Next generation informatics to elucidate viral ecology and ecosystem impacts in nature

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Microbes are now appreciated for their roles in human health and disease, in promoting plant growth, and cycling nutrients in the oceans and soils. More recently, it has been recognized that the viruses that infect these microbes influence both the microbes and their communities through selective killing, moving genes between them, and reprogramming their host's metabolism during infection. Because viruses are so tiny, and most cannot be currently grown in laboratories, we are reliant upon decoding their biology through "reading" their stories via molecular sequencing techniques. This project seeks to augment iVirus, a collection of software tools (apps) and databases that leverages the NSF-funded CyVerse CyberInfrastructure (CI) to help researchers store, read and interpret these viral stories. Through development of new apps and curation of existing databases, the project will establish new analyses and features for researchers, directly train several undergraduate students, graduate students, and postdocs, and will provide two international training workshops to better "see" the viruses in their research.The microbiome is increasingly recognized to drive the nutrient and energy cycles that fuel Earth's diverse ecosystems, with their viruses modulating these impacts through killing, horizontal gene transfer, and metabolic reprogramming during infection. With the recent emergence of quantitative, sequence-based methods to comprehensively explore virus diversity in nature, the precise roles that viruses play can be increasingly elucidated. To perform these analyses, the iVirus platform was established in 2017 as part of the NSF-funded CyVerse CyberInfrastructure. iVirus currently includes apps, databases, and live documentation designed to enable researchers to better identify and analyze virus sequences by integrating and enhancing access to (meta)genomic sequence datasets and functions in the context of the NSF-funded CyVerse CyberInfrastructure. This project seeks to significantly augment iVirus in three ways: (i) aggregate and upgrade current viral ecogenomic capabilities, (ii) develop an integrated viral ecogenomic analytical pipeline, and (iii) establish direct connections and inter-operability across key databases and independent cyberinfrastructure environments. Beyond augmenting iVirus capabilities at CyVerse, we will actively seek to maximize its impact and utility for researchers through key partnerships with other existing tools (e.g., DOE Joint Genome Institute IMG/VR database). We will also continue to collect and be responsive to feedback provided through the CyVerse and the protocols.io reporting platforms, as well as collaborator and general user beta-testing and subsequent feedback on releases. Finally, we'll provide training at all levels through peer-reviewed publications, talks, and dedicated international workshops to enable the broader research community. The results of this project can be found at the iVirus website, http://ivirus.us/ .This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.