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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
KU Leuven, Department of Microbiology & Immunology, Rega Institute, Leuven BE3000, Belgium
Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
Lab of Cellular Oncology, NCI, NIH, Bethesda, MD 20892-4263, USA
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
D’Amour & Associates, 11839 Hilltop Drive, Los Altos Hills, CA 94024, USA
Department of Genetics, University Medical Center Groningen, Groningen 9713AV, The Netherlands
Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA
Bioinformatics and Systems Biology Program, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Department of Laboratory Medicine, University of Washington Virology, 1616 Eastlake Ave E, Seattle, WA 98102, USA
Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85716, USA
MITRE Corporation, 7515 Colshire Drive, McLean, VA 22102-7539, USA
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
University of Tsukuba, Ibaraki 305-8575, Japan
Boyce Thompson Institute, Ithaca, NY 14853, USA
Bioscience Division, Los Alamos National Lab, Los Alamos, NM 87545, USA
Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA
School of Natural Sciences, University of California Merced, Merced, CA 95343, USA
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 714;
Received: 26 July 2019 / Revised: 5 September 2019 / Accepted: 5 September 2019 / Published: 16 September 2019
(This article belongs to the Special Issue Viral Diagnostics Using Next-Generation Sequencing)
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. View Full-Text
Keywords: metagenomic; viruses; SRA; STRIDES; hackathon; infrastructure; cloud computing metagenomic; viruses; SRA; STRIDES; hackathon; infrastructure; cloud computing
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MDPI and ACS Style

Connor, R.; Brister, R.; Buchmann, J.P.; Deboutte, W.; Edwards, R.; Martí-Carreras, J.; Tisza, M.; Zalunin, V.; Andrade-Martínez, J.; Cantu, A.; D’Amour, M.; Efremov, A.; Fleischmann, L.; Forero-Junco, L.; Garmaeva, S.; Giluso, M.; Glickman, C.; Henderson, M.; Kellman, B.; Kristensen, D.; Leubsdorf, C.; Levi, K.; Levi, S.; Pakala, S.; Peddu, V.; Ponsero, A.; Ribeiro, E.; Roy, F.; Rutter, L.; Saha, S.; Shakya, M.; Shean, R.; Miller, M.; Tully, B.; Turkington, C.; Youens-Clark, K.; Vanmechelen, B.; Busby, B. NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes 2019, 10, 714.

AMA Style

Connor R, Brister R, Buchmann JP, Deboutte W, Edwards R, Martí-Carreras J, Tisza M, Zalunin V, Andrade-Martínez J, Cantu A, D’Amour M, Efremov A, Fleischmann L, Forero-Junco L, Garmaeva S, Giluso M, Glickman C, Henderson M, Kellman B, Kristensen D, Leubsdorf C, Levi K, Levi S, Pakala S, Peddu V, Ponsero A, Ribeiro E, Roy F, Rutter L, Saha S, Shakya M, Shean R, Miller M, Tully B, Turkington C, Youens-Clark K, Vanmechelen B, Busby B. NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes. 2019; 10(9):714.

Chicago/Turabian Style

Connor, Ryan, Rodney Brister, Jan P. Buchmann, Ward Deboutte, Rob Edwards, Joan Martí-Carreras, Mike Tisza, Vadim Zalunin, Juan Andrade-Martínez, Adrian Cantu, Michael D’Amour, Alexandre Efremov, Lydia Fleischmann, Laura Forero-Junco, Sanzhima Garmaeva, Melissa Giluso, Cody Glickman, Margaret Henderson, Benjamin Kellman, David Kristensen, Carl Leubsdorf, Kyle Levi, Shane Levi, Suman Pakala, Vikas Peddu, Alise Ponsero, Eldred Ribeiro, Farrah Roy, Lindsay Rutter, Surya Saha, Migun Shakya, Ryan Shean, Matthew Miller, Benjamin Tully, Christopher Turkington, Ken Youens-Clark, Bert Vanmechelen, and Ben Busby. 2019. "NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements" Genes 10, no. 9: 714.

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