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

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 open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.

SUBMITTER: Baker D

PROVIDER: S-EPMC7425854 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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

Baker Dannon D van den Beek Marius M Blankenberg Daniel D Bouvier Dave D Chilton John J Coraor Nate N Coppens Frederik F Eguinoa Ignacio I Gladman Simon S Grüning Björn B Keener Nicholas N Larivière Delphine D Lonie Andrew A Kosakovsky Pond Sergei S Maier Wolfgang W Nekrutenko Anton A Taylor James J Weaver Steven S

PLoS pathogens 20200813 8

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 yea ...[more]

PMID: 32790776

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Dataset Information

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

Publications

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

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