High Performance Computing Instrumentation for Yale University Biomedical HPC Cen

描述(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、电子显微结构确定、分子动力学、结构生物学、高通量药物筛选和蛋白质组学)，这些进步越来越受到耶鲁大学研究人员可用的“个人计算机”和小型部门群无法充分和及时地分析所产生的海量数据的限制。在生物医学研究中使用更高吞吐量技术的必然趋势是产生越来越多的海量数据集，这导致耶鲁生物医学高性能计算(HPC)中心的使用量大幅增加，以至于其仪器设备不再能满足激增的需求。虽然最近的生物技术突破将我们带到了令人兴奋的系统级生物医学研究的门槛，但要利用这些技术，耶鲁大学的研究人员将需要获得比HPC中心现在更强大的高性能计算机，以及相应水平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生物医学HPC中心能够满足日益增长的需求，即使用更强大的计算机来处理阻碍生物医学研究的具有挑战性的但可服从的问题。该应用程序的优势包括：将继续支持Biomedical HPC中心的非常多样化和富有成效的研究人员用户基础；Keck实验室近30年来证明的监督、持续操作和维护尖端生物技术仪器并将其带到数百名耶鲁大学和非耶鲁大学研究人员手中的能力；可用于使所需仪器上线并监督和支持其持续使用的广泛基础设施和专业知识；将容纳所需仪器的Biomedical HPC中心已证明成功，以及耶鲁大学及其医学院的精心规划和非常坚定的支持，以确保这一应用程序代表着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回应。 公共卫生相关性：如果该应用程序得到资助，所请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，以分析耶鲁大学校园内将由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海量数据。拟议的研究结果将对生物医学研究做出非常实质性的贡献，这些研究将扩展和增加我们对胚胎发育、表观遗传学、造血分化、炎症、转移、蛋白质弹性、蛋白质折叠；感染性疾病，如艾滋病毒和流感，以及非传染性疾病，如高血压、癌症、糖尿病、肾脏疾病、哮喘、淀粉样蛋白疾病、冠状动脉疾病、药物成瘾、阅读困难、肺气肿和青光眼的知识。 创造就业机会 对这项申请的资助将使耶鲁大学及其医学院(见所附的支持函)维持一名系统管理人员(年成本为125,000美元)和四名博士级别工作人员的三年雇佣，其中两人在Keck实验室的HPC和生物信息学资源(每年补贴600,000美元)，三年总计2,175,000美元。 环境影响 我们认为，与现有仪器相比，所请求的高性能计算仪器的电气使用/CPU-hr计算时间更少，如果为该应用程序提供资金，现有仪器将被替换。

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.