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Model Composition for Macromolecular Regulatory Networks
April-June 2010 (vol. 7 no. 2)
pp. 278-287
Ranjit Randhawa, Virginia Tech, Blacksburg
Clifford A. Shaffer, Virginia Tech, Blacksburg
John J. Tyson, Virginia Tech, Blacksburg
Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Large models are usually built up from smaller models, representing subsets of reactions within the larger network. To assist modelers in this composition process, we present a formal approach for model composition, a wizard-style program for implementing the approach, and suggested language extensions to the Systems Biology Markup Language to support model composition. To illustrate the features of our approach and how to use the JigCell Composition Wizard, we build up a model of the eukaryotic cell cycle "engine” from smaller pieces.

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Index Terms:
Modeling, composition, fusion, flattening, SBML.
Ranjit Randhawa, Clifford A. Shaffer, John J. Tyson, "Model Composition for Macromolecular Regulatory Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 278-287, April-June 2010, doi:10.1109/TCBB.2008.64
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