iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
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 Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1835644
- Resource Type:
- Published Article
- Journal Name:
- ISME Communications
- Additional Journal Information:
- Journal Name: ISME Communications Journal Volume: 1 Journal Issue: 1; Journal ID: ISSN 2730-6151
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Bolduc, Benjamin, Zablocki, Olivier, Guo, Jiarong, Zayed, Ahmed A., Vik, Dean, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam, Merchant, Nirav, Pett-Ridge, Jennifer, Roux, Simon, Vaughn, Matthew, and Sullivan, Matthew B. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. United States: N. p., 2021.
Web. doi:10.1038/s43705-021-00083-3.
Bolduc, Benjamin, Zablocki, Olivier, Guo, Jiarong, Zayed, Ahmed A., Vik, Dean, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam, Merchant, Nirav, Pett-Ridge, Jennifer, Roux, Simon, Vaughn, Matthew, & Sullivan, Matthew B. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. United States. https://doi.org/10.1038/s43705-021-00083-3
Bolduc, Benjamin, Zablocki, Olivier, Guo, Jiarong, Zayed, Ahmed A., Vik, Dean, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam, Merchant, Nirav, Pett-Ridge, Jennifer, Roux, Simon, Vaughn, Matthew, and Sullivan, Matthew B. Tue .
"iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology". United States. https://doi.org/10.1038/s43705-021-00083-3.
@article{osti_1835644,
title = {iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology},
author = {Bolduc, Benjamin and Zablocki, Olivier and Guo, Jiarong and Zayed, Ahmed A. and Vik, Dean and Dehal, Paramvir and Wood-Charlson, Elisha M. and Arkin, Adam and Merchant, Nirav and Pett-Ridge, Jennifer and Roux, Simon and Vaughn, Matthew and Sullivan, Matthew B.},
abstractNote = {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.},
doi = {10.1038/s43705-021-00083-3},
journal = {ISME Communications},
number = 1,
volume = 1,
place = {United States},
year = {Tue Dec 14 00:00:00 EST 2021},
month = {Tue Dec 14 00:00:00 EST 2021}
}
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