No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker; Marius van den Beek; Daniel Blankenberg; Dave Bouvier; John Chilton; Nate Coraor; Frederik Coppens; Ignacio Eguinoa; Simon Gladman; Bjoern Gruening; Nicholas Keener; Delphine Lariviere; Andrew Lonie; Sergei Kosakovsky Pond; Wolfgang Maier; Anton Nekrutenko; James Taylor; Steven Weaver

Journal article

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Bjoern Gruening, Nicholas Keener, Delphine Lariviere, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver

PLOS PATHOGENS | PUBLIC LIBRARY SCIENCE | Published : 2020

DOI: 10.1371/journal.ppat.1008643

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Abstract

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an ope..

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University of Melbourne Researchers

Simon Gladman Author Medicine, Dentistry and Health Sciences

Andrew Lonie Author Medicine, Dentistry and Health Sciences

Grants

Awarded by NIH

Awarded by NSF ABI Grant

Awarded by German Federal Ministry of Education and Research

Awarded by Research Foundation-Flanders (FWO)

Funding Acknowledgements

This work is funded by NIH Grant U41 HG006620 and NSF ABI Grant 1661497 to AN and JT. Usegalaxy.eu is supported by the German Federal Ministry of Education and Research grants 031L0101C and de.NBI-epi to BG. Galaxy and HyPhy integration is supported by NIH Grant R01 AI134384 to AN. Usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons through funding from the Australian Government National Collaborative Research Infrastructure Strategy. Hyphy.org development team is supported by NIH Grant R01GM093939 to SKP. Usegalaxy.be is supported by the Research Foundation-Flanders (FWO) grant I002919N and the Flemish Supercomputer Center (VSC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.