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Name of Collaboratory :


Biomedical Informatics Research Network: Coordination Center (BIRN CC)


Logo :


URL :  

Collaboratory Status :

Completed   Start Date : 2001 End Date : 2004 Info Last Updated : Fri, Dec 3 2010 3:00am PST

Primary Collaboratory Function :

  Distributed Research Center  

Secondary Collaboratory Functions :


Domain(s) :

  Neuroscience--> Brain Imaging--> Diseases of the brain and the treatment thereof  

Brief Description of the Collaboratory :


BIRN's goal is to enable data sharing across neuroimaging databases and image archives throughout the nation. To do this requires development of new and ambitious national-scale information infrastructure to store and compare a vast number of data objects. BIRN's scientific goal is to integrate a wide variety of types of data, acquired by the most advanced biomedical imaging and General Clinical Research Centers around the US, into a extensible knowledge system. To make this possible, BIRN CC is designing and implementing a hardware and software infrastructure, supported by the necessary expertise, to manage, provide access to, and support analysis across geographically distributed data sets.

Data sharing will enable better understanding of the underpinnings of neurological disease, including multiple sclerosis, schizophrenia, Alzheimer's, and Parkinson's, some of the the diseases slated for study during the early years of the project.

Altogether, there are four grants:

BIRN Coordinating Center (this description)
Mouse BIRN, looking at neuroimaging of the mouse brain, which is a mamallian counterpart to the reactions the human brain has in these diseases.
Brain Morphometry BIRN, looking at these diseases in human brains.
Function BIRN (also called FIRST BIRN) where the data is functional imaging of brain activity.

Day to day operations for the BIRN infrastructure are overseen by UCSD BIRN Coordinating Center (BIRN CC). The key is the ability to integrate various images at various scales so researchers can get a "big picture" and aggregate over data widely collected data

The CC is responsible for deploying the network infrastructure, developing software tools and the common Web portal interface, sharing tools/code across institutions, converting data between tools, and providing support services, such as network monitoring, performance measurement, statistical analysis, a help desk, problem tracking and resolution, and documentation.


Access to Instruments :


Access to Information Resources :

  The whole point of BIRN is to gather data from distributed resources so that a researcher can gather correlating information about disease and its consequences. It uses a distributed data repository using mediator technology to allow a researcher to find information even though it is stored in various places with various views (scales) and formats.  

Access to People as Resources :

  The people building the visualization and statistical analysis software talk with the researchers to understand their needs. Those doing the translation software need to understand the issues at the data site, what kind of data, measurements, etc. so it can be properly translated. They all communicate at various meetings and workshops in breakout sessions about issues of building the facility as well as its governance.  

Funding Agency or Sponsor :

United States Department of Health and Human Services
National Institutes of Health (NIH)
National Center for Research Resources (NCRR)

Notes on Funding Agencies/Sponsors:

Organizations with Funded Participants:
Organization name:
Approx # of participants:
Description of organization's role(s):
University of California, San Diego (UCSD)
   National Center for Microscopy and Imaging Research (NCMIR)
Dr. Mark Ellisman, UCSD Mr. Steven Peltier, UCSD ï Project Manager: Mark James
   San Diego Supercomputer Center (SDSC)
   California Institute for Telecommunications and Information Technology (Cal-(IT)≤)
National Partnership for Advanced Computational Infrastructure (NPACI)
Organizations Otherwise Associated:
Organization name:
Approx # of participants:
Description of organization's role(s):
University of California, San Diego (UCSD)
   National Biomedical Computation Resource

Notes on Participants/Organizations:
84 individual accounts (includes scientists and developers)as of June 2003

34 people are in the BIRN CC, 3 more at Internet2, and 2 at Ohio State. Typically each site has a system administrator as well


Communications Technology Used :

  Public and Secure Website & Video Conferencing via a MCU unit. They also utilize face-to-face meetings, email and phone.  

Technical Capabilities :

  Asynchronous conversation
Synchronous conversation
Audio, Video, Instant messaging/chat
  Key Articles :  

Ackerman, S. P. (2003). BIRN: Putting heads together in cyberspace NCRR Reporter, 27(4), 5-7.

Ellisman, Mark H. (2005). Cyberinfrastructure and the future of collaborative work Issues in Science and Technology, 22(1), 43-50.

Marx, V. (2002). Beautiful bioimages for the eyes of many beholders Science, 297, 39-40.

Newman, H. B., Ellisman, M. H., & Orcutt, J. A. (2003). Data-intensive e-science frontier research Communications of the ACM, 46(11), 68-77.


Project-reported performance data :

  As of June 2003, there are 200,971 files (images and other analyses) with 60 GB.
The Mediator works but is not in production; Atlases exist (they have the Mouse one, but are still deciding on the Human one); Individuals have various visualization and statistical analysis tools--that will be made available on the portal.
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