"Biomedical research is undergoing a rapid transformation that can be traced to the explosion in the size of data sets ranging from DNA and protein sequences to high-resolution images mapping the architecture of cells, tissues, cellular components, organs, and whole organisms", said Judith Vaitukaitis, director of NCRR. "Information technology is becoming essential for the management and analysis of these data."
The Biomedical Informatics Research Network (BIRN), will be the first test bed for sharing and mining data effectively in a site-independent manner for both basic and clinical research. BIRN will enable researchers to put into practice a multi-institutional, collaborative, technology-enabled approach that will be key to progress in neuroscience and medical science generally. The BIRN project will share digital magnetic resonance images (MRI) and advanced 3D microscope images using high-bandwidth networking technologies. They will equally share related genomic, structural, and gene expression data. Eventually, BIRN capabilities will scale across additional data repositories, resource centres, and regional core facilities.
"BIRN will create an environment for organising and presenting data in a way that makes it accessible and useful to other researchers", stated Mark Ellisman, director of the UCSD Center for Research on Biological Structure (CRBS) and principal investigator for the BIRN Co-ordinating Center. "All of us will be able to study linkages between animal models of human diseases and data from patients suffering with these diseases. We will establish a test bed to determine the software and hardware requirements for achieving meaningful access to shared databases. Special attention must be given to issues of quality of service, reliability, confidentiality, scalability, and data ownership."
UCSD will establish the Co-ordinating Center for the national BIRN project with information technology contributions from the NSF-supported National Partnership for Advanced Computational Infrastructure (NPACI), the San Diego Supercomputer Center (SDSC), and the newly formed California Institute for Telecommunications and Information Technology (Cal-(IT)²). BIRN is a major extension of a current grant to the NCRR's National Biomedical Computational Resource (NBCR), operated by UCSD through CRBS. NBCR develops and deploys computational tools to benefit the biomedical community. CRBS will co-ordinate participation by the School of Medicine and campus researchers in biomedical areas.
The BIRN Co-ordinating Center at UCSD will work with Duke University, Caltech, Massachusetts General Hospital, Brigham and Women's Hospital, UCSD's School of Medicine, and UCLA to establish large-scale network connections and data-sharing facilities for the BIRN research projects. Investigators at each of these sites have ongoing studies involving brain imagery. Their objective will be to raise the statistical accuracy and medical incisiveness of all their experiments by comparing and contrasting imagery from animal and human subjects.
"The BIRN collaboration depends upon new technology that will allow this close coupling of such studies for the first time", Mr. Ellisman stated. The project will train and encourage researchers to access and share data from others' experiments in a co-ordinated way, and it will mark a new era for information technology-enabled, multi-institutional collaborative science, according to Mr. Ellisman.
"BIRN will allow research computations and data analysis to go forward on a scale never before possible", stated Edward Holmes, vice chancellor for health sciences and dean of the UCSD School of Medicine. "What is particularly exciting is that these steps, taken for brain research, will build collaborative models for the use of modern informatics and telescience in all areas of medicine."
Initially, data from ongoing experiments will be shared among two major BIRN subprojects. The Mouse BIRN Project is led by G. Allan Johnson, director of the Center for In Vivo Microscopy, an NCRR Resource at Duke University. Mouse BIRN will collaborate with Ellisman's National Center for Microscopy and Imaging Research, also an NCRR-supported resource at UCSD, the Laboratory of Neuro Imaging directed by Arthur Toga at UCLA, an NCRR Resource as well, and the Biological Imaging Center's MRI Division directed by Scott Fraser and Russell Jacobs at Caltech's Beckman Institute. They will extend studies by using two mouse models of human disease, one that develops a neurological disorder similar to multiple sclerosis and another in which one gene regulating the level of dopamine in the brain has been altered. Changes in brain dopamine levels occur in Parkinson's disease, schizophrenia, and several other brain disorders.
The Brain Morphology BIRN Project will be based on ongoing studies of human subjects. Led by Bruce Rosen, director of the Athinoula A. Martinos Center for Structural and Functional Biomedical Imaging (Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard Medical School) and colleague Anders Dale, the project will rely on collaborators led by Ferenc Jolesz and Ron Kikinis of Harvard's Center for Neuro-imaging Technologies (Brigham and Women's Hospital), Toga's group at UCLA, and three groups at NCRR-supported General Clinical Research Centers (GCRCs). One of these is at Duke, led by Ranga Krishnan; another is the GCRC at Massachusetts General Hospital, where the BIRN projects will be led by David Nathan and Randy Gollub.
The third GCRC group, which includes clinical investigators in the departments of psychiatry, neurosciences, and radiology at the UCSD School of Medicine, is led by Edward Holmes. A major goal of this project is to develop technologies for enabling seamless interoperability of algorithms and computational tools for analysis and visualisation of structural brain imaging data and for sharing of data and computational resources across the research network. The initial clinical focus of the project will be on depression and Alzheimer's disease.
Advanced networking for BIRN will be developed using the Internet 2/Abilene high-speed infrastructure. Eventually, BIRN will use the large-scale distributed supercomputing resources of the TeraGrid, being established by NSF under the Partnerships for Advanced Computational Infrastructure (PACI) programme. TeraGrid, the most powerful computing environment ever proposed for scientific research, will facilitate the acquisition and correlation of the huge, complex datasets. "It's a tremendous computational challenge to perform comparisons on the vast amount of data that will be collected by the BIRN sites", said Fran Berman, director of SDSC, one of four TeraGrid sites. "BIRN will be an ideal test bed for the national cyberinfrastructure, bringing together the hardware and software necessary for a scalable network of databases and computational resources."
Mark Ellisman is also looking forward to the participation of Cal-(IT)², a new partnership of UCSD and the University of California, Irvine, to extend the Internet throughout the physical world. Cal-(IT)² director Larry Smarr explained that "BIRN will be part of the Cal-(IT)² programme on Digitally Enabled Genomic Medicine, and BIRN will work with Cal-(IT)² to develop a high-speed wireless capability to enable anywhere/anytime access to BIRN data and images." Additional supporters of BIRN include industry partners Oracle Corporation, Compaq Computer Corporation, and Sun Microsystems, that are providing database, storage, server, and computer-cluster technologies.