Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges

Kyle Ellrott; Alex Buchanan; Allison Creason; Michael Mason; Thomas Schaffter; Bruce Hoff; James Eddy; John M. Chilton; Thomas Yu; Joshua M. Stuart; Julio Saez-Rodriguez; Gustavo Stolovitzky; Paul C. Boutros; Justin Guinney

doi:10.1186/s13059-019-1794-0

Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges

Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros, Justin Guinney

Biochemistry & Molecular Biology

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the diversity of software architectures, input and output file formats, and computing environments. To mitigate these problems, some challenges have leveraged new virtualization and compute methods, requiring participants to submit cloud-ready software packages. We review recent data challenges with innovative approaches to model reproducibility and data sharing, and outline key lessons for improving quantitative biomedical data analysis through crowd-sourced benchmarking challenges.

Original language	English (US)
Article number	195
Journal	Genome biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1794-0
State	Published - Sep 10 2019

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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Ellrott, K., Buchanan, A., Creason, A., Mason, M., Schaffter, T., Hoff, B., Eddy, J., Chilton, J. M., Yu, T., Stuart, J. M., Saez-Rodriguez, J., Stolovitzky, G., Boutros, P. C., & Guinney, J. (2019). Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges. Genome biology, 20(1), Article 195. https://doi.org/10.1186/s13059-019-1794-0

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AU - Schaffter, Thomas

AU - Hoff, Bruce

AU - Eddy, James

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AU - Yu, Thomas

AU - Stuart, Joshua M.

AU - Saez-Rodriguez, Julio

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AU - Guinney, Justin

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Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges

Abstract

All Science Journal Classification (ASJC) codes

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