A Framework for Individual-based Simulation of Heterogeneous Cell Populations

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dc.contributor.authorAbdennur, Nezar A
dc.date.accessioned2011-12-13T19:47:40Z
dc.date.available2011-12-13T19:47:40Z
dc.date.created2012
dc.date.issued2012
dc.identifier.urihttp://hdl.handle.net/10393/20478
dc.identifier.urihttp://dx.doi.org/10.20381/ruor-5079
dc.description.abstractAn object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.
dc.language.isoen
dc.publisherUniversité d'Ottawa / University of Ottawa
dc.subjectsimulation
dc.subjectcomputational biology
dc.subjectindividual-based models
dc.subjectsystems biology
dc.subjectpopulation dynamics
dc.subjectobject-oriented
dc.subjectconstant-number monte carlo
dc.subjectstochastic chemical kinetics
dc.subjectcell physiology
dc.subjectsimulation channels
dc.subjectscheduling protocols
dc.subjectcell populations
dc.subjectpopulation heterogeneity
dc.subjectdifferential reproduction
dc.subjectnoise
dc.subjectheritability
dc.subjectdynamics
dc.subjectcell lineages
dc.titleA Framework for Individual-based Simulation of Heterogeneous Cell Populations
dc.typeThesis
dc.faculty.departmentMédecine cellulaire et moléculaire / Cellular and Molecular Medicine
dc.contributor.supervisorKaern, Mads
dc.embargo.termsimmediate
dc.degree.nameMSc
dc.degree.levelmasters
dc.degree.disciplineMédecine / Medicine
thesis.degree.nameMSc
thesis.degree.levelMasters
thesis.degree.disciplineMédecine / Medicine
uottawa.departmentMédecine cellulaire et moléculaire / Cellular and Molecular Medicine
CollectionThèses, 2011 - // Theses, 2011 -

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