Extending Regulatory Network Modeling with Multistate Species

• Main Author: Mobassera, Umme Juka
• Other Authors: Computer Science
• Format: Others
• Published: Virginia Tech 2014
• Subjects: Modeling Tool; Software; JigCell; Computational Systems Biology; Multistate Species; SBML; Rule Based Modeling
• Online Access: http://hdl.handle.net/10919/35594; http://scholar.lib.vt.edu/theses/available/etd-11042011-165743/

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, maintain, 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 defined range for state variables, which refers to a group of different forms for a specific 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. === Master of Science