JigCell Model Connector: building large molecular network models from components. (November 2018)

• Record Type: Journal Article
• Authors: Jones, Thomas C; Hoops, Stefan; Watson, Layne T; Palmisano, Alida; Tyson, John J; Shaffer, Clifford A
• Is Part Of: Simulation. Volume 94:Number 11(2018)
• Page Start: 993
• Page End: 1008
• Publication Date: 2018-11
• Subjects: computational systems biology -- hierarchical model composition -- JigCell -- modeling tool -- SBML -- software; Computer simulation -- Periodicals; 003.3
• DOI: 10.1177/0037549717754121
• Languages: English
• ISSNs: 0037-5497

Abstract

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.