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Nat Commun. 2019 Mar 27;10(1):1393. doi: 10.1038/s41467-019-09406-4.

Systematic benchmarking of omics computational tools.

Author information

1
Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
2
Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E Young Drive East, Los Angeles, CA, 90095, USA. smangul@ucla.edu.
3
Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E Young Drive East, Los Angeles, CA, 90095, USA.
4
Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA.
5
Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
6
Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA.
7
The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
8
Department of Human Genetics, University of California Los Angeles, 695 Charles E. Young, Los Angeles, CA, USA.

Abstract

Computational omics methods packaged as software have become essential to modern biological research. The increasing dependence of scientists on these powerful software tools creates a need for systematic assessment of these methods, known as benchmarking. Adopting a standardized benchmarking practice could help researchers who use omics data to better leverage recent technological innovations. Our review summarizes benchmarking practices from 25 recent studies and discusses the challenges, advantages, and limitations of benchmarking across various domains of biology. We also propose principles that can make computational biology benchmarking studies more sustainable and reproducible, ultimately increasing the transparency of biomedical data and results.

PMID:
30918265
PMCID:
PMC6437167
DOI:
10.1038/s41467-019-09406-4
[Indexed for MEDLINE]
Free PMC Article

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