Formal Methods for Biochemical Signalling Pathways

Muffy Calder; Stephen Gilmore; Jane Hillston; Vladislav Vyshemirsky

doi:10.1007/978-1-84882-736-3_6

Formal Methods for Biochemical Signalling Pathways

Muffy Calder, Stephen Gilmore, Jane Hillston, Vladislav Vyshemirsky

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

Abstract

We apply quantitative formal methods to a domain from the life sciences: biochemical signalling pathways. The key idea is to model pathways as stochastic continuous time distributed systems. Components of the system are molecular species (rather than individual molecules) and are modelled by concurrent processes that interact with each other via biochemical reactions. Through an application, we show how high level languages and analysis techniques rooted in computer science theory add significantly to the analysis presently available to computational biologists.

Original language	English
Title of host publication	Formal Methods: State of the Art and New Directions
Editors	Paul Boca, Jonathan P. Bowen, Jawed Siddiqi
Publisher	Springer London
Pages	185-215
Number of pages	31
ISBN (Electronic)	978-1-84882-736-3
ISBN (Print)	978-1-84882-735-6
DOIs	https://doi.org/10.1007/978-1-84882-736-3_6
Publication status	Published - 2010

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10.1007/978-1-84882-736-3_6

http://dx.doi.org/10.1007/978-1-84882-736-3_6

SIGNAL: SIGNAL -Stochastic process algebra for biochemical signaling pathway analysis
Gilmore, S. & Hillston, J.
EPSRC
1/09/07 → 31/01/11
Project: Research
SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A., Beggs, J., Ghazal, P., Goryanin, I., Hillston, J., Plotkin, G., Tollervey, D., Walton, A. & Robertson, K.
BBSRC
8/01/07 → 31/12/12
Project: Research

Cite this

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title = "Formal Methods for Biochemical Signalling Pathways",

abstract = "We apply quantitative formal methods to a domain from the life sciences: biochemical signalling pathways. The key idea is to model pathways as stochastic continuous time distributed systems. Components of the system are molecular species (rather than individual molecules) and are modelled by concurrent processes that interact with each other via biochemical reactions. Through an application, we show how high level languages and analysis techniques rooted in computer science theory add significantly to the analysis presently available to computational biologists.",

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doi = "10.1007/978-1-84882-736-3_6",

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AU - Calder, Muffy

AU - Gilmore, Stephen

AU - Hillston, Jane

AU - Vyshemirsky, Vladislav

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AB - We apply quantitative formal methods to a domain from the life sciences: biochemical signalling pathways. The key idea is to model pathways as stochastic continuous time distributed systems. Components of the system are molecular species (rather than individual molecules) and are modelled by concurrent processes that interact with each other via biochemical reactions. Through an application, we show how high level languages and analysis techniques rooted in computer science theory add significantly to the analysis presently available to computational biologists.

U2 - 10.1007/978-1-84882-736-3_6

DO - 10.1007/978-1-84882-736-3_6

M3 - Chapter

SN - 978-1-84882-735-6

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EP - 215

BT - Formal Methods: State of the Art and New Directions

A2 - Boca, Paul

A2 - Bowen, Jonathan P.

A2 - Siddiqi, Jawed

PB - Springer London

ER -

Formal Methods for Biochemical Signalling Pathways

Abstract

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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