期刊
GENOME BIOLOGY
卷 20, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-019-1887-9
关键词
Benchmarking; Differential equation models; Optimization; Parameter estimation; Systems biology
资金
- German Ministry of Education and Research [EA:Sys FKZ031L0080]
- German Research Foundation (DFG) under Germany's Excellence Strategy -EXC-2189 [390939984]
Insufficient performance of optimization-based approaches for the fitting of mathematical models is still a major bottleneck in systems biology. In this article, the reasons and methodological challenges are summarized as well as their impact in benchmark studies. Important aspects for achieving an increased level of evidence for benchmark results 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 the establishment of a robust and reliable methodology for the systems biology community.
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