High Performance Computing Instrumentation for Yale University Biomedical HPC Cen

描述（由申请人提供）：本应用程序的原则是，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)，由于耶鲁大学的研究人员无法充分、及时地分析海量的结果数据，这些研究越来越受到“个人电脑”和小型部门集群的限制。在生物医学研究中使用高通量技术产生越来越多的海量数据集是不可阻挡的趋势，这导致耶鲁生物医学高性能计算（HPC）中心的使用大幅增加，以至于其仪器已经无法满足激增的需求。虽然最近的生物技术突破已经将我们带到了令人兴奋的系统级生物医学研究的门槛，但为了利用这些技术，耶鲁大学的研究人员将需要比现在的高性能计算机中心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高性能计算中心能够满足日益增长的需求，使更强大的计算机承担生物医学研究道路上具有挑战性但可解决的问题。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基础，这将继续支持生物医学高性能计算中心，凯克实验室近30年来证明了其监督、持续操作和维护复杂生物技术仪器的能力，并将其提供给数百名耶鲁大学和非耶鲁大学的研究人员，广泛的基础设施和专业知识，可以使所要求的仪器上线，并监督和支持其持续使用，将容纳所要求的仪器的生物医学高性能计算中心的成功展示；以及耶鲁大学及其医学院的精心规划和坚定支持，以确保这一应用程序代表了一个协调和深思熟虑的机构响应，以提供继续推动生物医学研究向前发展所需的高性能计算。

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.