The ever-growing size and complexity of molecular network models makes them 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 together 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 different types of ports. Not all modules connect together the same way, therefore multiple connection options need to exist. / Master of Science / Genes and proteins interact to control the functions of a living cell. In order to better understand these interactions, mathematical models can be created. A model is a representation of a cellular function that can be simulated on a computer. Results from the simulations can be used to gather insight and drive the direction of new laboratory experiments. As new discoveries are made, mathematical models continue to grow in size and complexity. 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 together 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 different types of ports. Not all modules connect together the same way, therefore multiple connection options need to exist.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/78277 |
| Date | 28 June 2017 |
| Creators | Jones, Thomas Carroll Jr. |
| Contributors | Computer Science, Shaffer, Clifford A., Tyson, John J., Hoops, Stefan, Watson, Layne T. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Detected Language | English |
| Type | Thesis |
| Format | ETD, application/pdf |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
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