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Bioinformatics. 2009 Dec 15;25(24):3289-95. doi: 10.1093/bioinformatics/btp581. Epub 2009 Oct 29.

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

Author information

  • 1Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.

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

CONTACT:

shaffer@vt.edu

PMID:
19880372
PMCID:
PMC2788926
DOI:
10.1093/bioinformatics/btp581
[PubMed - indexed for MEDLINE]
Free PMC Article
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