Attendees at the Ohio State University viromics workshop gather for a meal. (Photo by David Paez)
By Shelley Littin and Michaela Webb, 2016 NASA Space Grant Intern at CyVerse
A workshop on viral genomics – dubbed “viromics” – hosted October 18-20 at Ohio State University (OSU) by CyVerse collaborator Matthew Sullivan brought dozens of viral and microbial ecologists from nine different countries together for three days of community science empowerment.
Researchers affiliated with the Sullivan Lab created iVirus, a community-oriented platform that uses CyVerse cyberinfrastructure to offer big data storage capacity and a host of analytical tools specifically for viral ecologists.
“Previously viral ecologists had to partner with a bioinformatician or computer science person. A lot of the capabilities these tools offer were inaccessible to the researcher,” said Ben Bolduc, a postdoctoral researcher in the Sullivan Lab who is largely responsible for iVirus' creation along with University of Arizona assistant professor Bonnie Hurwitz, who spearheads the iMicrobe project, and her team. “iVirus is bringing a lot of challenging-to-use bioinformatics tools related to viral ecology and putting them in the hands of viral ecologists.”
Technological advances made in the field of viral ecology over the past decade have overcome many obstacles to collecting viral metagenomic data. This has led to a proliferation of data and a subsequent need for tools with analytical and storage capacity to handle that data. iVirus offers these tools, documented in the ISME Journal, a Nature publication, on a single platform that is easy for viral ecologists to use.
Biology has changed in important ways as a result of virome-enabled science, noted Sullivan, who is an OSU associate professor in microbiology and civil, environmental, and geodetic engineering. "We now know that viruses carry genes to directly manipulate carbon, nitrogen, and sulfur-cycling in the oceans,, and viruses best predict how the oceans sink carbon" he said. "Also, we have near-completely catalogued the ocean viruses globally, with some 800 viral genera."
iVirus uses CyVerse hardware and infrastructure, which makes more tools available to researchers than otherwise would be possible. These tools can be used together to analyze data, which eliminates the need for viral ecologists to use multiple programs, expensive hardware, and computer memory for their big data projects.
In addition to providing tools for data analysis, iVirus is linked to an archive of important viral datasets, including some collected by now-discontinued projects, stored in the CyVerse community folder and linked to the iVirus website.
Since it became available, iVirus has attracted dozens of users, Bolduc said. “It shows the enthusiasm when researchers realize that these tools that historically were only accessible to the ‘big labs’ are now available to individual researchers anywhere in the world.”
Support from the Gordon and Betty Moore Foundation and OSU College of Arts and Sciences and a venue provided by the OSU Mathematical Biosciences Institute enabled the hosts to offer the workshop to their international community free of charge.