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: 2149506
• 负责人: Kelly Wrighton
• 金额: $ 33.07万
• 依托单位: Colorado 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=2149506&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各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，以及在健康和生态失调状态之间调节动物和植物微生物群。然而，感染这些微生物的病毒越来越多地被认为通过杀死，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问：“病毒是如何影响我的系统的？”这导致了多样性目录的爆炸和病毒感染细胞的研究，或病毒细胞，作为另一个窗口，生态系统的影响。这些生态系统到行星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、共享和分析功能来理解它的能力。这些能力是由网络基础设施实现的，这些网络基础设施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，微生物分析平台的数量和复杂性随着公共数据库中积累的测序数据而稳步增加。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，代表了以病毒为重点的分析平台，它已经通过培训研讨会和网络研讨会，出版物和公开演示实现了民主化，以建立一个庞大，活跃和不断增长的用户群。通过这些场所，确定了新的能力需求。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病毒的新工具来增强主要是双链DNA病毒的工具包;改进研究病毒感染细胞（病毒细胞）的分析;并开发新的长读病毒组学分析。iVirus用户基础将通过广泛的培训、外联和iVirus门户网站的改进得到扩大，包括通过一个由25人组成的合作者教员咨询委员会提供反馈，以及通过protocols.io、VERVE-NET社区网页、专门的推特和电子邮件账户以及网上评论表提供iVirus“现场协议”;为直接参与该项目的各种学员提供培训机会（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，通过病毒组学模块/网络研讨会和当地实践课程;和被动参与的机会，从一个新的早期职业研究员世界病毒组学网络研讨会系列，和（ii）2个门户网站的具体技术支持（MAVERIC门户）以及iVirus的资源、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的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。要在网上找到iVirus，请访问https://www.ivirus.us/.This奖项反映了NSF的法定使命，并被认为值得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来支持。