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dc.contributor.authorAllen, Nicholas Alexanderen_US
dc.description.abstractThe cell is a highly ordered and intricate machine within which a wide variety of chemical processes take place. The full scientific understanding of cellular physiology requires accurate mathematical models that depict the temporal dynamics of these chemical processes. Modelers build mathematical models of chemical processes primarily from systems of differential equations. Although developing new biological ideas is more of an art than a science, constructing a mathematical model from a biological idea is largely mechanical and automatable.

This dissertation describes the practices and processes that biological modelers use for modeling and simulation. Computational biologists struggle with existing tools for creating models of complex eukaryotic cells. This dissertation develops new processes for biological modeling that make model creation, verification, validation, and testing less of a struggle. This dissertation introduces computational software that automates parts of the biological modeling process, including model building, transformation, execution, analysis, and evaluation. User and methodological requirements heavily affect the suitability of software for biological modeling. This dissertation examines the modeling software in terms of these requirements.

Intelligent, automated model evaluation shows a tremendous potential to enable the rapid, repeatable, and cost-effective development of accurate models. This dissertation presents a case study that indicates that automated model evaluation can reduce the evaluation time for a budding yeast model from several hours to a few seconds, representing a more than 1000-fold improvement. Although constructing an automated model evaluation procedure requires considerable domain expertise and skill in modeling and simulation, applying an existing automated model evaluation procedure does not. With this automated model evaluation procedure, the computer can then search for and potentially discover models superior to those that the biological modelers developed previously.

dc.publisherVirginia Techen_US
dc.rightsI hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Virginia Tech or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.en_US
dc.subjectsystems biologyen_US
dc.subjectbiological modelingen_US
dc.subjectmodeling processen_US
dc.subjectmodeling support environmenten_US
dc.titleComputational Software for Building Biochemical Reaction Network Models with Differential Equationsen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US D.en_US Polytechnic Institute and State Universityen_US Scienceen_US
dc.contributor.committeechairShaffer, Clifford A.en_US
dc.contributor.committeememberTyson, John J.en_US
dc.contributor.committeememberRamakrishnan, Narenen_US
dc.contributor.committeememberWatson, Layne T.en_US
dc.contributor.committeememberHeath, Lenwood S.en_US

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