A semantic equivalence for Bio-PEPA based on discretisation of continuous values

Vashti Galpin; Jane Hillston

doi:10.1016/j.tcs.2011.01.007

A semantic equivalence for Bio-PEPA based on discretisation of continuous values

Research output: Contribution to journal › Article › peer-review

Abstract

Bio-PEPA is a process algebra for modelling biological systems. An important aspect of Bio-PEPA is the ability it provides to discretise concentrations resulting in a smaller, more manageable state space. The discretisation is based on a step size which determines the size of each discrete level and also the number of levels. This paper considers the relationship between two discretisations of the same Bio-PEPA model that differ only in the step size and hence the number of levels, by using the idea of equivalence from concurrency and process algebra. We present a novel behavioural semantic equivalence, compression bisimilarity, and investigate when this equates two discretisations of the same model and the circumstances in which this equivalence is a congruence with respect to the synchronisation operator. (C) 2011 Elsevier B.V. All rights reserved.

Original language	English
Pages (from-to)	2142-2161
Number of pages	20
Journal	Theoretical Computer Science
Volume	412
Issue number	21
DOIs	https://doi.org/10.1016/j.tcs.2011.01.007
Publication status	Published - 6 May 2011

Keywords / Materials (for Non-textual outputs)

Process algebra
Biological modelling
Discretisation
Semantic equivalence
Compression bisimulation
Congruence
Stoichiometry

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10.1016/j.tcs.2011.01.007

http://www.sciencedirect.com/science/article/pii/S0304397511000338

Cite this

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title = "A semantic equivalence for Bio-PEPA based on discretisation of continuous values",

abstract = "Bio-PEPA is a process algebra for modelling biological systems. An important aspect of Bio-PEPA is the ability it provides to discretise concentrations resulting in a smaller, more manageable state space. The discretisation is based on a step size which determines the size of each discrete level and also the number of levels. This paper considers the relationship between two discretisations of the same Bio-PEPA model that differ only in the step size and hence the number of levels, by using the idea of equivalence from concurrency and process algebra. We present a novel behavioural semantic equivalence, compression bisimilarity, and investigate when this equates two discretisations of the same model and the circumstances in which this equivalence is a congruence with respect to the synchronisation operator. (C) 2011 Elsevier B.V. All rights reserved.",

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AU - Hillston, Jane

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KW - Biological modelling

KW - Discretisation

KW - Semantic equivalence

KW - Compression bisimulation

KW - Congruence

KW - Stoichiometry

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A semantic equivalence for Bio-PEPA based on discretisation of continuous values

Abstract

Keywords / Materials (for Non-textual outputs)

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

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

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A semantic equivalence for Bio-PEPA based on discretisation of continuous values

Abstract

Keywords / Materials (for Non-textual outputs)

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Other files and links

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Projects

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

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

Cite this