Type of Document	Master's Thesis
Author	Mobassera, Umme Juka
Author's Email Address	mobassera@vt.edu
URN	etd-11042011-165743
Title	Extending Regulatory Network Modeling with Multistate Species
Degree	Master of Science
Department	Computer Science
Advisory Committee	Advisor Name Title Shaffer, Clifford A. Committee Chair Tyson, John J. Committee Co-Chair Cao, Yang Committee Member
Keywords	Modeling Tool Software JigCell Computational Systems Biology Multistate Species SBML Rule Based Modeling
Date of Defense	2011-10-31
Availability	unrestricted
Abstract By increasing the level of abstraction in the representation of regulatory network models, we can hope to allow modelers to create models that are beyond the threshold of what can currently be expressed reliably. As hundreds of reactions are difficult to understand, main- tain, and extend, thousands of reactions become next to impossible without any automation or aid. Using the multistate-species concept we can reduce the number of reactions needed to represent certain systems and thus, lessen the cognitive load on modelers. A multistate species is an entity with a defined range for state variables, which refers to a group of different forms for a specific species. A multistate reaction involves one or more multistate species and compactly represents a group of similar single reactions. In this work, we have extended JCMB (the JigCell Model Builder) to comply with multistate species and reactions modeling and presented a proposal for enhancing SBML (the Systems Biology Markup Language) standards to support multistate models.
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