Journal Article

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

Ranjit Randhawa, Clifford A. Shaffer and John J. Tyson

in Bioinformatics

Volume 25, issue 24, pages 3289-3295
Published in print December 2009 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp581
Model aggregation: a building-block approach to creating large macromolecular regulatory networks

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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 are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu.

Contact: shaffer@vt.edu

Journal Article.  5701 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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