phenomena is an important yet non-trivial task. In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA process algebra as a modelling language and describing the verification steps that are supported by the Bio-PEPA tool. In particular, we elaborate on both static analysis based on the structure of models and dynamic analysis of generated stochastic simulation traces performed using the Traviando trace analyser. We illustrate the approach with a model of a JAK/STAT signalling pathway.

U2 - 10.1145/1839764.1839769

DO - 10.1145/1839764.1839769

M3 - Conference contribution

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SP - 23

EP - 32

BT - Proceedings of the 8th International Conference on Computational Methods in Systems Biology

PB - ACM

CY - New York, NY, USA

ER -

On verifying Bio-PEPA models

Abstract

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SIGNAL: SIGNAL -Stochastic process algebra for biochemical signaling pathway analysis

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