High Performance Computing Instrumentation for Yale University Biomedical HPC Cen

耶鲁大学生物医学 HPC 中心高性能计算仪器

• 批准号: 7841409
• 负责人: ROBERT DEAN BJORNSON
• 金额: $ 58.8万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2013-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7841409
• 关键词: Biomedical Research; Computers; DNA Sequence Analysis; Data; Data Set; Electrons; Ensure; Genome; Genomics; High Performance Computing; Housing; Image; Laboratories; Microscopic; Personal Computers; Preclinical Drug Evaluation; Proteomics; Research Infrastructure; Research Personnel; Structure; System; Technology; Universities; Ursidae Family; Variant; base; high end computer; high throughput technology; instrumentation; medical schools; meetings; molecular dynamics; next generation; programs; protein folding; response; simulation; structural biology; success; trend

DESCRIPTION (provided by applicant): The tenet of this application is that progress in biomedical research is increasingly dependent upon high throughput biotechnological advances (e.g., high throughput "next generation" DNA sequencing, analysis of genomic data for variants, cross-genome comparisons, statistical simulations, protein folding, imaging, electron microscopic structure determination, molecular dynamics, structural biology, high-throughput drug screening, and proteomics) that are increasingly limited by the inability of the "personal computers" and small departmental clusters available to Yale investigators to adequately and timely analyze the enormous volume of the resulting data. The inexorable trend toward the use of higher throughput technologies in biomedical research that produce ever more massive data sets has resulted in substantially increasing the use of the Yale Biomedical High Performance Computing (HPC) Center such that its instrumentation can no longer meet the surging demand. While recent biotechnological breakthroughs have brought us to the exciting threshold of systems level biomedical research, to take advantage of these technologies Yale investigators will need access to far more powerful high performance computers than are now within the HPC Center and a commensurate level of technical programming and systems administration support. The requested high performance computing instrumentation would enable the Yale Biomedical HPC Center to meet the ever increasing need for bringing more powerful computers to bear on challenging, yet amenable problems that stand in the way of biomedical research. The strengths of this application include the very diverse and productive investigator user base that would Continue to support the Biomedical HPC Center, the almost 30 years of demonstrated ability of the Keck Laboratory to oversee and continually operate and maintain sophisticated biotechnological instrumentation and to bring it within reach of hundreds of Yale and non-Yale researchers, the extensive infrastructure and expertise that is available to bring the requested instrumentation on-line and to oversee and support its continuous use, the demonstrated success of the Biomedical HPC Center that would house the requested instrumentation, and the careful planning and very firm support of both Yale University and its School of Medicine to ensure that this application represents a coordinated and well conceived institutional response to the challenge of providing the high performance computing needed to continue to drive biomedical research forward. PUBLIC HEALTH RELEVANCE: If this application is funded, the requested High Performance Computing instrumentation would provide biomedical researchers' with sufficient shared computing power to analyze the vast amounts of data that will be collected across the Yale campus by an ever increasing number of laboratories using state-of-the-art high throughput DNA sequencing, proteomics, and other technologies. The results of the proposed research would make a very substantial contribution to biomedical research that would extend to and increase our knowledge of embryonic development, epigenetic, hematopoietic differentiation, inflammation, metastasis, protein elasticity, protein folding; infectious diseases such as HIV and influenza, and non-infectious diseases such as hypertension, cancer, diabetes, renal diseases, asthma, amyloid diseases, coronary artery disease, drug addiction, dyslexia, emphysema, and glaucoma. Job Creation Funding of this application would commit Yale University and its Medical School (see attached support letters) to maintaining three years of employment for one Systems administration staff (annual cost is $125,000) and four Ph.D.-level staff, two each in the Keck Laboratory's HPC and Bioinformatics Resources (annual subsidy is $600,000) for a three year total of $2,175,000. Environmental Impact We believe that electrical use/CPU-hr of computing time is less on the requested HPC instrumentation than it is on the existing instrumentation that would be replaced if this application is funded.

描述（由申请人提供）：本申请的宗旨是生物医学研究的进展越来越依赖于高通量生物技术的进步（例如，高通量"下一代" DNA测序、变异体的基因组数据分析、跨基因组比较、统计模拟、蛋白质折叠、成像、电子显微镜结构测定、分子动力学、结构生物学、高通量药物筛选、和蛋白质组学），这些技术越来越受到"个人电脑"耶鲁大学的研究人员可以利用小型部门集群来充分和及时地分析大量的数据。在生物医学研究中使用更高吞吐量技术的必然趋势产生了越来越多的海量数据集，这导致耶鲁大学生物医学高性能计算（HPC）中心的使用量大幅增加，其仪器无法满足激增的需求。虽然最近的生物技术突破已经把我们带到了系统级生物医学研究的令人兴奋的门槛，但要利用这些技术，耶鲁大学的研究人员需要获得比HPC中心现在更强大的高性能计算机，以及相应的技术编程和系统管理支持。所要求的高性能计算仪器将使耶鲁大学生物医学HPC中心能够满足日益增长的需求，使更强大的计算机承担具有挑战性的，但经得起考验的问题，站在生物医学研究的道路上。 该应用程序的优势包括非常多样化和富有成效的研究者用户群，这将继续支持生物医学HPC中心，凯克实验室近30年来证明有能力监督和持续操作和维护复杂的生物技术仪器，并使其成为数百名耶鲁大学和非耶鲁大学研究人员的研究对象，广泛的基础设施和专业知识，可使所需的仪器上线，并监督和支持其持续使用，生物医学HPC中心的成功证明，将容纳所需的仪器，以及耶鲁大学及其医学院的精心规划和非常坚定的支持，以确保该应用程序代表了对提供继续推动生物医学研究所需的高性能计算的挑战的协调和精心设计的机构响应。 公共卫生关系：如果这项申请获得资助，所要求的高性能计算仪器将为生物医学研究人员提供足够的共享计算能力，以分析耶鲁校园内越来越多的实验室使用最先进的高通量DNA测序，蛋白质组学和其他技术收集的大量数据。拟议研究的结果将对生物医学研究作出非常重大的贡献，这将扩大和增加我们对胚胎发育、表观遗传、造血分化、炎症、转移、蛋白质弹性、蛋白质折叠的知识;感染性疾病如HIV和流感，和非感染性疾病如高血压、癌症、糖尿病、肾病、哮喘、淀粉样蛋白疾病、冠状动脉疾病，药物成瘾、诵读困难、肺气肿和青光眼。 创造就业 这项申请的资金将使耶鲁大学及其医学院（见所附的支持信）维持一名系统管理人员（每年费用为125，000美元）和四名博士的三年就业。该计划包括两名高级职员，分别在凯克实验室的HPC和生物信息学资源中心工作（每年补贴60万美元），三年共资助217.5万美元。 环境影响 我们认为，所要求的HPC仪器上的电气使用/CPU小时计算时间比现有仪器上的要少，如果该应用程序获得资助，现有仪器将被替换。

项目成果

Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.

使用 DNA 序列多态性和分歧检测蛋白质编码基因内选择强度的区域变异。

• DOI: 10.1093/molbev/msx213
• 发表时间: 2017
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Zhao,Zi-Ming;Campbell,MichaelC;Li,Ning;Lee,DanielSW;Zhang,Zhang;Townsend,JeffreyP
• 通讯作者: Townsend,JeffreyP