Article

Modeling and analysis of biological processes by mem(brane) calculi and systems

Authors:

Claudio ZandronAuthors Info & Claims

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

Pages 1646 - 1655

Published: 03 December 2006 Publication History

Abstract

In recent years, the modeling and analysis techniques developed in the area of formal languages and of concurrent process calculi have been successfully applied to the field of Systems Biology. In this setting, Brane Calculi and Membrane Systems are two of the most prominent approaches for the modeling of the behaviour of biological membranes. Membrane Systems have been introduced by Gh. Paun as a class of distributed parallel computing devices of a biochemical type, while Brane Calculi are a family of process calculi, based on a set of biologically inspired primitives of membrane interaction. In this paper we model the behaviour of a biological process - namely, the LDL Cholesterol Degradation Pathway - in both Brane Calculi and Membrane Systems. We also provide a brief discussion on the application of analysis techniques to this case study.

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Cited By

Bodei CBrodo LGori RHermith DLevi F(2015)A Global Occurrence Counting Analysis for Brane CalculiRevised Selected Papers of the 25th International Symposium on Logic-Based Program Synthesis and Transformation - Volume 952710.1007/978-3-319-27436-2_11(179-200)Online publication date: 13-Jul-2015
https://dl.acm.org/doi/10.1007/978-3-319-27436-2_11
Ciocchetta FHillston J(2008)Process algebras in systems biologyProceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology10.5555/1786698.1786707(265-312)Online publication date: 2-Jun-2008
https://dl.acm.org/doi/10.5555/1786698.1786707
Busi N(2006)Deciding behavioural properties in brane calculiProceedings of the 2006 international conference on Computational Methods in Systems Biology10.1007/11885191_2(17-31)Online publication date: 18-Oct-2006
https://dl.acm.org/doi/10.1007/11885191_2

Modeling and analysis of biological processes by mem(brane) calculi and systems

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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

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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

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Published: 03 December 2006

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WSC06: Winter Simulation Conference 2006

December 3 - 6, 2006

California, Monterey

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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

Bodei CBrodo LGori RHermith DLevi F(2015)A Global Occurrence Counting Analysis for Brane CalculiRevised Selected Papers of the 25th International Symposium on Logic-Based Program Synthesis and Transformation - Volume 952710.1007/978-3-319-27436-2_11(179-200)Online publication date: 13-Jul-2015
https://dl.acm.org/doi/10.1007/978-3-319-27436-2_11
Ciocchetta FHillston J(2008)Process algebras in systems biologyProceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology10.5555/1786698.1786707(265-312)Online publication date: 2-Jun-2008
https://dl.acm.org/doi/10.5555/1786698.1786707
Busi N(2006)Deciding behavioural properties in brane calculiProceedings of the 2006 international conference on Computational Methods in Systems Biology10.1007/11885191_2(17-31)Online publication date: 18-Oct-2006
https://dl.acm.org/doi/10.1007/11885191_2

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