NATIONAL BIOMEDICAL COMPUTATION RESOURCE SCIENCE GATEWAY FOR THE TERAGRID

这个子项目是众多研究子项目之一

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.