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: 8169339
• 负责人: PHILIP PAPADOPOULOS
• 金额: $ 26.8万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8169339
• 关键词: Address; Biology; Code; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Development; Ensure; Equilibrium; Funding; Grant; Individual; Institution; Linux; Logic; Operating System; Organ Model; Performance; Reproducibility; Research; Research Infrastructure; Research Personnel; Resources; Scientist; Services; Source; System; Testing; Time; Translational Research; United States National Institutes of Health; base; 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. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 目标 我们的核心目标是解决基于当前和新兴计算、数据和网络基础设施的药物发现、细胞和器官建模以及图像重建中适应、优化和配置生物医学应用的实际问题。与此同时，我们必须确保进行多尺度分析所需的大型软件集合的可访问性、可重复性和多功能性。 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“机器平衡”，其中各个节点成为大规模、共享内存对称多处理器 (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 生物医学代码：隐藏尽可能多的复杂性使科学家能够更轻松地推理进行研究所需的系统或工作流程的逻辑，而不是低级系统细节。 目标 3：定义、测试和支持完整的网络基础设施：通过了解外部提供的软件、组装成位于标准 Linux 操作系统之上的发行版以及定期、严格的测试来提供可复制的网络环境。 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”