High Performance Computing Instrumentation for the Yale Center for Genome Analysis

耶鲁大学基因组分析中心的高性能计算仪器

• 批准号: 10416696
• 负责人: SHRIKANT M MANE
• 金额: $ 119.81万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-25 至 2023-06-24
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10416696
• 关键词: 6 year old; Architecture; Basic Science; Biology; Biomedical Research; Brain Diseases; Capital; Cardiovascular Diseases; Cells; Communities; Country; Data; Data Storage and Retrieval; Development; Enhancers; Ensure; Funding; Genes; Genome; High Performance Computing; Infrastructure; Institution; Investigation; Investments; Life; Malignant Neoplasms; Medicine; MicroRNAs; Modeling; Nature; Performance; Production; Publications; Publishing; Reporting; Research; Research Personnel; Science; Talents; United States National Institutes of Health; Universities; autism spectrum disorder; base; cluster computing; congenital heart disorder; data infrastructure; genome analysis; high standard; improved; innovation; instrumentation; next generation sequencing; operation; success; technology development; tool

The advent of next-generation sequencing (NGS) is revolutionizing biology and medicine and is rapidly becoming a standard tool for investigation. Recognizing the tremendous potential of NGS, Yale University establish the Yale Center for Genome Analysis (YCGA) in 2009. YCGA has led the development of a new genome center model, focusing on a centralized facility with the highest standards of innovation, data production and analysis, but which is open access to the community rather than having projects selected by an oversight group. This scalable model has provided broad access to NGS, which has spurred innovation and eliminated barriers to experimentation by new users. By virtue of its substantial contribution to technology development for data production and analysis, accompanied by high profile scientific discoveries and success in competing for NIH funding, YCGA has emerged as one of the leading genome centers in the country. High-performance computation is indispensable for NGS operation. YCGA produces an average of more than 30 terabases of sequence data per month, necessitating infrastructure for data storage, analysis and interpretation. YCGA’s current dedicated HPC instrumentation has served more than 1,000 users from 327 institutions/departments as well as many non-Yale investigators, and is making an enormous contribution to biomedicine (since 2015 published >500 research articles including, >70 publications in Science, Nature, Cell, N Engl J Med) reporting new genes contributing to autism, cardiovascular disease, cancer, and congenital diseases of the heart and brain, as well as fundamental advances in understanding of enhancer function, mechanisms of microRNA formation, and mechanisms of evolutionary change. YCGA's dedicated compute cluster and storage is predominantly 6 years old and near the end of its productive life. This architecture must be replaced and upgraded if YCGA is to continue to serve its users. The requested HPC instrumentation will increase computational capacity to match growing demand, will greatly improve data storage and networking, and will reduce the power and cooling requirements. The strengths of this proposal include; (1) an efficient and effective centralized facility serving an extremely diverse, large and productive mostly NIH funded investigator user base; (2) the demonstrated ability of YCGA to effectively integrate cutting edge data production and analysis for the benefit of hundreds of NIH funded Yale and non-Yale researchers, (3) and the extensive infrastructure and expertise that is available to bring the requested instrumentation online and to oversee its continuous use. Yale University has made a major investment in capital and institutional talent to build a first-rate infrastructure that has proven highly successful. The requested instrumentation will be highly leveraged upon this existing infrastructure ensuring that it will be of high value and broad impact on NIH supported biomedical and basic research within and beyond the Yale community.

新一代测序 (NGS) 的出现正在迅速改变生物学和医学领域 成为调查的标准工具。耶鲁大学认识到 NGS 的巨大潜力 2009 年建立耶鲁大学基因组分析中心 (YCGA)。YCGA 领导了新的基因组分析中心的开发 基因组中心模型，专注于具有最高创新、数据生产标准的集中设施 和分析，但这是对社区的开放访问，而不是由监督选择项目 团体。这种可扩展的模型提供了对 NGS 的广泛访问，从而刺激了创新并消除了 新用户尝试的障碍。凭借其对技术发展的重大贡献 数据生产和分析，伴随着引人注目的科学发现和竞争的成功 在 NIH 的资助下，YCGA 已成为美国领先的基因组中心之一。 NGS运行离不开高性能计算。 YCGA 平均产出更多 每月超过 30 TB 的序列数据，需要数据存储、分析和分析的基础设施 解释。 YCGA 目前的专用 HPC 仪器已为 327 个国家和地区的 1,000 多名用户提供服务 机构/部门以及许多非耶鲁研究人员，并正在做出巨大贡献 生物医学（自 2015 年以来发表了超过 500 篇研究文章，其中包括超过 70 篇发表在 Science、Nature、Cell、 N Engl J Med）报告了导致自闭症、心血管疾病、癌症和先天性疾病的新基因 心脏和大脑疾病，以及对增强子功能理解的根本进展， microRNA 形成机制和进化变化机制。 YCGA的专用计算 集群和存储主要已经使用了 6 年，并且已接近其生产寿命的终点。该架构必须 如果 YCGA 要继续为其用户提供服务，则需要更换和升级。所需的 HPC 仪器将 增加计算能力以满足不断增长的需求，将大大改善数据存储和网络， 并将降低电力和冷却要求。 该提案的优点包括： (1) 一个高效、有效的集中设施，服务于 极其多样化、庞大且富有成效的、主要由 NIH 资助的研究者用户群； (2) 所表现出的能力 YCGA 有效整合尖端数据生产和分析，造福数百家 NIH 资助耶鲁大学和非耶鲁大学的研究人员，(3) 以及可用于的广泛基础设施和专业知识 将所需的仪器联网并监督其持续使用。 耶鲁大学在资金和机构人才方面进行了大量投资，打造一流的大学 事实证明非常成功的基础设施。所请求的仪器将被高度利用 现有的基础设施确保其对 NIH 支持的生物医学具有高价值和广泛影响 以及耶鲁大学社区内外的基础研究。