Established in 1994, the overall mission of the National Biomedical Computation Resource (NBCR) is to conduct, catalyze and enable multiscale biomedical research by harnessing forefront computational and information technologies. Over the past 5 years, one of our key foci was on the development of sophisticated application level middleware that enables the transparent access to the emerging cyberinfrastructure that includes compute, data, instrument, visualization and human resources. Combined with our effort in software tools and libraries that enable multiscale modeling, we have positioned ourselves to focus on a new theme of cyberinfrastructure for biomedicine in the current award period (2009-2014). By working closely with the biomedical research and multiscale modeling community, we have built upon our previous achievements, hardened our software tools, and further prepared us as the onramp to cyberinfrastructure for translational research and biomedicine.
The key objectives may be summarized as follows:
- Push forward the frontiers of integrative, multiscale modeling. We created collaborative and integrative projects that involve several core technologies, resulting in use of a prototype computer-aided drug discovery pipeline, new tools grounded on finite element (FE) codes to capture subcellular geometry, a new core project and several collaborative projects to tackle modeling opportunities with improved data, mathematical approaches, and cyberinfrastructure at the mesoscale.
- Accelerate the adoption and development of emerging information technologies by the biomedical science community; in particular, by providing transparent access to grid services. We create and deployed a toolkit, Opal, that allows providing existing codes as services, and through deployment of services using this tool, including MEME, APBS, and using this approach to create services for CAMERA, setting the stage for working collaboratively with PDB.
- Focus new activities on translational medicine related to the NIH mission. We worked with collaborative projects in drug discovery, surgeryor understanding treatments for Alzheimers. These are being reflected in new collaborative projects.
- Strengthen the multidisciplinarity of the resource. We start building tools to begin a serious multiscale modeling approach, and bring together pieces of the computer-aided drug discovery pipeline. The focus on a new core project will further strengthen our gains. Furthermore, several of the collaborative projects involve multiple technology cores.
- Expand service, training and dissemination. We created the NBCR Summer Institute that has over two summers engaged more than 100 individuals, the coordination of joint-booths at Supercomputing and Biophysical Society meetings involving several other Research Resources; and organization with the National Center for Physics-based Simulation of Biological Structures (Simbios) a series of two sessions at the Pacific Symposium of Biocomputing on areas of multiscale modeling. These activities will continue and we will leverage the NBCR Summer Institute for bringing collaborators together in targeted areas of cardiac or infectious diseases.
Over the past 5 years, we have made significant progress towards the above objectives, paid particular attention to the translational medicine theme, and channeled our new efforts into three technology research and development core themes:
- Multiscale Model Building and Visualization Tools (Tools), embodying objectives in i) and iv) above, establishing close interactions among experimental biologists, computer scientists specialized in image processing and visualization, mathematicians in multidimensional tomographic reconstruction, and mathematical mesh representation, and biophysicists, biochemists for advanced model building.
- Multiscale simulation software suites and pipelines (Simulations), encompassing objectives i) and iii), building upon the multidisciplinary nature of the core theme 1 by conduting real life computational simulations towards computer aided drug design and patient specific modeling and simulation based therapy, and bringing together experimental biologists for lead identification and validation, chemists for lead optimization, and computational biologists with clinicians for better therapeutic procedures and devices.
- Flexible, scalable cyberinfrastructure framework, (CI Framework) drawing upon objectives ii) and iii), supporting the requirements of the two other core themes, by bringing together skilled software engineers, scientific software developers and researchers to deliver tools that enhance the productivity of the researchers, driven by collaborative projects.
Core theme 1 provides the fundamental tools and data sources for core theme 2, which spearheads the multiscale modeling and simulation activities with strong translational emphasis, with core theme 3 ensuring the tools created are scalable and reusable by the wider biomedical community. We have demonstrated strong synergistic interactions among the three thematic areas, and it is our intention to make cross-disciplinary interactions even stronger in the current award period.
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