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.

现在，微生物被认为是潜水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，并调节健康和不良生物之间的动物和植物菌群。但是，感染这些微生物的病毒越来越多地通过杀伤，基因流和代谢重编程来认识到强大的生态系统相关性。那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爆炸，并研究了感染病毒的细胞或virocells，这是一个进入生态系统影响的窗口。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），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。这些功能由网络基础设施实现，这些网络基础设施使生物学家能够无需专家计划知识和硬件维护问题处理数据。在过去的十年中，随着公共数据存储库中积累的测序数据，微生物分析平台的数量和复杂性已悄然增加。尽管这样的平台广泛地赋予生物学家充分利用大数据，但以病毒为中心的工具在这些平台上实际上是不存在的，这极大地限制了病毒瘤和微生物组科学。 Ivirus是由NSF资助的应用程序和资源的生态系统，代表了以病毒为中心的分析平台，它通过培训研讨会和网络研讨会，出版物和公开演讲而被民主化，以建立大型，活跃的用户基础。通过这些场所，已经确定了新的功能。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；通过研究单链DNA和所有RNA病毒的新工具来增强主要双链DNA病毒工具包；改善研究病毒感染细胞的分析（Virocells）；并开发新的长阅读病毒分析。 Ivirus用户群将通过广泛的培训，外展和Ivirus Web门户网站改进来扩展，其中包括通过25人合作委员会的反馈以及通过Ivirus的“实时协议”通过protastios.io，Verve-Net社区页面，专门的Twitter和网络帐户和基于Web的评论的形式；为直接参与该项目的潜水员学员的培训机会（6个数据分析的本科生，1名研究生，2名PostDocs 4研究科学家）和更广泛的研究社区通过病毒学模块 /网络研讨会和当地的动手课程；以及新的早期职业生涯研究员世界病毒式网络研讨会系列的被动参与机会，以及（ii）2 Web门户网站（Maveric Portal），以及意识以及ivirus资源，数据集，工具/应用程序和协议（Ivirus Portal）的意识和位置。预计这些努力将把ivirus用户群增长到数以万计的病毒瘤和微生物科学领域的研究人员，以及相关领域。要在线查找Ivirus，请访问https://www.ivirus.us/.this奖，反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响评估标准，被认为是珍贵的支持。