NATIONAL BIOMEDICAL COMPUTATION RESOURCE SCIENCE GATEWAY FOR THE TERAGRID

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH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 中心，不一定是研究者的机构。 网络基础设施的发展是由多尺度建模驱动的 应用，其重点是科学研究，范围从生物规模， 从亚原子到分子，从细胞到组织，从器官。应用例子包括 GAMESS量子力学建模，蛋白质静电场计算 电位与APBS和有限元工具包FETK，蛋白质配体对接 使用AutoDock进行研究，使用 使用PMV和可视化工作流程编程实现连续性和分子可视化 在幻视里真实的用例用于演示这些多尺度应用程序如何 可以在网格上透明地提供给生物医学研究人员 和转化研究竞技场，通过综合项目，从 了解HIV蛋白酶和整合酶的详细作用机制， 神经肌肉接头研究在肌病，心脏心律失常和衰竭， 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 能够高效地开发高度可重用的软件组件 利用国家和国际电网发展和云计算 活动通过使用Opal Web服务工具包，我们提供了一个简单的层 科学软件即服务。分布式计算被管理， 通过Globus、DRMAA或像CSF 4这样的元数据库。解决复杂问题的方法 可以使用协调不同的可互操作的工作流工具来封装 服务大规模计算问题可以透明地在 国家级基础设施，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.