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: 9239936
• 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/9239936
• 关键词: Address; Adopted; Area; Arts; Award; Big Data; Bioinformatics; Breeding; Cardiovascular Diseases; Chicago; Cloud Computing; Communities; Complex; Consensus; Data; Data Set; Development; Diabetes Mellitus; Ensure; Galaxy; Genomics; Grant; Human Resources; Institutes; Institution; Internet; Malignant Neoplasms; Maps; Methods; Modality; Monitor; Movement; Neurodevelopmental Disorder; Performance; Provider; Research; Research Infrastructure; Research Personnel; Resources; Running; Services; Specific qualifier value; System; Technology; Time; Universities; Variant; Washington; Work; computer framework; cost; dashboard; design; exome; genome analysis; genomic platform; innovation; meetings; novel; outreach; prospective; repository; research study; 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.

项目摘要 Globus基因组学是在芝加哥大学计算研究所开发的 基因组学分析平台作为Amazon Web服务上的软件服务，由Globus提供支持 和银河系。它的开发是为了满足需要一个需要一个的研究人员和核心实验室提供者的需求 具有最先进功能的高质量服务，可帮助简化数据移动，简化创建 基因组学分析管道，自动执行这些管道，并大规模运行分析 弹性计算基础架构。开发了三年的Globus基因组学已被使用 包括华盛顿大学芝加哥大学在内的主要机构的研究人员广泛 华盛顿大学圣路易斯，乔治敦大学和约翰·霍普金斯。有巨大的潜力和 扩大服务的需求，以满足现有的快速增长的基因组分析需求 用户和大型新用户社区。现在，我们提出的工作将扩大 通过（1）通过1000秒的用户提供（1）同时分析，（2）支持通过（1）提供（1）支持，（2）支持通过（1）支持，（2）支持通过（1）支持，（1）支持，（1）支持，（2） 用于最先进的高性能工作流程和工具，包括大规模的归纳分析和共识 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观点。 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基因组学计算框架，以实现高性能的标准执行和 大型且极大的数据集上的新型NGS分析工作流程；创建和维护最先进的 用于变异调用的管道，整个基因组分析，RNASEQ和CHIPSEQ，涉及计算 分析工具的最新版本，并了解不同的计算方式以进行最佳执行 在亚马逊网络服务上；创建分析和优化框架以启用自动化，成本和/或 大型云系统上NGS应用程序和工作流程的时间优势配置；并创建一个 自动计算供应框架。赠款裁决将使我们能够满足 当前和潜在的用户，因此为研究人员提供重要的生物信息学平台 否则，无法轻易访问此类功能。