Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Autor: Dillon MR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Bolyen E; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Adamov A; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Zürich, Switzerland., Belk A; Department of Animal Sciences, Cell and Molecular Biology Special Academic Unit, Colorado State University, Fort Collins, Colorado, United States of America., Borsom E; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Burcham Z; Department of Animal Sciences, Cell and Molecular Biology Special Academic Unit, Colorado State University, Fort Collins, Colorado, United States of America., Debelius JW; Centre for Translational Microbiome Research, Department of Microbiology, Tumor, and Cancer Biology, Karolinska Institutet, Stockholm, Sweden., Deel H; Department of Animal Sciences, Cell and Molecular Biology Special Academic Unit, Colorado State University, Fort Collins, Colorado, United States of America., Emmons A; Department of Animal Sciences, Cell and Molecular Biology Special Academic Unit, Colorado State University, Fort Collins, Colorado, United States of America., Estaki M; Department of Pediatrics, University of California San Diego, San Diego, California, United States of America., Herman C; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Keefe CR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Morton JT; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, United States of America., Oliveira RRM; Environmental Genomics, Instituto Tecnológico Vale, Belém, Pará, Brazil., Sanchez A; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Simard A; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Vázquez-Baeza Y; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, California, United States of America., Ziemski M; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Zürich, Switzerland., Miwa HE; Academic Programs, Foundation for Advanced Education in the Sciences at the National Institutes of Health, Bethesda, Maryland, United States of America., Kerere TA; Academic Programs, Foundation for Advanced Education in the Sciences at the National Institutes of Health, Bethesda, Maryland, United States of America., Coote C; Academic Programs, Foundation for Advanced Education in the Sciences at the National Institutes of Health, Bethesda, Maryland, United States of America., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, United States of America., Knight R; Department of Pediatrics, University of California San Diego, San Diego, California, United States of America.; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, California, United States of America., Oliveira G; Environmental Genomics, Instituto Tecnológico Vale, Belém, Pará, Brazil., Gopalasingam P; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom., Kaehler BD; School of Science, University of New South Wales, Canberra, Australia., Cope EK; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America., Metcalf JL; Department of Animal Sciences, Cell and Molecular Biology Special Academic Unit, Colorado State University, Fort Collins, Colorado, United States of America., Robeson Ii MS; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America., Bokulich NA; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Zürich, Switzerland., Caporaso JG; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2021 Jun 24; Vol. 17 (6), pp. e1009056. Date of Electronic Publication: 2021 Jun 24 (Print Publication: 2021).
DOI: 10.1371/journal.pcbi.1009056
Abstrakt: In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn't work well, and what we plan to do differently in future workshops.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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