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，是美国国立卫生研究院国家研究资源中心(NCRR)的国家资源中心，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。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。这些多尺度的应用可以在网格上透明地提供给生物医学和转化研究领域的研究人员，通过合作项目，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，以及新出现的公共卫生威胁，以及通过向生物医学研究人员提供服务项目。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。我们为生物医学和临床研究提供端到端的计算环境，利用开源软件的优势，使用GridSphere提供门户界面，使用GAMA提供透明的GSI身份验证，使用Opal工具包提供简单但强大的Web服务包装，使用Rock提供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。大规模的计算问题可以在国家规模的基础设施中透明地启动，例如TeraGrid资源。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), a national Resource Center of the National Center for Research Resources (NCRR), National Institutes of Health, NIH, 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. 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. These multiscale applications may be made available transparently on the grid to researchers in the biomedicine and translational research arena, through collaborative 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 service projects to biomedical researchers. The adoption of service oriented architecture enables the development of highly reusable software components, and efficiently leverages the international grid development activities. We provide an end to end computational environment for biomedical and clinical research, taking advantage of open source software to provide a portal interface using GridSphere, with transparent GSI authentication using GAMA, a simple yet powerful web service wrapper using the Opal toolkit, 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 computation problems may be launched transparently in national scale infrastructure such as the TeraGrid resource. NBCR Website URL: http://nbcr.net.