Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

实施基因组数据科学分析、可视化和信息学实验室空间 (AnVIL)

• 批准号: 9789931
• 负责人: VINCENT JAMES CAREY
• 金额: $ 240.24万
• 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 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9789931
• 关键词: 3-Dimensional; Accounting; Advisory Committees; Agave; Authorization documentation; Bioconductor; Biological Models; Biomedical Research; Communities; Computer Analysis; Computer software; Cost Savings; Coupling; Data; Data Aggregation; Data Science; Data Set; Data Storage and Retrieval; Disease; Education and Outreach; Educational workshop; Engineering; Ensure; Environment; FAIR principles; Foundations; Future; Galaxy; Genetic; Genome; Genomics; Genotype-Tissue Expression Project; Goals; Health; Human; Human Resources; Image; Imagery; Informatics; Infrastructure; Leadership; Life; Methods; National Human Genome Research Institute; Pattern; Persons; Provider; Research; Research Infrastructure; Research Personnel; Resources; Running; Scheme; Science; Secure; Security; Self-Direction; Services; Standardization; Structure; Supercomputing; The Cancer Genome Atlas; Training; Training Support; Update; Visualization software; Work; cloud based; computational platform; cost; cyber infrastructure; data access; data space; design; experience; flexibility; genome sciences; genomic data; indexing; innovation; interoperability; next generation; novel; precision genomic medicine; programs; scientific computing; statistics; tool

Project Summary: The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab‐space (AnVIL) will power the next generation of computational genomic research. We will develop the AnVIL environment using the leading national‐scale cyberinfrastructure as the foundation supporting the most widely‐used analysis environments and frameworks vetted by NHGRI researchers. Our user‐centered solution for data access, analysis, and visualization will enable 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. Aim 1: Engineer the AnVIL Data and Compute Platform. We will leverage the TACC Science Cloud and the Agave Science‐As‐A‐Service platform to deploy a cloud‐based environment supporting the data storage, access, and compute needs of the NHGRI research community. Aim 2. Develop APIs for Data and Compute Access. To maximize the domain‐wide impact of AnVIL, we will draw on community efforts and our own collective experience supporting diverse genomic analyses to define access standards and to design and implement AnVIL APIs. Aim 3. Build an AnVIL metaportal integrating widely used analysis platforms. We will create a single metaportal residing within TACC's Science Cloud providing a unified view of users' data and activities, provenance and billing, and access to several of the most widely used workbenches for genomic research. These workbenches include Bioconductor, Galaxy, the Genome Modeling System, Juypter, and RStudio. The metaportal will also provide access to the most popular genomic visualization tools. Aim 4. Develop novel data aggregation, indexing and query schemes to increase analysis efficiency and reduce cost. We will build approaches, including indexing and pre‐computation of key statistics, to make better use of existing (e.g., TCGA, GTEx) and future large datasets with the goal of increasing data utility and decreasing the cost of posing scientific queries against massive datasets. Aim 5: Develop training and outreach infrastructure and materials. We will build support for training directly in the AnVIL platform, including tight coupling to MOOC style courses, self‐directed training materials, and support materials for conducting online and in‐person training workshops. Aim 6: Engage in effective project governance and assessment. We will establish a leadership and management structure involving key stakeholders from NHGRI, including program staff and the NHGRI appointed Data Steering Committee and External Advisory Committee. The key innovation of this work is our leveraging of existing hardware, software, and human resources to create a practical and pragmatic solution to the challenge of building the AnVIL.

项目摘要：NHGRI基因组数据科学分析，可视化和信息学实验室空间 （Anvil）将为下一代计算基因组研究提供动力。我们将发展砧 使用领先的国家范围网络基础设施作为支持最大的基金会的环境 NHGRI研究人员审查的广泛分析环境和框架。我们以用户为中心的解决方案 为了进行数据访问，分析和可视化将使各个级别的专业知识的研究人员充分利用 基因组数据集使用他们已经熟悉的环境，利用良好设计和 优化的科学计算基础设施，以提高效率和较低的成本。 AIM 1：工程砧数据和计算平台。我们将利用TACC科学云和 Agave Science-As-A-Service平台部署基于云的环境，支持数据存储， 访问和计算NHGRI研究社区的需求。 AIM 2。开发用于数据的API并计算访问。为了最大化砧座的范围范围的影响，我们将 利用社区努力和我们自己的集体经验，支持潜水员基因组分析以定义 访问标准并设计和实施砧API。 AIM 3。建立一个砧式元皮质整合广泛使用的分析平台。我们将创建一个 居住在TACC的科学云中的元皮托尔提供了对用户数据和活动的统一视图， 出处和计费，并访问一些用于基因组研究的最广泛使用的工作台。 这些工作台包括生物导体，银河系，基因组建模系统，Juypter和Rstudio。这 Metaportal还将提供最受欢迎的基因组可视化工具。 目标4。开发新的数据聚合，索引和查询方案，以提高分析效率和 降低成本。我们将建立方法，包括关键统计数据的索引和预先计算，以使 更好地利用现有（例如TCGA，GTEX）和未来的大型数据集，目的是增加数据实用程序和 降低对大量数据集提出科学查询的成本。 目标5：开发培训和外展基础设施和材料。我们将支持培训 直接在砧台上，包括与MOOC风格课程的紧密耦合，自定向的培训 材料和支持材料，用于在线和人工培训研讨会。 目标6：进行有效的项目治理和评估。我们将建立领导 涉及NHGRI的主要利益相关者的管理结构，包括计划人员和NHGRI 指定的数据指导委员会和外部咨询委员会。 这项工作的关键创新是我们利用现有的硬件，软件和人力资源来 为建立砧座的挑战创建实用且务实的解决方案。