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: 7601497
• 负责人: Wilfred Wenfeng Li
• 金额: $ 0.07万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601497
• 关键词: Address; Adoption; Architecture; Arrhythmia; Biological; Biomedical Computing; Biomedical Research; Cardiac; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Development; Docking; Electrostatics; Elements; Environment; Failure; Funding; Grant; HIV Protease; Imagery; Institution; Integrase; International; Internet; Ligands; Mediation; Mission; Modeling; Molecular; Myopathy; Neuromuscular Junction; Ontology; Organ; Physiology; Process; Proteins; Public Health; Quantum Mechanics; Range; Research; Research Personnel; Resources; Running; Science; Semantics; Services; Solutions; Source; Systems Biology; Tissues; Translational Research; United States National Institutes of Health; Vision; Visual; biocomputing; data integration; interoperability; multi-scale modeling; open source; programs; prototype; research and development; tool; virtual

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. Begun in 1994, the mission of the National Biomedical Computation Resource (NBCR) is to conduct, catalyze and enable multiscale biomedical research by harnessing advanced computation and data cyberinfrastructure through multidiscipline and multi-institutional integrative research and development activities. We aim to contribute to the development of cyberinfrastructure for multiscale modeling activities. 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 international grid development activities. We are in the process of developing an end to end prototype environment, exemplified by the adoption of key components by the Telescience project, that allows existing applications to run transparently on the grid, taking advantage of open source software that provides a portal interface using GridSphere, with transparent GSI authentication using GAMA, a web service wrapper using Opal, a metascheduler using CSF4, a virtual filesystem using Gfarm, and a grid-enabled cluster environment using Rocks. Solutions to complex problems may be developed using workflow tools that coordinate different interoperable services. Large scale problems that can't be solved using local computational resources will need to be made available transparently to our users. This proposal aims to address the specific requirements and add support of transparent access to TeraGrid resources through the TeraGrid Science Gateway program. In addition, we also intend to make such a science gateway available through web services, through the development of ontology and semantic mediation tools such as Pathsys and OntoQuest for data integration and interoperability. 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。 国家生物医学计算资源（NBCR）的使命始于1994年，是通过通过多阶层和多机构综合研究和发展活动来利用先进的计算和数据网络基础结构来进行多尺度生物医学研究。我们的目标是为多尺度建模活动的网络基础设施的发展做出贡献。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，并有效利用国际网格开发活动。 We are in the process of developing an end to end prototype environment, exemplified by the adoption of key components by the Telescience project, that allows existing applications to run transparently on the grid, taking advantage of open source software that provides a portal interface using GridSphere, with transparent GSI authentication using GAMA, a web service wrapper using Opal, a metascheduler using CSF4, a virtual filesystem using使用岩石的GFARM和启用网格的集群环境。可以使用协调不同可互操作服务的工作流量工具来开发复杂问题的解决方案。无法使用本地计算资源解决的大规模问题将需要向我们的用户透明地提供。该提案旨在通过Teragrid Science Gateway计划来满足特定要求，并增加对Teragrid资源的透明访问。此外，我们还打算通过Web Services，开发诸如PATHSYS和Quest的语义中介工具的开发，以提供数据集成和互操作性，使其通过Web服务提供这样的科学网关。 NBCR网站URL：http：//nbcr.net。