Stochastic Modelling of the Kai-based Circadian Clock

Christopher Banks; Allan Clark; Anastasios-Andreas Georgoulas; Stephen Gilmore; Jane Hillston; Dimitrios Milios; Ian Stark

doi:10.1016/j.entcs.2013.07.004

Stochastic Modelling of the Kai-based Circadian Clock

Christopher Banks, Allan Clark, Anastasios-Andreas Georgoulas, Stephen Gilmore, Jane Hillston, Dimitrios Milios, Ian Stark

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

Abstract / Description of output

We present two process algebra models of a Kai-protein based circadian clock. Our models are represented in the Bio-PEPA and the continuous pi-calculus process algebras. The circadian clock is not based on transcription and has been shown to persist with a rhythmic signal when removed from a living cell. Our models allow us to speculate as to the mechanisms which allow for the rhythmic signals. We reproduce previous results based on ODE models and then use our models as the basis for stochastic simulation.

Original language	English
Title of host publication	Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).
Publisher	Elsevier
Pages	43-60
Number of pages	18
Volume	296
DOIs	https://doi.org/10.1016/j.entcs.2013.07.004
Publication status	Published - 17 Sept 2012
Event	Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC) - UK, London, United Kingdom Duration: 1 Sept 2012 → …

Publication series

Name	Electronic Notes in Theoretical Computer Science
ISSN (Print)	1571-0661

Conference

Conference	Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC)
Country/Territory	United Kingdom
City	London
Period	1/09/12 → …

Access to Document

10.1016/j.entcs.2013.07.004

1-s2.0-S1571066113000352-main
Elsevier Open Access paper.
Final published version, 421 KB

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

Banks, C., Clark, A., Georgoulas, A.-A., Gilmore, S., Hillston, J., Milios, D., & Stark, I. (2012). Stochastic Modelling of the Kai-based Circadian Clock. In Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC). (Vol. 296, pp. 43-60). (Electronic Notes in Theoretical Computer Science). Elsevier. https://doi.org/10.1016/j.entcs.2013.07.004

Banks, Christopher ; Clark, Allan ; Georgoulas, Anastasios-Andreas et al. / Stochastic Modelling of the Kai-based Circadian Clock. Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).. Vol. 296 Elsevier, 2012. pp. 43-60 (Electronic Notes in Theoretical Computer Science).

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title = "Stochastic Modelling of the Kai-based Circadian Clock",

abstract = "We present two process algebra models of a Kai-protein based circadian clock. Our models are represented in the Bio-PEPA and the continuous pi-calculus process algebras. The circadian clock is not based on transcription and has been shown to persist with a rhythmic signal when removed from a living cell. Our models allow us to speculate as to the mechanisms which allow for the rhythmic signals. We reproduce previous results based on ODE models and then use our models as the basis for stochastic simulation.",

author = "Christopher Banks and Allan Clark and Anastasios-Andreas Georgoulas and Stephen Gilmore and Jane Hillston and Dimitrios Milios and Ian Stark",

year = "2012",

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Banks, C, Clark, A, Georgoulas, A-A , Gilmore, S , Hillston, J, Milios, D & Stark, I 2012, Stochastic Modelling of the Kai-based Circadian Clock. in Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).. vol. 296, Electronic Notes in Theoretical Computer Science, Elsevier, pp. 43-60, Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC), London, United Kingdom, 1/09/12. https://doi.org/10.1016/j.entcs.2013.07.004

Stochastic Modelling of the Kai-based Circadian Clock. / Banks, Christopher; Clark, Allan; Georgoulas, Anastasios-Andreas et al.
Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).. Vol. 296 Elsevier, 2012. p. 43-60 (Electronic Notes in Theoretical Computer Science).

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

TY - GEN

T1 - Stochastic Modelling of the Kai-based Circadian Clock

AU - Banks, Christopher

AU - Clark, Allan

AU - Georgoulas, Anastasios-Andreas

AU - Gilmore, Stephen

AU - Hillston, Jane

AU - Milios, Dimitrios

AU - Stark, Ian

PY - 2012/9/17

Y1 - 2012/9/17

N2 - We present two process algebra models of a Kai-protein based circadian clock. Our models are represented in the Bio-PEPA and the continuous pi-calculus process algebras. The circadian clock is not based on transcription and has been shown to persist with a rhythmic signal when removed from a living cell. Our models allow us to speculate as to the mechanisms which allow for the rhythmic signals. We reproduce previous results based on ODE models and then use our models as the basis for stochastic simulation.

AB - We present two process algebra models of a Kai-protein based circadian clock. Our models are represented in the Bio-PEPA and the continuous pi-calculus process algebras. The circadian clock is not based on transcription and has been shown to persist with a rhythmic signal when removed from a living cell. Our models allow us to speculate as to the mechanisms which allow for the rhythmic signals. We reproduce previous results based on ODE models and then use our models as the basis for stochastic simulation.

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DO - 10.1016/j.entcs.2013.07.004

M3 - Conference contribution

AN - SCOPUS:84883385936

VL - 296

T3 - Electronic Notes in Theoretical Computer Science

SP - 43

EP - 60

BT - Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).

PB - Elsevier

T2 - Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC)

Y2 - 1 September 2012

ER -

Banks C, Clark A, Georgoulas AA , Gilmore S , Hillston J, Milios D et al. Stochastic Modelling of the Kai-based Circadian Clock. In Proceedings the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC).. Vol. 296. Elsevier. 2012. p. 43-60. (Electronic Notes in Theoretical Computer Science). doi: 10.1016/j.entcs.2013.07.004

Stochastic Modelling of the Kai-based Circadian Clock

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Projects

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh

Cite this