DEVELOPMENT AND DEPLOYMENT OF FLEXIBLE AND SCALABLE CI FOR BIOMED RESEARCH

为 BIOMED 研究开发和部署灵活且可扩展的 CI

• 批准号: 8362790
• 负责人: PHILIP PAPADOPOULOS
• 金额: $ 31.99万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8362790
• 关键词: Address; Biology; Biomedical Computing; Cell model; Code; Computer software; Data; Development; Ensure; Equilibrium; Funding; Grant; Individual; Linux; Logic; National Center for Research Resources; Operating System; Organ Model; Performance; Principal Investigator; Reproducibility; Research; Research Infrastructure; Resources; Scientist; Services; Source; System; Testing; Time; Translational Research; United States National Institutes of Health; base; cost; drug discovery; flexibility; image reconstruction; multicore processor; shared memory; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Objectives Our objective in this core is to address the practical issues of adapting, optimizing and provisioning biomedical applications in drug discovery, cellular and organ modeling, and image reconstruction based upon current and emerging computing, data and network infrastructures. At the same time, we must ensure the accessibility, reproducibility and versatility of the large ensembles of software that are required to carry out multiscale analysis. Specific Aims Aim 1: Scaling and Adapting Multiscale Biology Codes to High-Performance Clusters and Multicore Processors: To allow application codes to take advantage of a new "balance of machines where individual nodes become large-scale, shared-memory symmetric multiprocessors (SMPs). Aim2: Providing Transparent and Service-Based Access to Multiscale and Multiphysics Biomedical Codes: To hide as much complexity as possible allows scientists to reason more easily about the logic of the systems or workflows required to carry out their research  and less about the low-level system details. Aim 3: Defining, Testing, and Supporting a Complete Cyberinfrastructure: To provide a reproducible cyberenvironment by understanding externally-supplied software, assembling into a distribution that sits on top of a standard Linux operating system, and regularly and rigorously testing. Aim 4: Integrating and Delivering Tools for Translational Research: To integrate and test selected "suites" of software application pipelines

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的主要研究者可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 目标 我们的核心目标是解决适应、优化和 提供药物发现、细胞和器官建模方面的生物医学应用，以及 基于当前和新兴计算、数据和网络的图像重建 基础设施。同时，我们必须确保可访问性、可重复性和 执行多尺度任务所需的大型软件集合的多功能性 分析。 具体目标 目标 1：扩展和调整多尺度生物学代码以适应高性能集群和 多核处理器：允许应用程序代码利用新的“平衡” 单个节点变得大规模、共享内存对称的机器 多处理器 (SMP)。 目标 2：提供对多尺度和多物理场的透明且基于服务的访问 生物医学密码：隐藏​​尽可能多的复杂性，使科学家能够进行更多推理 轻松了解进行研究所需的系统或工作流程的逻辑 较少涉及底层系统细节。 目标 3：定义、测试和支持完整的网络基础设施：提供 通过了解外部提供的软件、组装可重现的网络环境 进入一个位于标准 Linux 操作系统之上的发行版，并定期和 严格测试。 目标 4：集成和提供转化研究工具：集成和提供转化研究工具 测试选定的软件应用程序管道“套件”