Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA.
Bioinformatics. 2009 Dec 15;25(24):3289-95. doi: 10.1093/bioinformatics/btp581. Epub 2009 Oct 29.
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.
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.
Java implementations are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu.
随着监管网络的规模和复杂性的增长，构建和理解这些模型变得更加困难。建模者自然会从较小的组件构建大型模型，每个组件代表较大网络中反应的子集。为了帮助建模者完成此过程，我们提出了模型聚合，它根据旨在组合的组件来定义模型。
我们已经实现了一个包含模型聚合的模型编辑器，并建议对系统生物学标记语言（SBML）级别 3 进行支持扩展。我们使用从小部分创建的真核细胞周期“引擎”模型来说明聚合。
Java 实现可在 JigCell Aggregation Connector 中获得。请访问 http://jigcell.biol.vt.edu。
