Extending Regulatory Network Modeling with Multistate Species

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dc.contributor.authorMobassera, Umme Jukaen
dc.contributor.committeechairShaffer, Clifford A.en
dc.contributor.committeecochairTyson, John J.en
dc.contributor.committeememberCao, Yangen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2014-03-14T20:47:28Zen
dc.date.adate2011-12-20en
dc.date.available2014-03-14T20:47:28Zen
dc.date.issued2011-10-31en
dc.date.rdate2011-12-20en
dc.date.sdate2011-11-04en
dc.description.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, 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.en
dc.description.degreeMaster of Scienceen
dc.identifier.otheretd-11042011-165743en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-11042011-165743/en
dc.identifier.urihttp://hdl.handle.net/10919/35594en
dc.publisherVirginia Techen
dc.relation.haspartMobassera_UJ_T_2011.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectModeling Toolen
dc.subjectSoftwareen
dc.subjectJigCellen
dc.subjectComputational Systems Biologyen
dc.subjectMultistate Speciesen
dc.subjectSBMLen
dc.subjectRule Based Modelingen
dc.titleExtending Regulatory Network Modeling with Multistate Speciesen
dc.typeThesisen
thesis.degree.disciplineComputer Scienceen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen

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