iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Benjamin Bolduc; Olivier Zablocki; Jiarong Guo; Ahmed A Zayed; Dean Vik; Paramvir Dehal; Elisha M Wood-Charlson; Adam Arkin; Nirav Merchant; Jennifer Pett-Ridge; Simon Roux; Matthew Vaughn; Matthew B Sullivan

doi:10.1038/s43705-021-00083-3

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

ISME Commun. 2021 Dec 14;1(1):77. doi: 10.1038/s43705-021-00083-3.

Authors

Benjamin Bolduc^{1

2

3}, Olivier Zablocki^{1

2

3}, Jiarong Guo^{1

2

3}, Ahmed A Zayed^{1

2

3}, Dean Vik¹, Paramvir Dehal⁴, Elisha M Wood-Charlson⁴, Adam Arkin^{4

5}, Nirav Merchant⁶, Jennifer Pett-Ridge^{7

8}, Simon Roux⁹, Matthew Vaughn¹⁰, Matthew B Sullivan^{11

12

13

14}

Affiliations

¹ Department of Microbiology, The Ohio State University, Columbus, OH, USA.
² Center of Microbiome Science, Columbus, OH, USA.
³ EMERGE Biology Integration Institute, Columbus, OH, USA.
⁴ Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁵ Department of Bioengineering, University of California, Berkeley, CA, USA.
⁶ The University of Arizona, Tucson, AZ, USA.
⁷ Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
⁸ Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA.
⁹ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁰ Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA.
¹¹ Department of Microbiology, The Ohio State University, Columbus, OH, USA. [email protected].
¹² Center of Microbiome Science, Columbus, OH, USA. [email protected].
¹³ EMERGE Biology Integration Institute, Columbus, OH, USA. [email protected].
¹⁴ Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA. [email protected].

Abstract

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into 'iVirus' on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus's functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy's Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as "live" protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Publication types

Review

Abstract

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