Abstract — 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. Here we report the more recent research and technology advances in building cyberinfrastructure for multiscale modeling activities.
The development of the cyberinfrastructure is driven by multiscale modeling applications, which focus 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 the detailed mechanism of HIV protease and integrase action, 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 describe an end to end prototype environment, exemplified by the adoption of key components of the Telescience project, that allows existing applications to run transparently on the grid, taking advantage of open source software that provides the following:
- a portal interface using GridSphere,
- 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. In addition, we also describe the development of ontology and semantic mediation tools such as Pathsys and OntoQuest for data integration and interoperability, which may be efficiently coupled with the application services provided to the biomedical community.
