Hardening Globus Genomics to make large-scale genomics analysis available for everybody

强化 Globus Genomics 使每个人都可以进行大规模基因组学分析

• 批准号: 9766875
• 负责人: Ian Foster
• 金额: $ 39.5万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-28 至 2020-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9766875
• 关键词: Address; Adopted; Area; Award; Big Data; Bioinformatics; Cardiovascular Diseases; Chicago; Cloud Computing; Communities; Complex Analysis; Consensus; Data; Data Analyses; Data Set; Development; Diabetes Mellitus; Docking; Ensure; Galaxy; Genomics; Grant; Human Resources; Infrastructure; Institutes; Institution; Internet; Intuition; Malignant Neoplasms; Maps; Methods; Modality; Monitor; Movement; Neurodevelopmental Disorder; Performance; Provider; Research; Research Personnel; Resources; Running; Services; Specific qualifier value; Structure; System; Technology; Time; Universities; Variant; Washington; Work; analysis pipeline; computer framework; cost; dashboard; design; exome; experimental study; genome analysis; genome-wide; genomic data; genomic platform; innovation; novel; outreach; prospective; repository; scale up; software as a service; software systems; success; terabyte; tool; transcriptome sequencing; web services; whole genome

Project Summary Globus Genomics has been developed at the Computation Institute, University of Chicago as an advanced genomics analysis platform running as a Software-as-a-Service on Amazon Web Services, powered by Globus and Galaxy. It was developed to meet the needs of both researchers and core lab providers who require a high-quality service with state-of-the-art capabilities to help streamline data movement, simplify the creation of genomics analysis pipelines, automate the execution of those pipelines, and run analysis at very large scale on elastic compute infrastructure. Globus Genomics, under development for three years, has been used extensively by researchers at leading institutions, including University of Washington, University of Chicago, Washington University St. Louis, Georgetown University, and Johns Hopkins. There is significant potential and demand to expand use of the service to meet the rapidly growing genomics analysis needs of both existing users and large communities of new users. We now propose work that will amplify the utility and impact of Globus Genomics by providing (1) scalability to 1000s of simultaneous analyses by 1000s of users, (2) support for state-of-art high performance workflows and tools, including large-scale imputation analysis and consensus calling on structural variants, (3) automated cost and performance optimization to slash cloud computing costs and turnaround times, and (4) powerful dashboards for end-to-end and summary views of large-scale analyses. These enhancements will be enabled by development in the following key areas: enhancing and extending the Globus Genomics computational framework to enable high-performance reliable execution of standard and novel NGS analysis workflows on large and extremely large datasets; creating and maintaining state-of-the-art pipelines for variant calling, whole genome analysis, RNASeq and ChipSeq, which involves computationally profiling the latest versions of tools and understanding different computational modalities for optimal execution on Amazon Web Services; creating a profiling and optimization framework to enable automated, cost- and/or time-optimal configuration of NGS applications and workflows on large cloud systems; and creating an automatic computational provisioning framework. The grant award would allow us to address key needs of current and prospective users and thus to provide an important bioinformatics platform to researchers who otherwise could not easily access such capabilities.

项目概要 Globus Genomics 是由芝加哥大学计算研究所开发的一种先进的基因组学技术。 基因组学分析平台作为软件即服务在 Amazon Web Services 上运行，由 Globus 提供支持 和银河。它的开发是为了满足研究人员和核心实验室提供商的需求，他们需要 具有最先进功能的高质量服务，有助于简化数据移动、简化数据创建 基因组学分析管道，自动执行这些管道，并在 弹性计算基础设施。 Globus Genomics 历时三年开发，现已使用 受到华盛顿大学、芝加哥大学等领先机构研究人员的广泛关注 华盛顿大学圣路易斯分校、乔治城大学和约翰霍普金斯大学。有巨大的潜力和 需要扩大该服务的使用，以满足现有和快速增长的基因组分析需求 用户和大型新用户社区。我们现在提出的工作将扩大以下方面的效用和影响： Globus Genomics 提供 (1) 可扩展性，可让 1000 个用户同时进行 1000 个分析，(2) 支持 用于最先进的高性能工作流程和工具，包括大规模插补分析和共识 呼吁结构变体，（3）自动化成本和性能优化以削减云计算成本 和周转时间，以及 (4) 强大的仪表板，用于大规模分析的端到端和摘要视图。 这些增强功能将通过以下关键领域的开发来实现：增强和扩展 Globus Genomics 计算框架可实现标准和标准的高性能可靠执行 针对大型和超大型数据集的新颖 NGS 分析工作流程；创造并保持最先进的 用于变异调用、全基因组分析、RNASeq 和 ChipSeq 的管道，其中涉及计算 分析最新版本的工具并了解不同的计算模式以实现最佳执行 在亚马逊网络服务上；创建一个分析和优化框架，以实现自动化、成本和/或 大型云系统上 NGS 应用程序和工作流程的时间优化配置；并创建一个 自动计算配置框架。赠款将使我们能够满足以下人员的关键需求： 当前和潜在的用户，从而为研究人员提供一个重要的生物信息学平台 否则无法轻松访问此类功能。