Jones Thomas C, Hoops Stefan, Watson Layne T, Palmisano Alida, Tyson John J, Shaffer Clifford A
Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA.
Simulation. 2018 Nov;94(11):993-1008. doi: 10.1177/0037549717754121. Epub 2018 Feb 14.
The growing size and complexity of molecular network models makes them increasingly difficult to construct and understand. Modifying a model that consists of tens of reactions is no easy task. Attempting the same on a model containing hundreds of reactions can seem nearly impossible. We present the JigCell Model Connector, a software tool that supports large-scale molecular network modeling. Our approach to developing large models is to combine smaller models, making the result easier to comprehend. At the base, the smaller models (called modules) are defined by small collections of reactions. Modules connect together to form larger modules through clearly defined interfaces, called ports. In this work, we enhance the port concept by defining three types of ports. An output port is linked to an internal component that will send a value. An input port is linked to an internal component that will receive a value. An equivalence port is linked to an internal component that will both receive and send values. Not all modules connect together in the same way; therefore, multiple connection options need to exist.
分子网络模型规模的不断扩大及其复杂性的日益增加，使得构建和理解这些模型变得越来越困难。修改一个包含数十个反应的模型并非易事。而要对一个包含数百个反应的模型进行同样的操作，几乎是不可能的。我们展示了JigCell模型连接器，这是一种支持大规模分子网络建模的软件工具。我们开发大型模型的方法是将较小的模型组合起来，使结果更易于理解。从根本上说，较小的模型（称为模块）由少量反应集合定义。模块通过明确定义的接口（称为端口）连接在一起，形成更大的模块。在这项工作中，我们通过定义三种类型的端口来强化端口概念。输出端口链接到一个将发送值的内部组件。输入端口链接到一个将接收值的内部组件。等效端口链接到一个既接收又发送值的内部组件。并非所有模块都以相同的方式连接在一起；因此，需要存在多种连接选项。
