Title page for ETD etd-05312006-175717


Type of Document Master's Thesis
Author Panning, Thomas D
Author's Email Address tpanning@vt.edu
URN etd-05312006-175717
Title Deterministic Parallel Global Parameter Estimation for a Model of the Budding Yeast Cell Cycle
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Watson, Layne T. Committee Chair
Shaffer, Clifford A. Committee Member
Tyson, John J. Committee Member
Keywords
  • computational biology
  • MADS algorithm
  • direct search
  • DIRECT algorithm
Date of Defense 2006-05-25
Availability unrestricted
Abstract
Two parallel deterministic direct search algorithms are combined to find improved parameters for a system of differential equations designed to simulate the cell cycle of budding yeast. Comparing the model simulation results to experimental data is difficult because most of the experimental data is qualitative rather than quantitative. An algorithm to convert simulation results to mutant phenotypes is presented. Vectors of the 143 parameters defining the differential equation model are rated by a discontinuous objective function. Parallel results on a 2200 processor supercomputer are presented for a global optimization algorithm, DIRECT, a local optimization algorithm, MADS, and a hybrid of the two. A second formulation is presented that uses a system of smooth inequalities to evaluate the phenotype of a mutant. Preliminary results of this formulation are given.

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