No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
Genre
Journal articleDate
2020-08-13Author
Baker, Dannonvan den Beek, Marius
Blankenberg, Daniel
Bouvier, Dave
Chilton, John
Coraor, Nate
Coppens, Frederik
Eguinoa, Ignacio
Gladman, Simon
Grüning, Björn
Keener, Nicholas
Larivière, Delphine
Lonie, Andrew
Pond, Sergei

Maier, Wolfgang
Nekrutenko, Anton
Taylor, James
Weaver, Steven

Department
BiologySubject
SARS CoV 2Genome analysis
Genomics
COVID 19
SARS
Transmissible gastroenteritis coronavirus
Open source software
Preprocessing
Permanent link to this record
http://hdl.handle.net/20.500.12613/230
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https://doi.org/10.1371/journal.ppat.1008643Abstract
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.Citation
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.1008643Citation to related work
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PLOS Pathogens, Vol. 16, Issue 8ADA compliance
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http://dx.doi.org/10.34944/dspace/214