NATIONAL BIOMEDICAL COMPUTATION RESOURCE SCIENCE GATEWAY FOR THE TERAGRID

太格网国家生物医学计算资源科学网关

• 批准号: 7956144
• 负责人: Wilfred Wenfeng Li
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956144
• 关键词: Adoption; Architecture; Arrhythmia; Biological; Biomedical Computing; Biomedical Research; Cardiac; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Development; Docking; Electrostatics; Elements; Encapsulated; Failure; Funding; Grant; HIV Protease; High Performance Computing; Imagery; Institution; Integrase; International; Internet; Ligands; Modeling; Molecular; Myopathy; Neuromuscular Junction; Organ; Physiology; Proteins; Public Health; Quantum Mechanics; Research; Research Infrastructure; Research Personnel; Resources; Science; Services; Solutions; Source; Systems Biology; Tissues; Translational Research; United States National Institutes of Health; Vision; Visual; cluster computing; multi-scale modeling; programs; tool; web site

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. The development of the cyberinfrastructure is driven by multiscale modeling applications, which focuses on scientific research ranging in biological scale from the subatomic, to molecular, cellular, tissue to organ level. Application examples include quantum mechanics modeling with GAMESS, calculation of protein electrostatic potentials with APBS and the finite element toolkit FETK, protein-ligand docking studies with AutoDock, cardiac systems biology and physiology modeling with Continuity, and molecular visualizations using PMV and visual workflow programming in Vision. Real use cases are used to demonstrate how these multiscale applications may be made available transparently on the grid to researchers in the biomedicine and translational research arena, through integrative projects ranging from the understanding of detailed mechanism of action of HIV protease and integrase, to neuromuscular junction research in myopathy, to heart arrhythmia and failure, and to emerging public health threats, as well as through collaborative projects with other research teams across the world. The adoption of service oriented architecture enables the development of highly reusable software components, and efficiently leverages the national and international grid development and cloud computing activities. Through the use of the Opal web service toolkit, we provide a simple layer for scientific software as a service. The distributed computing is managed either through Globus, DRMAA or a metascheduler like CSF4. Solutions to complex problems may be encapsulated using workflow tools that coordinate different interoperable services. Large scale computation problems may be launched transparently in national scale infrastructure such as the TeraGrid resource. NBCR Website URL: http://nbcr.net.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 网络基础设施的发展是由多尺度建模应用驱动的，该应用的介于从亚原子到分子，细胞，组织到器官水平的生物规模的科学研究。应用示例包括使用游戏机进行量子力学建模，使用APB的蛋白质静电势计算以及有限的元素工具包FETK，使用Autodock的蛋白质配体对接研究，具有连续性的心脏系统生物学和生理学建模，以及使用PMV和Visual Wormflow在视觉中进行的分子可视化。 Real use cases are used to demonstrate how these multiscale applications may be made available transparently on the grid to researchers in the biomedicine and translational research arena, through integrative projects ranging from the understanding of detailed mechanism of action of HIV protease and integrase, to neuromuscular junction research in myopathy, to heart arrhythmia and failure, and to emerging public health threats, as well as through collaborative projects with other research teams在世界范围内。采用面向服务的体系结构可以开发高度可重复使用的软件组件，并有效利用国家和国际网格开发以及云计算活动。通过使用Opal Web服务工具包，我们为科学软件作为服务提供了一个简单的层。分布式计算是通过Globus，Drmaa或CSF4（例如CSF4）进行管理的。可以使用协调不同互操作服务的工作流量工具来封装解决复杂问题的解决方案。大规模计算问题可以在国家规模的基础架构（例如Teragrid资源）中透明地启动。 NBCR网站URL：http：//nbcr.net。