iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon; Hurwitz, Bonnie L.; Sullivan, Matthew B.

doi:10.1038/ismej.2016.89

Title: iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Journal Article · 15 July 2016 · The ISME Journal

DOI: https://doi.org/10.1038/ismej.2016.89 · OSTI ID:1473902

Bolduc, Benjamin ^[1]; Youens-Clark, Ken ^[2];

^[1]; Hurwitz, Bonnie L. ^[2]; Sullivan, Matthew B. ^[3]

The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
Univ. of Arizona, Tucson, AZ (United States). Dept. of Agricultural and Biosystems Engineering
The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. Dept. of Civil, Environmental and Geodetic Engineering

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

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Research Organization:: Univ. of Arizona, Tucson, AZ (United States); The Ohio State Univ., Columbus, OH (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Gordon and Betty Moore Foundation (United States)

Grant/Contract Number:: SC0010580; GBMF4491; GBMF4733; GBMF3305; GBMF3790

OSTI ID:: 1473902

Journal Information:: The ISME Journal, Vol. 11; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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