High Performance Computer System for Biomolecular and Systems Modeling

用于生物分子和系统建模的高性能计算机系统

• 批准号: 7793018
• 负责人: Jason Robert Banfelder
• 金额: $ 48.07万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-10 至 2011-08-11
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7793018
• 关键词: Address; Advisory Committees; Alzheimer' s Disease; Arrhythmia; Award; Biochemistry; Biological Models; Biophysics; Cells; Cellular Structures; Communicable Diseases; Complement; Computer Systems; Computers; Data; Disease; Drug abuse; Environment; Equipment; Gender; Head; High Performance Computing; Housing; Human; Imagery; Institutes; Lead; Learning; Maintenance; Malignant Neoplasms; Molecular; Molecular Structure; N.I.H. Research Support; National Institute of Allergy and Infectious Disease; National Institute of Drug Abuse; National Institute of General Medical Sciences; National Institute of Neurological Disorders and Stroke; Nerve Degeneration; Occupations; Parkinson Disease; Physiology; Prevention therapy; Process; Research; Research Infrastructure; Research Personnel; Research Project Grants; Resources; Science; System; Technology; United States National Institutes of Health; Virus; Woman; Work; base; cluster computing; computing resources; density; experience; heart function; high end computer; innovation; instrumentation; member; men; professor; public health relevance; scientific computing; structural biology

DESCRIPTION (provided by applicant): This application for the acquisition of High Performance Computing (HPC) instrumentation is submitted by a Consortium of Investigators (COI) whose NIH-supported research is either entirely dependent on access to, or would benefit greatly from, the availability of such instrumentation. The COI represents a diverse spectrum of users from experienced major users of computation (e.g., Weinstein, Mehler, Shi, Andersen), to members whose research is turning towards computation driven by the underlying science (e.g., Boudker, Wu, Eliezer) and with the guidance of the experienced colleagues and an expert administrative and infrastructure management team headed by the PI. The group represents diversity in academic rank (5 Full Professors, 4 Assistant Professors), as well as gender (6 men, 3 women). Most importantly, the scope, breadth and depth of the science represented by the research of this COI are remarkable. Ranging from molecular biophysics (Andersen, Mehler, Shi, Weinstein) and structural biology (Blanchard, Boudker, Wu) to cell biochemistry (Eliezer), and integrated systems physiology (Clancy), the research addresses disease mechanisms in cancer (Blanchard, Wu), neurodegeneration (Eliezer), drug abuse (Weinstein), and infectious diseases (Wu); it is therefore being supported by several NIH Institutes (NIGMS, NIDA, HBLI, NINDS, NIAID, NIA). The application describes in detail how the requested computational resource, if awarded, will enable significant progress on the important research projects supported by the mentioned NIH institutes in the labs of the COI members. The proposed HPC compute cluster comprises a total of nearly 600 cores dedicated to HPC job processing, and has been tailored to the specific needs of the COI. Visualization and interactive graphics based analysis are major components of the work of this COI and are complemented by the advanced immersive visualization environment (CAVE) that will be integrated with the requested HPC cluster to enable the COI's many projects requiring interactive visualization. Taking advantage of the established human and infrastructure resources made available by the Institute for Computational Biomedicine (ICB) in which the cluster will be housed in a ready, dedicated high-density HPC data center located on the Weill Cornell campus, the cluster will be maintained for the COI by the staff of professionals in the Technology Management Team (TMT) headed by the PI. This professional team is fully supported by the ICB and is dedicated to the efficient maintenance of scientific computing resources and infrastructure in a well organized manner, adhering to the highest professional standards, as detailed in the application. The resource will be supervised by a Management and Advisory Committee (MAC) composed of cluster users, as well as an outside member with computational experience. Integrated with the infrastructure already available to maintain, manage and enhance it with related resources, the availability of the requested equipment will create a scientific and academic synergy within a diverse but highly collaborative group of outstanding investigators. PUBLIC HEALTH RELEVANCE: The high performance computer requested in this application will serve a group of experienced researchers supported by the NIH to make faster progress and deeper discoveries and innovation in their research on the mechanisms of various diseases including cancer, Alzheimer's, Parkinson's, drug abuse and infectious diseases. Their work depends on computers to learn the structure of molecular components of cells and viruses, and to describe mechanisms of heart function and cardiac arrhythmias. The advanced computer will make their work more productive and should lead to fast leads for therapies and prevention.

描述（由申请人提供）：本高性能计算（HPC）仪器采购申请由研究者联盟（COI）提交，其NIH支持的研究完全依赖于此类仪器的使用，或将从此类仪器的可用性中受益匪浅。COI代表了从有经验的主要计算用户（例如，Weinstein，Mehler，Shi，Andersen），其研究转向由基础科学驱动的计算的成员（例如，Boudker，Wu，Eliezer），并在经验丰富的同事和由PI领导的专家行政和基础设施管理团队的指导下进行。该小组在学术级别（5名正教授，4名助理教授）和性别（6名男子，3名妇女）方面表现出多样性。最重要的是，这个COI的研究所代表的科学的范围，广度和深度是显着的。从分子生物物理学（Andersen，Mehler，Shi，Weinstein）和结构生物学（Blanchard、Boudker、Wu）到细胞生物化学（Eliezer）和综合系统生理学（Clancy），该研究解决了癌症的疾病机制（Blanchard，Wu），神经变性（Eliezer），药物滥用（Weinstein）和传染病（Wu）;因此，它得到了几个NIH研究所（NIGMS，NIDA，HBLI，NINDS，NIAID，NIA）的支持。该申请详细描述了所请求的计算资源，如果被授予，将如何在COI成员实验室中由上述NIH研究所支持的重要研究项目上取得重大进展。拟议的HPC计算集群包括总共近600个专用于HPC作业处理的核心，并已根据COI的特定需求进行了量身定制。可视化和基于交互式图形的分析是COI工作的主要组成部分，并由高级沉浸式可视化环境（CAVE）补充，该环境将与所要求的HPC集群集成，以支持COI的许多需要交互式可视化的项目。利用计算生物医学研究所（ICB）提供的现有人力和基础设施资源，该集群将位于威尔康奈尔校园内的一个现成的专用高密度HPC数据中心，该集群将由PI领导的技术管理团队（TMT）的专业人员为COI进行维护。该专业团队得到ICB的全力支持，致力于以组织良好的方式有效维护科学计算资源和基础设施，遵守最高的专业标准，如申请中所述。该资源将由一个管理和咨询委员会（MAC）监督，该委员会由群集用户以及一名具有计算经验的外部成员组成。与现有的基础设施相结合，利用相关资源维护，管理和加强它，所要求的设备的可用性将在一个多样化但高度协作的优秀调查人员小组中产生科学和学术协同作用。 公共卫生关系：本申请中要求的高性能计算机将服务于NIH支持的一组经验丰富的研究人员，以便在癌症、阿尔茨海默氏症、帕金森氏症、药物滥用和传染病等各种疾病的机制研究中取得更快的进展和更深入的发现和创新。他们的工作依赖于计算机来学习细胞和病毒的分子成分的结构，并描述心脏功能和心律失常的机制。先进的计算机将使他们的工作更有成效，并应导致快速的治疗和预防。