Type of Document Master's Thesis Author Mobassera, Umme Juka Author's Email Address firstname.lastname@example.org 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
- Computational Systems Biology
- Multistate Species
- Rule Based Modeling
Date of Defense 2011-10-31 Availability unrestricted AbstractBy 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 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.
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