The National Centers for Biomedical Computation
In May 2002, Elias Zerhouni, the newly appointed Director, changed the traditional paradigm for the National Institutes of Health (NIH) by creating a roadmap for medical research for the next century. Traditionally, medical research has been funded by the individual institutes within NIH but challenges too large for any individual institute or disciplines which fell between gaps in institutional missions were often neglected.
Three major funding areas were defined under the Roadmap: New Pathways to Discovery, Research Teams of the Future and Reengineering the Clinical Research Enterprise. Emerging disciplines, such as, Bioinformatics and Computational Biology, not traditionally affiliated with any one of the National Institutes were identified as high priority areas for Roadmap funding under New Pathways to Discovery.
At this time, NIH has funded seven National Centers for Biomedical Computing. Each Center's mission is to develop computational tools to support biological discovery. These Centers define the current state of the art in the field and represents a significant fraction of the national effort directed towards biomedical computation. Stanford University hosts two of these seven centers and the Principal Investigators are Russ Altman, the Director of the Biomedical Informatics (BMI) Training Program and Mark Musen, the Co-Director of the program, respectively.
Physics-based Simulation of Biological Structures: Simbios
Russ B. Altman, MD, PhD,
Director of the Biomedical Informatics Training Program, Professor of Genetics, Medicine, Bioengineering and (by courtesy) Computer Science
The NIH Center for Simulation of Biological Structures (Simbios) supports scientific research of physics-based simulation of biological structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions.
Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating can apply for NIH funding (http://simbios.stanford.edu/collab.htm) targeted to this purpose.
Simbios is developing and disseminating the SimTK simulation toolkit. SimTK is open-source software developed by experienced professionals. The software will include advanced capabilities for modeling the geometry and physics of biological systems and comparing simulation results with experimental data. SimTK seeks to be fast, efficient, and easy-to-use. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists.
To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with www.simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repository.
Simbios also provides a broad dissemination effort, including the Biomedical Computation Review (www.BiomedicalComputationReview.org), a magazine devoted to the science and tools in biocomputation; Simbiome (www.Simbiome.org) an inventory of high-quality commercial and academic bio-simulation tools; curriculum material; and onsite and distance training to biomedical scientists and students.
In the context of other NIH centers concentrating on complementary elements of biomedicine, Simbios is focused on the physical reality of biological structures and provides a critical piece of a national biomedical computing infrastructure.
National Center for Biomedical Ontology: cBIO
Mark A. Musen, MD, PhD, Co-Director, Biomedical Informatics Training Program, Head of Stanford Medical Informatics, Professor, Department of Medicine.
The National Center for Biomedical Ontology (cBIO) will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research.
Our Center is truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores: (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center's technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group.
cBio will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.