Reduction of a biochemical model with preservation of its basic dynamic properties.
The complexity of full-scale metabolic models is a major obstacle for their effective use in computational systems biology. The aim of model reduction is to circumvent this problem by eliminating parts of a model that are unimportant for the properties of interest. The choice of reduction method is influenced both by the type of model complexity and by the objective of the reduction; therefore, no single method is superior in all cases. In this study we present a comparative study of two different methods applied to a 20D model of yeast glycolytic oscillations. Our objective is to obtain biochemically meaningful reduced models, which reproduce the dynamic properties of the 20D model. The first method uses lumping and subsequent constrained parameter optimization. The second method is a novel approach that eliminates variables not essential for the dynamics. The applications of the two methods result in models of eight (lumping), six (elimination) and three (lumping followed by elimination) dimensions. All models have similar dynamic properties and pin-point the same interactions as being crucial for generation of the oscillations. The advantage of the novel method is that it is algorithmic, and does not require input in the form of biochemical knowledge. The lumping approach, however, is better at preserving biochemical properties, as we show through extensive analyses of the models.
Danø
Sune
S
Department of Medical Biochemistry and Genetics, University of Copenhagen, Denmark.
Madsen
Mads F
MF
Schmidt
Henning
H
Cedersund
Gunnar
G
D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D006019:Glycolysis; D008954:Models, Biological; D015003:Yeasts / Q000378:metabolism*