National Biomedical Computation Resource

National Biomedical Computation Resource

Research Emphasis

The mission of the National Biomedical Computation Resource (NBCR) is to conduct, catalyze, and enable multiscale biomedical research by harnessing advanced computational technology. To fulfill this mission, NBCR efforts are focused on four key activities: 1) integrate computational, data, and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments, and people; 2) develop and deploy advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing, and interactive visualization; 3) deliver and support advanced grid/cyber-infrastructure for biomedical researchers; and 4) train a cadre of new researchers such that they have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists.

Current Research

The key aim of this resource is to provide transparent access to the new and emerging grid infrastructure that will deliver integrated computer, data, physical, experimental, and human resources to biomedical scientists investigating a wide range of medically important problems spanning scales of biological organization from small-molecule drug design and comparative genomics to diagnostic brain imaging and cardiovascular disease. The NBCR is currently organized into five core projects: 1) Integrative Modeling of Subcellular Processes: Application to Synaptic Activity and Pharmaceutical Discovery; 2) Data Integration and Analytic Tools for Biological Networks; 3) Structurally and Functionally Integrated Modeling of Cell and Organ Biophysics; 4) Creating Visualization Environments for Multiscale Biomedical Modeling; and 5) Grid Computing and Analysis for Multiscale Biomedical Applications.

Resource Capabilities

Methods

NBCR is developing three key technologies in the context of several pressing biological needs from important applications at various ranges of scales (e.g., atomic to macromolecular, molecular to cellular, and tissue to organ). This approach will deliver concrete products used by biomedical and translational medicine research communities as well as ensure a more robust, scalable problem-solving environment supporting multiple applications: 1) Cluster and grid computing: enables effective scheduling of three classes of applications, ranging from computationally intensive to simple scheduled update computations, to impulse or on-demand computing; 2) Data and Web services: includes data modeling, data access—including wrapping of information sources, use of XML-based standards, and data integration across multiple sources; and 3) Visualization and interfaces: facilitates the rapid development, reconfiguration, and novel utilization of multidisciplinary and multiscale applications for biological research.

Software

Numerous Analytical Services, Databases, and Software Tools are available to assist researchers in studying biomedical phenomena at and across multiple scales of biological complexity.

Key applications: 1) Finite Element toolkit (FEtk): continued development by NBCR and actively used in a suite of applications, such as the adaptive Poisson-Boltzman Solver (APBS) and the Smoluchowski equation solver (SMOL); 2) Biological Networks: a bioinformatics software platform for visualizing molecular interaction networks, data integration, and data query using graph query engines developed by NBCR; 3) Continuity: a multiscale computational platform for continuum problems in bioengineering and physiology, especially those related to cardiac mechanics and electrocardiology research, with continuous development by NBCR since 1994; 4) Python Molecular Viewer: continued development by NBCR and used in a suite of applications, such as AutoDock Tools, and Continuity; and 5) Grid toolkit: a suite of tools such as Opal for Web services deployment, myMPI for efficient parallel communication between FORTRAN and Python, and ATOMIC for transparent access of grid.

Available Resources

NBCR provides Web portals to a variety of analyses performed on its high-performance computing systems and servers.

Special Features

NBCR is part of the University of California San Diego's Center for Research in Biological Systems, and its technology development activities involve collaborations among researchers at the university, including the San Diego Supercomputer Center, the California Institute of Telecommunications and Information Technology (Calit2), the Scripps Research Institute, and Washington University in Saint Louis, with a general interest in performing basic and translational biomedical research from atomic to organismal levels.

Training Opportunities and Workshops

The annual NBCR Summer Institute provides weeklong training sessions on key NBCR software and tools (see http://nbcr.net/si).

Publications

1. Baitaluk, M., Qian, X., Godbole, S., Raval, A., Ray, A., and Gupta, A., PathSys: Integrating molecular interaction graphs for systems biology. BMC Bioinformatics 7:55, 2006.

2. Healy, S. N. and McCulloch, A. D., An ionic model of stretch-activated and stretch-modulated currents in rabbit ventricular myocytes. Europace 7:128–134, 2005.

3. Krishnan, S., Baldridge, K. K., Greenberg, J. P., Stearn, B., and Bhatia, K., In an end-to-end web services-based infrastructure for biomedical applications, Grid 2005. Seattle, Washington, 2005. nbcr.net/services.

4. Law, R. J., Henchman, R. H., and McCammon, J. A., A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proceedings of the National Academy of Sciences U S A 102:6813–6818, 2005.

5. Li, W. W., Yeo, C. L., Jeong, K., Hwang, S., Date, S., Kwak, J., Sekiguchi, S., Ang, L., and Arzberger, P. W., In: Proteome Analysis using iGAP in Gfarm., Life Sciences Grid Workshop, 2005.

6. Lin, A. W., Dai, L., Ung, K., Peltier, S., and Ellisman, M., The Telescience Project: Applications to Middleware Interaction Components: Proceedings of the 18th IEEE International Symposium on Computer-Based Medical Systems, 543–548, 2005.

7. Sanner, M. F., Stolz, M., Burkhard, P., et al., Visualizing nature at work from the nano to the macro scale. New York, NY: John Wiley & Sons, Ltd., Vol. 1, 7-11, 2005.