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。 网络基础设施的发展是由多尺度建模驱动的 应用程序，其重点是从生物规模的科学研究 从亚原子到分子、细胞、组织到器官层面。应用示例包括 用GAMESS进行量子力学建模，计算蛋白质静电 APBS和有限元工具包FETK的势能，蛋白质-配体对接 AutoDock、心脏系统生物学和生理学建模的研究 连续性和使用PMV和可视化工作流编程的分子可视化 在愿景中。我们使用实际使用案例来演示这些多规模应用程序如何 可以在网格上透明地提供给生物医学的研究人员 和翻译研究领域，通过从 了解HIV蛋白水解酶和整合酶的详细作用机制， 肌病、心律失常和心力衰竭的神经肌肉接头研究 新出现的公共卫生威胁，以及通过与其他 世界各地的研究团队。采用面向服务的体系结构 支持高度可重复使用的软件组件的开发，并且高效 利用国内和国际网格开发和云计算 活动。通过使用Opal Web服务工具包，我们提供了一个简单的层 将科学软件作为一种服务。分布式计算被管理为 通过Globus、DRMAA或CSF4等元调度器。复杂问题的解决方案 可以使用协调不同互操作的工作流工具进行封装 服务。大规模计算问题可以透明地在 全国性的基础设施，如TeraGrid资源。NBCR网站URL： 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. 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.