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SIMULATION
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Simulation Methods for Optimal Experimental Design in Systems Biology

D. Faller

Freiburg Center for Data Analysis and Modeling Eckerstr. 1, 79104 Freiburg, Germany

U. Klingmüller

Max-Planck-Institute for Immunology Stübeweg 51, 79108 Freiburg, Germany

J. Timmer

Freiburg Center for Data Analysis and Modeling Eckerstr. 1, 79104 Freiburg, Germany, jeti{at}fdm.uni-freiburg.de

To obtain a systems-level understanding of a biological system, the authors conducted quantitative dynamic experiments from which the system structure and the parameters have to be deduced. Since biological systems have to cope with different environmental conditions, certain properties are often robust with respect to variations in some of the parameters. Hence, it is important to use optimal experimental design considerations in advance of the experiments to improve the information content of the measurements. Using the MAP-Kinase pathway as an example, the authors present a simulation study investigating the application of different optimality criteria. It is demonstrated that experimental design significantly improves the parameter estimation accuracy and also reveals difficulties in parameter estimation due to robustness.

Key Words: Experimental design • systems biology • simulation methods

SIMULATION, Vol. 79, No. 12, 717-725 (2003)
DOI: 10.1177/0037549703040937
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