Collaborative Research: Updating iVirus - the CyVerse-powered analytical toolkit for viruses of microbes

微生物现在被认为是多种生态系统过程的基础，包括海洋生物地球化学循环，土壤肥力和功能的播种和维持，以及在健康和非生态状态之间调节动植物微生物群。然而，人们越来越认识到感染这些微生物的病毒通过杀死、基因流动和代谢重编程与生态系统有很强的相关性。因此，越来越多的研究人员提出“病毒是如何影响我的系统的？”这导致了多样性目录的爆炸式增长，以及对病毒感染细胞或病毒细胞的研究，作为研究生态系统影响的另一个窗口。这些从生态系统到行星规模的进步的根本是大数据（即下一代测序），以及我们通过可扩展的存储、搜索、共享和分析能力来理解它的能力。这些能力是由网络基础设施实现的，使生物学家能够在没有专业编程知识和硬件维护问题的情况下处理数据。在过去的十年中，随着公共数据库中测序数据的积累，微生物分析平台的数量和复杂性稳步增加。虽然这些平台广泛地使生物学家能够充分利用大数据，但在这些平台上几乎不存在以病毒为重点的工具，这极大地限制了病毒组和微生物组科学。iVirus是美国国家科学基金会（nsf）资助的应用程序和资源生态系统，代表了以病毒为重点的分析平台，它通过培训研讨会、网络研讨会、出版物和公开演讲实现了民主化，建立了一个庞大、活跃且不断增长的用户群。通过这些场所，已经确定了新的功能需求。该奖项旨在通过组织病毒序列空间以创建参考基因组和分类资源来满足这些需求；用研究单链DNA和所有RNA病毒的新工具增强以双链DNA为主的病毒工具箱；改进研究病毒感染细胞（病毒细胞）的分析方法；发展新的长读病毒组学分析。iVirus的用户基础将通过广泛的培训、推广和iVirus门户网站的改进来扩大，其中包括一个由25人组成的教员顾问委员会的反馈，以及通过协议从iVirus的“实时协议”中获得的反馈。io， VERVE-NET社区页面，专用twitter和电子邮件帐户，以及基于web的评论表单；通过病毒组学模块/网络研讨会和当地实践课程，为直接参与项目的不同学员（6名数据分析本科生，1名研究生，2名博士后，4名研究科学家）和更广泛的研究社区提供培训机会；（ii） 2个专门提供技术支持的门户网站（MAVERIC门户网站），以及了解和定位iVirus的资源、数据集、工具/应用程序和协议（iVirus门户网站）。这些努力预计将使iVirus的用户群增加到数万名病毒组和微生物组科学及相关领域的研究人员。要在线查找iVirus，请访问https://www.ivirus.us/.This该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Microbes are now recognized as fundamental to diverse ecosystem processes, including oceanic biogeochemical cycling, the seeding and maintenance of soil fertility and function, and modulating animal and plant microbiota between healthy and dysbiotic states. However, viruses that infect these microbes are increasingly recognized for strong ecosystem relevance through killing, gene flow, and metabolic reprogramming. Thus, more and more researchers ask ‘how are viruses affecting my system?’. This has led to diversity catalogs exploding and the study of virus-infected cells, or virocells, as another window into ecosystem impacts. At the root of these ecosystem- to planetary-scale advances are big data (i.e., Next Generation Sequencing) and our ability to make sense of it through scalable storage, searching, sharing, and analytical capabilities. These capabilities are enabled by cyberinfrastructures that empower biologists to handle data without expert programmatic knowledge and hardware maintenance concerns. Over the last decade, the number and complexity of microbial analysis platforms have steadily increased alongside sequencing data accumulating in public data repositories. While such platforms are broadly empowering biologists to make the most of big data, virus-focused tools are virtually non-existent across these platforms, which greatly limits virome and microbiome science. iVirus is an NSF-funded ecosystem of apps and resources that represent the go-to virus-focused analytical platform and it has been democratized through training workshops and webinars, publications, and public presentations to establish a large, active, and growing user-base. Through these venues, new capabilities needs have been identified. This award seeks to fill these needs by organizing virus sequence space to create reference genome and taxonomic resources; augmenting the predominantly double-stranded DNA virus toolkit with new tools for studying single-stranded DNA and all RNA viruses; improving analyses for studying virus-infected cells (virocells); and developing new long-read viromics analytics. The iVirus user-base will be broadened through extensive training, outreach, and iVirus web portal improvements that include feedback via a 25-person faculty advisory committee of collaborators, as well as from iVirus ‘live protocols’ via protocols.io, VERVE-NET community pages, dedicated twitter and email accounts, and a web-based comments form; training opportunities for diverse trainees directly involved in the project (6 data analytics undergraduates, 1 graduate student, 2 postdocs 4 research scientists) and the broader research community through viromics modules / webinars and a local hands-on course; and passive engagement opportunities from a new early career researcher World Viromics Webinar Series, and (ii) 2 web portals specific for technical support (the MAVERIC portal) and awareness and location for iVirus’ resources, datasets, tools/apps, and protocols (the iVirus portal). Together these efforts are expected to grow the iVirus user base to tens of thousands of researchers in virome and microbiome science, and related fields. To find iVirus online go to https://www.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.