  Insufficient performance of optimization approaches for fitting of
mathematical models is still a major bottleneck in systems biology. In this
manuscript, the reasons and methodological challenges are summarized as well as
their impact in benchmark studies. Important aspects for increasing evidence of
outcomes of benchmark analyses are discussed. Based on general guidelines for
benchmarking in computational biology, a collection of tailored guidelines is
presented for performing informative and unbiased benchmarking of
optimization-based fitting approaches. Comprehensive benchmark studies based on
these recommendations are urgently required for establishing of a robust and
reliable methodology for the systems biology community.
