Title page for ETD etd-11042011-165743

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
  • Modeling Tool
  • Software
  • JigCell
  • Computational Systems Biology
  • Multistate Species
  • SBML
  • Rule Based Modeling
Date of Defense 2011-10-31
Availability unrestricted
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 di fferent 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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