No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics
- Author
- Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens (UGent) , Ignacio Eguinoa (UGent) , Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor and Steven Weaver
- Organization
- 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.
- Keywords
- Immunology, Genetics, Molecular Biology, Microbiology, Parasitology, Virology, CORONAVIRUS
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8687394
- MLA
- Baker, Dannon, et al. “No More Business as Usual : Agile and Effective Responses to Emerging Pathogen Threats Require Open Data and Open Analytics.” PLOS PATHOGENS, edited by Carolyn B. Coyne, vol. 16, no. 8, 2020, doi:10.1371/journal.ppat.1008643.
- APA
- Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Chilton, J., Coraor, N., … Weaver, S. (2020). No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics. PLOS PATHOGENS, 16(8). https://doi.org/10.1371/journal.ppat.1008643
- Chicago author-date
- Baker, Dannon, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, et al. 2020. “No More Business as Usual : Agile and Effective Responses to Emerging Pathogen Threats Require Open Data and Open Analytics.” Edited by Carolyn B. Coyne. PLOS PATHOGENS 16 (8). https://doi.org/10.1371/journal.ppat.1008643.
- Chicago author-date (all authors)
- Baker, Dannon, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, and Steven Weaver. 2020. “No More Business as Usual : Agile and Effective Responses to Emerging Pathogen Threats Require Open Data and Open Analytics.” Ed by. Carolyn B. Coyne. PLOS PATHOGENS 16 (8). doi:10.1371/journal.ppat.1008643.
- Vancouver
- 1.Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, et al. No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics. Coyne CB, editor. PLOS PATHOGENS. 2020;16(8).
- IEEE
- [1]D. Baker et al., “No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics,” PLOS PATHOGENS, vol. 16, no. 8, 2020.
@article{8687394,
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.}},
articleno = {{e1008643}},
author = {{Baker, Dannon and van den Beek, Marius and Blankenberg, Daniel and Bouvier, Dave and Chilton, John and Coraor, Nate and Coppens, Frederik and Eguinoa, Ignacio and Gladman, Simon and Grüning, Björn and Keener, Nicholas and Larivière, Delphine and Lonie, Andrew and Kosakovsky Pond, Sergei and Maier, Wolfgang and Nekrutenko, Anton and Taylor, James and Weaver, Steven}},
editor = {{Coyne, Carolyn B.}},
issn = {{1553-7366}},
journal = {{PLOS PATHOGENS}},
keywords = {{Immunology,Genetics,Molecular Biology,Microbiology,Parasitology,Virology,CORONAVIRUS}},
language = {{eng}},
number = {{8}},
pages = {{8}},
title = {{No more business as usual : agile and effective responses to emerging pathogen threats require open data and open analytics}},
url = {{http://doi.org/10.1371/journal.ppat.1008643}},
volume = {{16}},
year = {{2020}},
}
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