Expanding the AnVIL (Analysis, Visualization, and Informatics Lab-space)

扩展 AnVIL（分析、可视化和信息学实验室空间）

• 批准号: 10748042
• 负责人: Enis Afgan
• 金额: $ 308.81万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-21 至 2028-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10748042
• 关键词: Acceleration; Bioconductor; Biomedical Research; Clinical; Clinical Research; Cloud Computing; Collaborations; Communities; Complex; Data; Data Science; Development; Disease; Education; Education and Outreach; Educational Curriculum; Educational process of instructing; Educational workshop; Engineering; Ensure; Environment; Ethnic Origin; Event; Galaxy; Genetic; Genome; Genomics; Genotype-Tissue Expression Project; Goals; Health; Human; Individual; Informatics; Infrastructure; Joints; Knowledge; Leadership; Lifting; Machine Learning; Medical; Mendelian disorder; Metadata; Methods; Minority-Serving Institution; Modeling; Monitor; Monograph; National Human Genome Research Institute; Needs Assessment; Participant; Persons; Phase; Property; Publishing; Research; Research Personnel; Resources; Running; Sampling; Secure; Services; Slide; Software Engineering; Software Tools; Students; System; Tissues; Training; Translating; Variant; Visualization; Work; cloud based; community partnership; computing resources; cost; cost efficient; dashboard; data access; data harmonization; data ingestion; design; empowerment; experience; genomic data; genomic platform; improved; innovation; interoperability; machine learning model; massive open online courses; new technology; next generation; online delivery; outreach; programs; reference genome; repository; scientific computing; success; systems research; task analysis; telomere; tool; usability

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) powers the next generation of computational genomic research. The AnVIL makes available several of the the most widely used analysis environments for genomics and biomedical research including Bioconductor, RStudio, Galaxy, Jupyter, Cromwell, and IGV in a secure, scalable, and accessible cloud-based environment. It currently houses >600,000 genomic samples from the largest NHGRI projects including the Centers for Common Disease Genomics (CCDG), the Centers for Mendelian Disease Genomics (CMG), the Telomere-to-Telomere (T2T) consortium, and the Genotype Tissue Expression (GTEx) project. Our user centered solution for data access, analysis, and visualization enables investigators across all levels of expertise to fully utilize genomic datasets using environments they are already familiar with, leveraging well engineered and optimized scientific computing infrastructure for greater efficiency and lower costs. In this second phase of the AnVIL, we will expand the AnVIL experience with several additional high-value services and capabilities with the goal of expanding the number of researchers using the platform and the depth of their research. In Aim 1, we will enhance the core platform in several innovative ways. First to support researchers transitioning into the cloud environment, we will work to simplify and optimize the research environment with new dashboards for monitoring costs and managing teams, along with optimizations to the APIs to run in a multi-cloud environment. Next we will optimize Galaxy in AnVIL to improve the user experience, enable cost-efficient computing, develop a workflow recommender system, and enable interoperability by integrating computing services across multiple clouds. Within Bioconductor, we will introduce new capabilities for reliable software engineering practices, enhance accessibility through monographs, curriculum authoring, and shiny apps; and optimize Bioconductor infrastructure and development for the cloud. Additionally, we will design and implement standards to ensure AnVIL is interoperable with other cloud-based research systems. In Aim 2, we will introduce four new scientific services to support critical analysis tasks. This includes services for enhanced machine learning capabilities, data harmonization and metadata autocompletion, new liftover services to translate genomic knowledge between reference genomes, and comprehensive variant discovery and analysis using long read sequencing. In Aim 3, we will expand our efforts for training and outreach. This will begin with focused high-impact events including community workshops and the AnVIL Champions Program, with the goal of seeding and developing community-driven support. We will also create scalable accessible videos and massive open online courses (MOOCs) leveraging new educational infrastructure we are developing. In Aim 4, we will continue our joint leadership with our AnVIL partners at the Broad, as well as welcome our new partners in the forthcoming AnVIL Clinical Resource (ACR) program.

NHGRI基因组数据科学分析，可视化和信息学实验室空间（AnVIL）为 下一代计算基因组研究AnVIL提供了几个最广泛的 用于基因组学和生物医学研究的分析环境，包括Bioconductor，RStudio，Galaxy， 在一个安全、可扩展且可访问的基于云的环境中使用EQUIPYTER、Cromwell和IGV。目前，房屋 来自最大的NHGRI项目的超过600，000个基因组样本，包括常见疾病中心 基因组学（CCDG），孟德尔疾病基因组学中心（CMG），端粒到端粒（T2 T） 基因型组织表达（Genotype Tissue Expression，GTEx）我们以用户为中心的数据访问解决方案， 分析和可视化使所有专业水平的研究人员能够充分利用基因组数据集 使用他们已经熟悉的环境，利用精心设计和优化的科学 计算基础设施，以提高效率和降低成本。在AnVIL的第二阶段，我们将 通过几项附加的高价值服务和功能扩展AnVIL体验，目标是 扩大使用该平台的研究人员数量和研究深度。在目标1中，我们 以多种创新方式加强核心平台。首先支持研究人员过渡到云计算 环境，我们将努力简化和优化研究环境， 监控成本和管理团队，沿着优化API以在多云环境中运行 环境接下来我们将在AnVIL中优化Galaxy，提升用户体验，实现高性价比 计算，开发工作流推荐系统，并通过集成计算实现互操作性 跨多个云的服务。在Bioconductor内部，我们将为可靠的软件引入新功能 工程实践，通过专著、课程编写和闪亮的应用程序增强可访问性; 优化Bioconductor基础设施和云开发。此外，我们将设计和 实施标准，以确保AnVIL与其他基于云的研究系统互操作。在目标2中， 将推出四项新的科学服务，以支持关键分析任务。这包括增强的服务 机器学习功能，数据协调和元数据自动完成，新的提升服务， 在参考基因组之间转换基因组知识，以及全面的变异发现和分析 使用长读取测序。在目标3中，我们将扩大培训和外联工作。这将开始 通过集中的高影响力活动，包括社区研讨会和AnVIL冠军计划， 播种和发展社区驱动的支持的目标。我们还将创建可扩展的无障碍视频 以及利用我们正在开发的新教育基础设施的大规模开放式在线课程（MOOC）。在 目标4，我们将继续与我们在Broad的AnVIL合作伙伴共同领导，并欢迎我们的 在即将到来的AnVIL临床资源（ACR）计划的新伙伴。