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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 van den Beek, Marius Blankenberg, Daniel Bouvier, Dave Chilton, John Coraor, Nate Coppens, Frederik Eguinoa, Ignacio Gladman, Simon Grüning, Björn
Baker, Dannon
van den Beek, Marius
Blankenberg, Daniel
Bouvier, Dave
Chilton, John
Coraor, Nate
Coppens, Frederik
Eguinoa, Ignacio
Gladman, Simon
Grüning, Björn
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Journal article
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2020-08-13
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Biology
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https://doi.org/10.1371/journal.ppat.1008643
Abstract
The current state of much of the Wuhan pneumonia virus (COVID-19) 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 ten 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 COVID-19 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and to (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.
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Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, et al. (2020) No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS Pathog 16(8): e1008643. https://doi.org/10.1371/journal.ppat.1008643
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PLOS
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PLOS Pathogens, Vol. 16, Issue 8
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