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

Galaxy and HyPhy developments teams, View ORCID ProfileAnton Nekrutenko, Sergei L Kosakovsky Pond
doi: https://doi.org/10.1101/2020.02.21.959973
1The Pennsylvania State University, USA
Anton Nekrutenko
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  • ORCID record for Anton Nekrutenko
  • For correspondence: anton@nekrut.org spond@temple.edu
Sergei L Kosakovsky Pond
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  • For correspondence: anton@nekrut.org spond@temple.edu
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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.

Footnotes

  • usegalaxy.org1,2,3, usegalaxy.eu4, usegalaxy.org.au5,6, usegalaxy.be7,8 and hyphy.org9 development teams

  • General edits and updates to author affiliations and funding

  • https://github.com/galaxyproject/SARS-CoV-2

  • https://doi.org/10.5281/zenodo.3685264

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 25, 2020.
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No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics
Galaxy and HyPhy developments teams, Anton Nekrutenko, Sergei L Kosakovsky Pond
bioRxiv 2020.02.21.959973; doi: https://doi.org/10.1101/2020.02.21.959973
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No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics
Galaxy and HyPhy developments teams, Anton Nekrutenko, Sergei L Kosakovsky Pond
bioRxiv 2020.02.21.959973; doi: https://doi.org/10.1101/2020.02.21.959973

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