tetano
Editor, Senior Moderator
PLoS Pathog
. 2020 Aug 13;16(8):e1008643.
doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug.
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
Dannon Baker[SUP] 1 [/SUP], Marius van den Beek[SUP] 2 [/SUP], Daniel Blankenberg[SUP] 3 [/SUP], Dave Bouvier[SUP] 2 [/SUP], John Chilton[SUP] 2 [/SUP], Nate Coraor[SUP] 2 [/SUP], Frederik Coppens[SUP] 4 5 [/SUP], Ignacio Eguinoa[SUP] 4 5 [/SUP], Simon Gladman[SUP] 6 7 [/SUP], Bj?rn Gr?ning[SUP] 8 [/SUP], Nicholas Keener[SUP] 2 [/SUP], Delphine Larivi?re[SUP] 2 [/SUP], Andrew Lonie[SUP] 6 [/SUP], Sergei Kosakovsky Pond[SUP] 9 [/SUP], Wolfgang Maier[SUP] 8 [/SUP], Anton Nekrutenko[SUP] 2 [/SUP], James Taylor[SUP] 1 [/SUP], Steven Weaver[SUP] 9 [/SUP]
Affiliations
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.
. 2020 Aug 13;16(8):e1008643.
doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug.
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
Dannon Baker[SUP] 1 [/SUP], Marius van den Beek[SUP] 2 [/SUP], Daniel Blankenberg[SUP] 3 [/SUP], Dave Bouvier[SUP] 2 [/SUP], John Chilton[SUP] 2 [/SUP], Nate Coraor[SUP] 2 [/SUP], Frederik Coppens[SUP] 4 5 [/SUP], Ignacio Eguinoa[SUP] 4 5 [/SUP], Simon Gladman[SUP] 6 7 [/SUP], Bj?rn Gr?ning[SUP] 8 [/SUP], Nicholas Keener[SUP] 2 [/SUP], Delphine Larivi?re[SUP] 2 [/SUP], Andrew Lonie[SUP] 6 [/SUP], Sergei Kosakovsky Pond[SUP] 9 [/SUP], Wolfgang Maier[SUP] 8 [/SUP], Anton Nekrutenko[SUP] 2 [/SUP], James Taylor[SUP] 1 [/SUP], Steven Weaver[SUP] 9 [/SUP]
Affiliations
- PMID: 32790776
- DOI: 10.1371/journal.ppat.1008643
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.