Article

Simulation and verification for computational modelling of signalling pathways

Authors:

Marta Kwiatkowska,

Oksana Tymchyshyn,

Eamonn GaffneyAuthors Info & Claims

WSC '06: Proceedings of the 38th conference on Winter simulation

Pages 1666 - 1674

Published: 03 December 2006 Publication History

Abstract

Modelling of the dynamics of biochemical reaction networks typically proceeds by solving ordinary differential equations or stochastic simulation via the Gillespie algorithm. More recently, computational methods such as process algebra techniques have been successfully applied to the analysis of signalling pathways. One advantage of these is that they enable automatic verification of the models, via model checking, against qualitative and quantitative temporal logic specifications, for example, "what is the probability that the protein eventually degrades?". Such verification is exhaustive, that is, the analysis is carried out over all paths, producing exact quantitative measures. In this paper, we give an overview of the simulation, verification and differential equation approaches to modelling biochemical reaction networks. We discuss the advantages and disadvantages of the respective methods, using as an illustration a fragment of the FGF signalling pathway.

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Cited By

Fisher JHarel DHenzinger T(2011)Biology as reactivityCommunications of the ACM10.1145/2001269.200128954:10(72-82)Online publication date: 1-Oct-2011
https://dl.acm.org/doi/10.1145/2001269.2001289
Danos VFeret JFontana WKrivine J(2008)Abstract interpretation of cellular signalling networksProceedings of the 9th international conference on Verification, model checking, and abstract interpretation10.5555/1787526.1787537(83-97)Online publication date: 7-Jan-2008
https://dl.acm.org/doi/10.5555/1787526.1787537
van Bakel SKhan IVigliotti MHeath J(2008)Modelling Intracellular Fate of FGF Receptors With BioAmbientsElectronic Notes in Theoretical Computer Science (ENTCS)10.1016/j.entcs.2008.11.026220:3(181-197)Online publication date: 1-Dec-2008
https://dl.acm.org/doi/10.1016/j.entcs.2008.11.026
Show More Cited By

Simulation and verification for computational modelling of signalling pathways

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Information & Contributors

Information

Published In

cover image ACM Conferences

WSC '06: Proceedings of the 38th conference on Winter simulation

December 2006

2429 pages

ISBN:1424405017

Editors:
L. Felipe Perrone
Bucknell University
,
Barry G. Lawson
University of Richmond
,
Jason Liu
Colorado School of Mines
,
Frederick P. Wieland
Sensis Corporation
,
General Chair:
David Nicol
University of Illinois, Urbana-Champaign
,
Program Chair:
Richard Fujimoto
College of Computing, Georgia Tech

Sponsors

IIE: Institute of Industrial Engineers
ASA: American Statistical Association
IEICE ESS: Institute of Electronics, Information and Communication Engineers, Engineering Sciences Society
IEEE-CS\DATC: The IEEE Computer Society
SIGSIM: ACM Special Interest Group on Simulation and Modeling
NIST: National Institute of Standards and Technology
(SCS): The Society for Modeling and Simulation International
INFORMS-CS: Institute for Operations Research and the Management Sciences-College on Simulation

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Winter Simulation Conference

Publication History

Published: 03 December 2006

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WSC06

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IIE
ASA
IEICE ESS
IEEE-CS\DATC
SIGSIM
NIST
(SCS)
INFORMS-CS

WSC06: Winter Simulation Conference 2006

December 3 - 6, 2006

California, Monterey

Acceptance Rates

WSC '06 Paper Acceptance Rate 177 of 252 submissions, 70%;

Overall Acceptance Rate 3,413 of 5,075 submissions, 67%

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Cited By

Fisher JHarel DHenzinger T(2011)Biology as reactivityCommunications of the ACM10.1145/2001269.200128954:10(72-82)Online publication date: 1-Oct-2011
https://dl.acm.org/doi/10.1145/2001269.2001289
Danos VFeret JFontana WKrivine J(2008)Abstract interpretation of cellular signalling networksProceedings of the 9th international conference on Verification, model checking, and abstract interpretation10.5555/1787526.1787537(83-97)Online publication date: 7-Jan-2008
https://dl.acm.org/doi/10.5555/1787526.1787537
van Bakel SKhan IVigliotti MHeath J(2008)Modelling Intracellular Fate of FGF Receptors With BioAmbientsElectronic Notes in Theoretical Computer Science (ENTCS)10.1016/j.entcs.2008.11.026220:3(181-197)Online publication date: 1-Dec-2008
https://dl.acm.org/doi/10.1016/j.entcs.2008.11.026
Langmead CJha S(2007)Predicting protein folding kinetics via temporal logic model checkingProceedings of the 7th international conference on Algorithms in Bioinformatics10.5555/2391870.2391894(252-264)Online publication date: 8-Sep-2007
https://dl.acm.org/doi/10.5555/2391870.2391894
Kuttler CLhoussaine CNiehren J(2007)A stochastic pi calculus for concurrent objectsProceedings of the 2nd international conference on Algebraic biology10.5555/1769026.1769043(232-246)Online publication date: 2-Jul-2007
https://dl.acm.org/doi/10.5555/1769026.1769043
Sauro HHarel DKwiatkowska MShaffer CUhrmacher AHucka MMendes PStrömback LTyson JNicol DFujimoto R(2006)Challenges for modeling and simulation methods in systems biologyProceedings of the 38th conference on Winter simulation10.5555/1218112.1218425(1720-1730)Online publication date: 3-Dec-2006
https://dl.acm.org/doi/10.5555/1218112.1218425

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