New Concepts for Evaluating the Performance of Computational Methods*

In this paper, new concepts for assessing methods which were developed for analyzing experimental data in the context of systems biology will be introduced. Some ideas are illustrated by evaluating the impact of the logarithmic transformation for parameter estimation. A strong benefit of the log-transformation was observed for five different ODE models. The suggested framework enables less biased and more reliable and valid assessment and comparison of competing approaches than currently performed in the literature. The presented concepts could serve as basis for developing decision guidelines for optimal selection of analysis methods and thereby enhancing the transfer of systems biological procedures and reverse engineering methods to industrial applications like drug development.