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Systematic benchmarking of omics computational tools.


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.

SUBMITTER: Mangul S 

PROVIDER: S-EPMC6437167 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Systematic benchmarking of omics computational tools.

Mangul Serghei S   Martin Lana S LS   Hill Brian L BL   Lam Angela Ka-Mei AK   Distler Margaret G MG   Zelikovsky Alex A   Eskin Eleazar E   Flint Jonathan J  

Nature communications 20190327 1


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, adva  ...[more]

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