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Genes (Basel). 2019 Sep 16;10(9). pii: E714. doi: 10.3390/genes10090714.

NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. connorrp@ncbi.nlm.nih.gov.
2
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. jamesbr@ncbi.nlm.nih.gov.
3
Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia. jan.buchmann@sydney.edu.au.
4
KU Leuven, Department of Microbiology & Immunology, Rega Institute, Leuven BE3000, Belgium. ward.deboutte@kuleuven.be.
5
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. redwards@sdsu.edu.
6
KU Leuven, Department of Microbiology & Immunology, Rega Institute, Leuven BE3000, Belgium. joan.marti@kuleuven.be.
7
Lab of Cellular Oncology, NCI, NIH, Bethesda, MD 20892-4263, USA. mike.tisza@nih.gov.
8
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. zaluninvv@ncbi.nlm.nih.gov.
9
Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia. Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá 111711, Colombia. js.andrade10@uniandes.edu.co.
10
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. vcantualessioroble@sdsu.edu.
11
D'Amour & Associates, 11839 Hilltop Drive, Los Altos Hills, CA 94024, USA. mike@damourventures.com.
12
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. efremova2@ncbi.nlm.nih.gov.
13
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. fleischmannlc@ncbi.nlm.nih.gov.
14
Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia. Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá 111711, Colombia. lm.forero10@uniandes.edu.co.
15
Department of Genetics, University Medical Center Groningen, Groningen 9713AV, The Netherlands. s.garmaeva@umcg.nl.
16
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. mgiluso@sdsu.edu.
17
Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA. cody.glickman@ucdenver.edu.
18
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. margaret.henderson@sdsu.edu.
19
Bioinformatics and Systems Biology Program, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA. bkellman@eng.ucsd.edu.
20
Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA. dk1313t63@gmail.com.
21
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. leubsdor@ncbi.nlm.nih.gov.
22
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. klevi@sdsu.edu.
23
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA. slevi3509@sdsu.edu.
24
Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA. suman.b.pakala@vumc.org.
25
Department of Laboratory Medicine, University of Washington Virology, 1616 Eastlake Ave E, Seattle, WA 98102, USA. vpeddu@uw.edu.
26
Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85716, USA. aponsero@email.arizona.edu.
27
MITRE Corporation, 7515 Colshire Drive, McLean, VA 22102-7539, USA. eribeiro@mitre.org.
28
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. froy@hsph.harvard.edu.
29
University of Tsukuba, Ibaraki 305-8575, Japan. lindsayannerutter@gmail.com.
30
Boyce Thompson Institute, Ithaca, NY 14853, USA. ss2489@cornell.edu.
31
Bioscience Division, Los Alamos National Lab, Los Alamos, NM 87545, USA. migun@lanl.gov.
32
Department of Laboratory Medicine, University of Washington Virology, 1616 Eastlake Ave E, Seattle, WA 98102, USA. rcs333@uw.edu.
33
Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85716, USA. mattmiller899@email.arizona.edu.
34
Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA. tully.bj@gmail.com.
35
School of Natural Sciences, University of California Merced, Merced, CA 95343, USA. cturkington@ucmerced.edu.
36
Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85716, USA. kyclark@email.arizona.edu.
37
KU Leuven, Department of Microbiology & Immunology, Rega Institute, Leuven BE3000, Belgium. bert.vanmechelen@kuleuven.be.
38
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA. ben.busby@nih.gov.

Abstract

A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.

KEYWORDS:

SRA; STRIDES; cloud computing; hackathon; infrastructure; metagenomic; viruses

PMID:
31527408
DOI:
10.3390/genes10090714
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