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Open Access Research article

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model

Cihan Oguz1, Teeraphan Laomettachit2, Katherine C Chen1, Layne T Watson3, William T Baumann4 and John J Tyson1*

Author Affiliations

1 Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA

2 Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand

3 Departments of Computer Science and Mathematics, Virginia Tech, Blacksburg, Virginia 24061, USA

4 Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA

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BMC Systems Biology 2013, 7:53  doi:10.1186/1752-0509-7-53

Published: 28 June 2013

Abstract

Background

Parameter estimation from experimental data is critical for mathematical modeling of protein regulatory networks. For realistic networks with dozens of species and reactions, parameter estimation is an especially challenging task. In this study, we present an approach for parameter estimation that is effective in fitting a model of the budding yeast cell cycle (comprising 26 nonlinear ordinary differential equations containing 126 rate constants) to the experimentally observed phenotypes (viable or inviable) of 119 genetic strains carrying mutations of cell cycle genes.

Results

Starting from an initial guess of the parameter values, which correctly captures the phenotypes of only 72 genetic strains, our parameter estimation algorithm quickly improves the success rate of the model to 105–111 of the 119 strains. This success rate is comparable to the best values achieved by a skilled modeler manually choosing parameters over many weeks. The algorithm combines two search and optimization strategies. First, we use Latin hypercube sampling to explore a region surrounding the initial guess. From these samples, we choose ∼20 different sets of parameter values that correctly capture wild type viability. These sets form the starting generation of differential evolution that selects new parameter values that perform better in terms of their success rate in capturing phenotypes. In addition to producing highly successful combinations of parameter values, we analyze the results to determine the parameters that are most critical for matching experimental outcomes and the most competitive strains whose correct outcome with a given parameter vector forces numerous other strains to have incorrect outcomes. These “most critical parameters” and “most competitive strains” provide biological insights into the model. Conversely, the “least critical parameters” and “least competitive strains” suggest ways to reduce the computational complexity of the optimization.

Conclusions

Our approach proves to be a useful tool to help systems biologists fit complex dynamical models to large experimental datasets. In the process of fitting the model to the data, the tool identifies suggestive correlations among aspects of the model and the data.

Keywords:
Optimization; Budding yeast; Cell cycle; ODE model; Model reduction; Phenotypic constraints; Latin hypercube sampling; Differential evolution; Sensitivity analysis; Phenotype competition