Office of Intramural Research Scientific Computing Facility

校内研究办公室科学计算设施

• 批准号: 10004480
• 负责人: Anthony Fletcher
• 金额: $ 92.44万
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10004480
• 关键词: Architecture; Authorization documentation; Biological; Catalogs; Collaborations; Communities; Complement; Computational Science; Computer Security; Computer Systems; Computer software; Computers; Custom; Data; Data Analyses; Database Management Systems; Databases; Development; Engineering; Environment; Exons; Funding; Gap Junctions; Gene Expression; Grant; Health; Home environment; Human; Image; Imagery; Infrastructure; Intramural Research; Joints; Laboratories; Linux; Maintenance; Molecular Structure; National Heart, Lung, and Blood Institute; National Institute of Allergy and Infectious Disease; National Institute of Dental and Craniofacial Research; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of General Medical Sciences; Policies; Process; Proteome; Reporting; Research; Research Personnel; Resource Sharing; Resources; Rodent; Running; Salivary; Salivary Proteins; Science; Security; Single Nucleotide Polymorphism; Software Tools; Speed; Study Section; System; Testing; Time; United States National Institutes of Health; Work; analysis pipeline; bioinformatics tool; computing resources; data sharing; design; laboratory facility; molecular modeling; next generation sequencing; operation; outreach; programs; research and development; scientific computing; tool; transcriptome; transcriptome sequencing; web services; web site

The Office of Intramural Research (OIR) Scientific Computing Facility (SCF) collaborates with OIR staff and their NIH investigators to build a diverse and robust scientific computing system. This system provides the infrastructure needed by the collaborations at the same time as complying with all security, confidentiality and integrity requirements, especially those concerned with storing PII and other sensitive data. The SCF manages hardware refreshes and software upgrades allowing collaborators to work uninterrupted. Expert staff are able to provide centralised support and advice to enable the best use of resources in support of OIR's research program. As a central part of a computational science research and development organization, the SCF acts as OIR's computational laboratory, contributing on many of OIR's collaborative efforts and providing many NIH investigators and leaders with a key resource. The SCF supports some 80 OIR staff and collaborators across approximately 100 systems, running a variety of web services, databases, file storage, computational clusters and large core count single image machines. The SCF has separate racks for machines used for storing and processing sensitive information, such as personal health information and grant information, with appropriate extra layers of protection. A common and federated environment across all computational systems, enables OIR staff to quickly build the data analysis tools they need throughout the lifetime of a collaboration. Common file systems, unified authentication, system management, and other system coordinating features are fully integrated into an infrastructure containing the required variety of supporting software. Commodity hardware, free software and commercial software are integrated into efficient and sustainable solutions. SCF Staff perform the many common security, maintenance, backup and reporting tasks that are required for the day to day operation of scientific computational systems on behalf of OIR. In particular, managing the Federally mandated Assessment and Authorization process on OIR's Computational Facility that would otherwise be a significant burden to OIR developers and investigators as well as their collaborators. When an collaborative project is concluded, the SCF is central in relocating systems to space within the ICs or the CIT Data Center as appropriate. In collaboration with NHLBI, the SCF provides strategic outreach to the wider Linux community at NIH, working with CIT to provide infrastructure support. Over the last 5 years we have developed AD integration configurations, stand-alone server configurations, two-factor authentication solutions, NFS/Krb5 integrations, as well as general Linux support for the NHLBI Division of Intramural Research. In 2019, supported collaborations include: . The Human Salivary Protein Catalog, with NIDCR, supporting the Salivary Proteome community. . Molecular Structure Determination (NIDDK, NIDCR, NCI, NHLBI). . The Center for Molecular Modeling's MMIGNET programme supporting NIH as a whole. . Microarray Database System (mAdb) with NCI and NIAID. . Portfolio analysis and portfolio visualization resources supporting many groups throughout NIH, including OD, CSR and NIGMS. . an Assisted Referral Tool (ART) project, with the Center for Scientific Review (CSR) to help NIH grant applicants choose appropriate study sections for their applications. . OIR's SCORHE (System for Continuous Observation of Rodents in Home-cage Environment) project. . A collaborative effort with NHLBI to design and execute a program which computes billions of SNP-gene expression association tests, in an effort to find expression - single nucleotide polymorphisms, eSNPs. Efforts so far are producing a 20-fold speed up over previous efforts. . A joint project, with NCI and a NCI-funded consortium, implementing an analysis pipeline and providing the necessary bioinformatics tools for transcriptome analysis and biological interpretation of RNA-seq/Exon capture data from next generation sequencing. . A joint project with NHLBI and other ICs to provide a nexus of computational system administration support and set policies and standards for NIH.

校内研究办公室（OIR）科学计算设施（SCF）与OIR工作人员及其NIH研究人员合作，建立一个多样化和强大的科学计算系统。该系统提供了合作所需的基础设施，同时符合所有安全性，机密性和完整性要求，特别是与存储PII和其他敏感数据有关的要求。SCF管理硬件更新和软件升级，允许协作者不间断地工作。专家工作人员能够提供集中的支持和建议，使资源的最佳利用，以支持OIR的研究计划。 作为计算科学研究和开发组织的核心部分，SCF充当OIR的计算实验室，为OIR的许多合作努力做出贡献，并为许多NIH研究人员和领导者提供关键资源。SCF支持大约100个系统中的大约80名OIR工作人员和协作者，运行各种Web服务，数据库，文件存储，计算集群和大型核心计数单映像机器。SCF有单独的机架，用于存储和处理敏感信息（如个人健康信息和赠款信息）的机器，并有适当的额外保护层。 跨所有计算系统的通用联合环境使OIR员工能够在整个协作生命周期中快速构建所需的数据分析工具。通用文件系统、统一身份验证、系统管理和其他系统协调功能完全集成到包含所需各种支持软件的基础架构中。商品硬件、免费软件和商业软件被整合到高效和可持续的解决方案中。 SCF工作人员代表OIR执行科学计算系统日常运行所需的许多常见安全、维护、备份和报告任务。特别是管理联邦授权的OIR计算设施评估和授权流程，否则这将成为OIR开发人员和调查人员及其合作者的重大负担。当一个合作项目结束时，SCF在将系统重新定位到IC或CIT数据中心（视情况而定）内的空间中发挥核心作用。 SCF与NHLBI合作，向NIH更广泛的Linux社区提供战略性外联，与CIT合作提供基础设施支持。在过去的5年里，我们开发了AD集成配置，独立服务器配置，双因素身份验证解决方案，NFS/Krb 5集成，以及为NHLBI内部研究部门提供一般Linux支持。 2019年，支持的合作包括： .人类唾液蛋白质目录，与NIDCR，支持唾液蛋白质组社区。 .分子结构测定（NIDDK、NIDCR、NCI、NHLBI）。 .分子建模中心的MMIGNET计划支持NIH作为一个整体。 .微阵列数据库系统（mAdb）与NCI和NIAID。 .投资组合分析和投资组合可视化资源支持整个NIH的许多团体，包括OD，CSR和NIGMS。 .一个辅助转介工具（ART）项目，与科学审查中心（CSR）合作，帮助NIH资助申请人为他们的申请选择合适的研究部分。 . OIR的SCORHE（家庭笼环境中啮齿动物连续观察系统）项目。 .与NHLBI合作设计并执行一个程序，该程序计算数十亿个SNP-基因表达关联测试，以寻找表达-单核苷酸多态性，eSNP。迄今为止的努力正在产生比以前的努力快20倍的速度。 .与NCI和NCI资助的财团的联合项目，实施分析管道并提供必要的生物信息学工具，用于转录组分析和下一代测序的RNA-seq/外显子捕获数据的生物解释。 .与NHLBI和其他IC的联合项目，为NIH提供计算系统管理支持并制定政策和标准。