NATIONAL BIOMEDICAL COMPUTATION RESOURCE SCIENCE GATEWAY FOR THE TERAGRID

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 国家生物医学计算资源(NBCR)成立于1994年，其使命是通过多学科和多机构的综合研究和开发活动，利用先进的计算和数据网络基础设施，进行、催化和实现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程序推动的，该应用程序侧重于从亚原子到分子、细胞、组织到器官层面的生物尺度的科学研究。应用实例包括使用GAMESS的量子力学建模，使用APBS和有限元工具包FEtk计算蛋白质静电势，使用AutoDock进行蛋白质-配体对接研究，使用连续性进行心脏系统生物学和生理学建模，以及使用PMV和Vision中的可视化工作流编程进行分子可视化。实际使用案例被用来展示如何通过综合项目，从了解艾滋病毒蛋白水解酶和整合酶的详细作用机制，到肌病的神经肌肉连接研究，到心律失常和衰竭，以及通过与世界各地的其他研究团队合作的项目，如何在网格上向生物医学和转化研究领域的研究人员透明地提供这些多尺度应用程序。采用面向服务的体系结构可以开发高度可复用的软件组件，并有效地利用国际网格开发活动。我们正在开发端到端的原型环境，Telescience项目采用的关键组件就是一个例子，它允许现有的应用程序在网格上透明地运行，利用开放源码软件，该软件提供使用GridSphere的门户界面、使用GAMA的透明GSI身份验证、使用Opal的Web服务包装、使用CSF4的元调度器、使用Gfield的虚拟文件系统，以及使用Rock的支持网格的集群环境。复杂问题的解决方案可以使用协调不同互操作服务的工作流工具来开发。使用本地计算资源无法解决的大规模问题将需要透明地提供给我们的用户。该提案旨在解决具体要求，并通过TeraGrid Science Gateway计划增加对TeraGrid资源的透明访问的支持。此外，我们还打算通过开发本体和语义中介工具，如用于数据集成和互操作性的Pathsys和OntoQuest，通过网络服务提供这样一个科学门户。Nbcr网站网址：http://nbcr.net.

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.