학술논문

Model Composition for Macromolecular Regulatory Networks
Document Type
Periodical
Source
IEEE/ACM Transactions on Computational Biology and Bioinformatics IEEE/ACM Trans. Comput. Biol. and Bioinf. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 7(2):278-287 Jun, 2010
Subject
Bioengineering
Computing and Processing
Biological system modeling
Proteins
Differential equations
Systems biology
Markup languages
Fungi
Chemical products
Mathematical model
Stochastic processes
Modeling
composition
fusion
flattening
SBML.
Language
ISSN
1545-5963
1557-9964
2374-0043
Abstract
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.