Article

Introducing variable ports and multi-couplings for cell biological modeling in DEVS

Authors:

Adelinde M. Uhrmacher,

Jan Himmelspach,

Roland EwaldAuthors Info & Claims

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

Pages 832 - 840

Published: 03 December 2006 Publication History

Abstract

Motivated by the requirements of molecular biological applications, we are suggesting an extension of the DEVS formalism. Starting with DYNDEVS a reflective variant of DEVS which supports dynamic behavior, composition, and interaction pattern, we develop ρ-DEVS. Dynamic ports and multi-couplings are introduced whose combination allows models to reflect significant state changes to the outside world and enabling or disabling certain interactions at the same time. An abstract simulator describes the operational semantics of the developed formalism, and the Tryptophan operon model illustrates the developed ideas and concepts.

References

[1]

Barros, F. 1997. Modeling Formalism for Dynamic Structure Systems. ACM Transactions on Modeling and Computer Simulation 7 (4): 501--514.

Digital Library

[2]

Degenring, D., M. Röhl, and A. Uhrmacher. 2004. Discrete Event, Multi-Level Simulation of Metabolite Channeling. BioSystems 75 (1--3): 29--41.

[3]

Gillespie, D. T. 1976. A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. Journal of Computational Physics 22:403--434.

[4]

Harel, D., and A. Naamad. 1996, October. The STATEMATE semantics of statecharts. ACM Transactions on Software Engineering and Methodology 5 (4): 293--333.

Digital Library

[5]

Himmelspach, J., and A. M. Uhrmacher. 2004, October. Processing dynamic PDEVS models. In Proceedings of the 12th IEEE International Symposium on MASCOTS, ed. D. DeGroot and P. Harrison, 329--336. Volendam, The Netherlands: IEEE Computer Society.

Digital Library

[6]

Himmelspach, J., and A. M. Uhrmacher. 2006. Sequential processing of pdevs models. In Proceedings of the EMSS 06.

[7]

Hu, X., B. Zeigler, and S. Mittal. 2005. Variable structure in devs component-based modeling and simulation. Simulation 81 (2).

Digital Library

[8]

Kuttler, C., and A. Uhrmacher. 2006. Multi-level modeling in systems biology by discrete event approaches. IT Themenheft Systems Biology.

[9]

Pawletta, T., B. Lampe, S. Pawletta, and W. Drewelow. 1996. A new approach for simulation of variable structure systems. In Proc. 41th KoREMA, Volume 2, 57--62. Opatija, Croatia.

[10]

Priami, C. 1995. Stochastic π-calculus. Computer Journal 6:578--589.

[11]

Priami, C., and P. Quaglia. 2005. Beta binders for biological interactions. Transactions on Computationa Systems Biology.

[12]

Uhrmacher, A. 2001. Dynamic Structures in Modeling and Simulation - A Reflective Approach. ACM Transactions on Modeling and Simulation 11 (2): 206--232.

Digital Library

[13]

Uhrmacher, A., and C. Priami. 2005, December 4--7. Discrete event systems specification in Systems Biology - a discussion of stochastic pi-calculus and DEVS. In Proc. of the Winter Simulation Conference.

Digital Library

[14]

Zeigler, B. 1986. Toward a simulation methodology for variable structure modelling. In Modelling and Simulation Methodology in the Artificial Intelligence Era, ed. M. Elzas, T. Ören, and B. Zeigler, 195--210. North-Holland.

[15]

Zeigler, B., H. Praehofer, and T. Kim. 2000. Theory of Modeling and Simulation. London: Academic Press.

Digital Library

Cited By

Steiniger AUhrmacher A(2016)Intensional Couplings in Variable-Structure ModelsACM Transactions on Modeling and Computer Simulation10.1145/281864126:2(1-27)Online publication date: 29-Jan-2016
https://dl.acm.org/doi/10.1145/2818641
Barros F(2014)On the representation of dynamic topologiesProceedings of the Symposium on Theory of Modeling & Simulation - DEVS Integrative10.5555/2665008.2665048(1-8)Online publication date: 13-Apr-2014
https://dl.acm.org/doi/10.5555/2665008.2665048
Hamri MBaati LMcGraw RImsand EChinni M(2010)On using design patterns for DEVS modeling and simulation toolsProceedings of the 2010 Spring Simulation Multiconference10.1145/1878537.1878664(1-9)Online publication date: 11-Apr-2010
https://dl.acm.org/doi/10.1145/1878537.1878664
Show More Cited By

Introducing variable ports and multi-couplings for cell biological modeling in DEVS
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

Recommendations

Modeling pedestrian behavior with Cell-DEVS

In this work, we provide an approach for Modeling and Simulation M&S of crowds using Cellular Discrete EVent System Specification Cell-DEVS. We present many examples of Cellular Discrete EVent System Specification entity-based crowd models, and we show ...
The DEVS-driven modeling language: syntax and semantics definition by meta-modeling and graph transformation
TMS/DEVS '12: Proceedings of the 2012 Symposium on Theory of Modeling and Simulation - DEVS Integrative M&S Symposium

This paper presents the syntax and semantics of the DEVS-Driven Modeling Language (DDML), a simulation modeling formalism that combines visual modeling, discrete event simulation and formal analysis. The use of visual notations makes DDML highly ...
Introduction to parallel DEVS modelling and simulation
Mod4Sim '18: Proceedings of the Model-driven Approaches for Simulation Engineering Symposium

DEVS is a popular formalism for modelling complex dynamic systems using a discrete-event abstraction. Main advantages of DEVS are its rigorous formal definition, and its support for modularity: models can be hierarchically nested. Thanks to these ...

Comments

Please enable JavaScript to view thecomments powered by Disqus.

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

Publisher

Winter Simulation Conference

Publication History

Published: 03 December 2006

Check for updates

Qualifiers

Article

Conference

WSC06

Sponsor:

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%

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

6
Total Citations
View Citations
111
Total Downloads

Downloads (Last 12 months)0
Downloads (Last 6 weeks)0

Reflects downloads up to 26 Nov 2024

Other Metrics

View Author Metrics

Citations

Cited By

Steiniger AUhrmacher A(2016)Intensional Couplings in Variable-Structure ModelsACM Transactions on Modeling and Computer Simulation10.1145/281864126:2(1-27)Online publication date: 29-Jan-2016
https://dl.acm.org/doi/10.1145/2818641
Barros F(2014)On the representation of dynamic topologiesProceedings of the Symposium on Theory of Modeling & Simulation - DEVS Integrative10.5555/2665008.2665048(1-8)Online publication date: 13-Apr-2014
https://dl.acm.org/doi/10.5555/2665008.2665048
Hamri MBaati LMcGraw RImsand EChinni M(2010)On using design patterns for DEVS modeling and simulation toolsProceedings of the 2010 Spring Simulation Multiconference10.1145/1878537.1878664(1-9)Online publication date: 11-Apr-2010
https://dl.acm.org/doi/10.1145/1878537.1878664
Maus CJohn MRöhl MUhrmacher A(2008)Hierarchical modeling for computational biologyProceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology10.5555/1786698.1786703(81-124)Online publication date: 2-Jun-2008
https://dl.acm.org/doi/10.5555/1786698.1786703
Baati LFrydman CGIAMBIASI NSeck MWainer G(2007)Low intensity conflicts modeling framework based on dynamic hierarchical structure DEVS approachProceedings of the 2007 Summer Computer Simulation Conference10.5555/1357910.1358145(1-6)Online publication date: 16-Jul-2007
https://dl.acm.org/doi/10.5555/1357910.1358145
Uhrmacher AEwald RJohn MMaus CJeschke MBiermann STew J(2007)Combining micro and macro-modeling in DEVS for computational biologyProceedings of the 39th conference on Winter simulation: 40 years! The best is yet to come10.5555/1351542.1351698(871-880)Online publication date: 9-Dec-2007
https://dl.acm.org/doi/10.5555/1351542.1351698

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Table of Contents