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: 9360135
• 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/9360135
• 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; Institutes; Institution; Internet; Intuition; 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; experimental study; genome analysis; genome-wide; 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.

项目摘要 Globus Genomics由芝加哥大学计算研究所开发， 基因组学分析平台作为Amazon Web Services上的软件即服务运行，由Globus提供支持 还有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， 高质量的服务，具有最先进的功能，可帮助简化数据移动， 基因组学分析管道，自动执行这些管道，并在非常大的规模上运行分析。 弹性计算基础设施。Globus Genomics公司开发了三年， 包括华盛顿大学，芝加哥大学， 华盛顿大学圣路易斯分校、乔治敦大学和约翰霍普金斯大学。潜力巨大， 扩大服务使用的需求，以满足现有的快速增长的基因组学分析需求 用户和新用户的大型社区。我们现在提出的工作，将扩大效用和影响， Globus Genomics通过提供（1）可扩展性，可由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 调用结构变体，（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）用于大规模分析的端到端和摘要视图的强大仪表板。 这些改进将通过以下关键领域的发展得以实现： Globus Genomics计算框架可实现标准和 针对大型和超大型数据集的新型NGS分析工作流程;创建和维护最先进的 用于变体调用、全基因组分析、RNASeq和ChipSeq的管道，这涉及计算 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Amazon Web Services上;创建分析和优化框架，以实现自动化、成本和/或 在大型云系统上对NGS应用程序和工作流进行时间优化配置; 自动计算供应框架。赠款将使我们能够满足以下关键需求： 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， 否则无法轻易获得这种能力。