Systems biology: model based evaluation and comparison of potential explanations for given biological data

Systems biology and its usage of mathematical modeling to analyse biological data is rapidly becoming an established approach to biology. A crucial advantage of this approach is that more information can be extracted from observations of intricate dynamics, which allows nontrivial complex explanations to be evaluated and compared. In this minireview we explain this process, and review some of the most central available analysis tools. The focus is on the evaluation and comparison of given explanations for a given set of experimental data and prior knowledge. Three types of methods are discussed: (a) for evaluation of whether a given model is sufficiently able to describe the given data to be nonrejectable; (b) for evaluation of whether a slightly superior model is significantly better; and (c) for a general evaluation and comparison of the biologically interesting features in a model. The most central methods are reviewed, both in terms of underlying assumptions, including references to more advanced literature for the theoretically oriented reader, and in terms of practical guidelines and examples, for the practically oriented reader. Many of the methods are based upon analysis tools from statistics and engineering, and we emphasize that the systems biology focus on acceptable explanations puts these methods in a nonstandard setting. We highlight some associated future improvements that will be essential for future developments of model based data analysis in biology.