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

协作研究：更新 iVirus - CyVerse 支持的微生物病毒分析工具包

• 批准号: 2149505
• 负责人: Matthew Sullivan
• 金额: $ 99.96万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-15 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2149505&HistoricalAwards=false
• 关键词: Collaborative; Research; Updating; iVirus; CyVerse

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.

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，以及在健康和失调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伤、基因流动和代谢重编程具有很强的生态系统相关性。因此，越来越多的研究人员问“病毒如何影响我的系统？”。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，成为了解生态系统影响的另一个窗口。这些生态系统到全球规模的进步的根源是大数据（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。这些功能是通过网络基础设施实现的，使生物学家能够处理数据，而无需专家编程知识和硬件维护问题。在过去的十年中，随着公共数据存储库中测序数据的积累，微生物分析平台的数量和复杂性也在稳步增加。虽然此类平台广泛地使生物学家能够充分利用大数据，但这些平台上几乎不存在以病毒为中心的工具，这极大地限制了病毒组和微生物组科学。 iVirus 是一个由 NSF 资助的应用程序和资源生态系统，代表着以病毒为中心的首选分析平台，它已通过培训研讨会和网络研讨会、出版物和公开演示实现民主化，以建立庞大、活跃且不断增长的用户群。通过这些场所，已经确定了新的能力需求。该奖项旨在通过组织病毒序列空间来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 病毒的新工具增强主要是双链 DNA 病毒的工具包；改进研究病毒感染细胞（virocell）的分析；并开发新的长读病毒组学分析。 iVirus 用户群将通过广泛的培训、推广和 iVirus 门户网站改进来扩大，其中包括通过 25 人合作者教职顾问委员会提供的反馈，以及通过 Protocols.io、VERVE-NET 社区页面、专用 Twitter 和电子邮件帐户以及基于网络的评论表提供 iVirus“实时协议”的反馈；通过病毒组学模块/网络研讨会和当地实践课程，为直接参与该项目的不同学员（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；以及来自新的早期职业研究员世界病毒组学网络研讨会系列的被动参与机会，以及 (ii) 2 个专门用于技术支持的门户网站（MAVERIC 门户）以及 iVirus 资源、数据集、工具/应用程序和协议的认知和位置（iVirus 门户）。这些努力预计将使 iVirus 用户群扩大到病毒组和微生物组科学及相关领域的数万名研究人员。要在线查找 iVirus，请访问 https://www.ivirus.us/。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。