Article

Symbolic modeling of signal transduction in pathway logic

Author:

Carolyn TalcottAuthors Info & Claims

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

Pages 1656 - 1665

Published: 03 December 2006 Publication History

Abstract

Pathway Logic is a step towards a vision of symbolic systems biology. It is an approach to modeling cellular processes based on formal methods. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a variety of formal tools are used to query these models. An important objective of Pathway Logic is to reflect the ways that biologists think about problems using informal models, and to provide bench biologists with tools for computing with and analyzing these models that are natural. In this paper we describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant tool to browse and query these models. The Rac1 signaling pathway is used to illustrate the concepts.

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Cited By

Talcott C(2008)Pathway logicProceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology10.5555/1786698.1786701(21-53)Online publication date: 2-Jun-2008
https://dl.acm.org/doi/10.5555/1786698.1786701
Tiwari ATalcott CKnapp MLincoln PLaderoute K(2007)Analyzing pathways using SAT-based approachesProceedings of the 2nd international conference on Algebraic biology10.5555/1769026.1769038(155-169)Online publication date: 2-Jul-2007
https://dl.acm.org/doi/10.5555/1769026.1769038

Symbolic modeling of signal transduction in pathway logic
1. Applied computing
  1. Life and medical sciences
2. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

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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

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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

Talcott C(2008)Pathway logicProceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology10.5555/1786698.1786701(21-53)Online publication date: 2-Jun-2008
https://dl.acm.org/doi/10.5555/1786698.1786701
Tiwari ATalcott CKnapp MLincoln PLaderoute K(2007)Analyzing pathways using SAT-based approachesProceedings of the 2nd international conference on Algebraic biology10.5555/1769026.1769038(155-169)Online publication date: 2-Jul-2007
https://dl.acm.org/doi/10.5555/1769026.1769038

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