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Bioinformatics Advance Access published online on October 29, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp581
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Model Aggregation: a building-block approach to creating large macromolecular regulatory networks

Ranjit Randhawa 1, Clifford A. Shaffer 1,* and John J. Tyson 2

1 Department of Computer Science, Virginia Tech, Blacksburg, VA 24061
2 Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061

*To whom correspondence should be addressed. Dr. Cliff Shaffer, E-mail: shaffer{at}vt.edu


  Abstract

Motivation: Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Modelers naturally build large models from smaller components that each represent subsets of reactions within the larger network. To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined.

Results: We have implemented a model editor that incorporates model aggregation, and we suggest supporting extensions to the Systems Biology Markup Language (SBML) Level 3. We illustrate aggregation with a model of the eukaryotic cell cycle ‘engine’ created from smaller pieces.

Availability: Java implementations of our SBML proposal are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu.

Contact: shaffer{at}vt.edu

Associate Editor: Dr. Trey Ideker

Received on April 29, 2009; revised on August 25, 2009; accepted on September 28, 2009

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