Deterministic Parallel Global Parameter Estimation for a Model of the Budding Yeast Cell Cycle

Panning, Thomas D. and Watson, Layne T. and Allen, Nicholas A. and Chen, Katherine C. and Shaffer, Clifford A. and Tyson, John J. (2006) Deterministic Parallel Global Parameter Estimation for a Model of the Budding Yeast Cell Cycle. Technical Report TR-06-01, Departments of Computer Science, Mathematics, and Biology, Virginia Tech.

Abstract

Two parallel deterministic direct search algorithms are used 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 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.