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Rules for Modeling Signal-Transduction Systems

Hlavacek, William S. and Faeder, James R. and Blinov, Michael L. and Posner, Richard G. and Hucka, Michael and Fontana, Walter (2006) Rules for Modeling Signal-Transduction Systems. Science's STKE: signal transduction knowledge environment, 2006 (344). re6. ISSN 1525-8882 . http://resolver.caltech.edu/CaltechAUTHORS:20121026-104604268

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Abstract

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic interaction map, but unlike most such maps, rules have precise interpretations. Rules can be processed to automatically generate a mathematical or computational model for a system, which enables explanatory and predictive insights into the system�s behavior. Rules are independent units of a model specification that facilitate model revision. Instead of changing a large number of equations or lines of code, as may be required in the case of a conventional mathematical model, a protein interaction can be introduced or modified simply by adding or changing a single rule that represents the interaction of interest. Rules can be defined and visualized by using graphs, so no specialized training in mathematics or computer science is necessary to create models or to take advantage of the representational precision of rules. Rules can be encoded in a machine- readable format to enable electronic storage and exchange of models, as well as basic knowledge about protein-protein interactions. Here, we review the motivation for rule-based modeling; applications of the approach; and issues that arise in model specification,simulation, and testing. We also discuss rule visualization and exchange and the software available for rule-based modeling.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1126/stke.3442006re6DOIArticle
http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2006/344/re6?view=abstractPublisherArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Contact Email Address:wish@lanl.gov
Additional Information:© 2006 American Association for the Advancement of Science. Published 18 July 2006. Revised 25 July 2006.
Record Number:CaltechAUTHORS:20121026-104604268
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20121026-104604268
Official Citation:W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, W. Fontana, Rules for modeling signal-transduction systems. Sci. STKE 2006, re6 (2006)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:35124
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:29 Oct 2012 15:28
Last Modified:21 Dec 2016 23:45

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