iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
Abstract
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 viromicsmore »
- Authors:
-
[1];
- 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
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States); The Ohio State Univ., Columbus, OH (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Gordon and Betty Moore Foundation (United States)
- OSTI Identifier:
- 1473902
- Grant/Contract Number:
- SC0010580; GBMF4491; GBMF4733; GBMF3305; GBMF3790
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 11; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; metagenomics; virology
Citation Formats
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B.. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States: N. p., 2016.
Web. doi:10.1038/ismej.2016.89.
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., & Sullivan, Matthew B.. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States. https://doi.org/10.1038/ismej.2016.89
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B.. Fri .
"iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure". United States. https://doi.org/10.1038/ismej.2016.89. https://www.osti.gov/servlets/purl/1473902.
@article{osti_1473902,
title = {iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure},
author = {Bolduc, Benjamin and Youens-Clark, Ken and Roux, Simon and Hurwitz, Bonnie L. and Sullivan, Matthew B.},
abstractNote = {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.},
doi = {10.1038/ismej.2016.89},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {2016},
month = {7}
}
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