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August 9, 2005

Berkeley Lab and QB3 Establish Joint Biological Data
Management Core

BERKELEY, CA – To help researchers turn the growing mountains of biological data into scientific knowledge, the California Institute for Quantitative Biomedical Research (QB3) and Lawrence Berkeley National Laboratory (Berkeley Lab) have agreed to turn the Lab’s Biological Data Management and Technology Center into a joint Biological Data Management Core Facility.

The California Institute for Quantitative Biomedical Research (QB3) hosts much of its computational biology work on the new Mission Bay campus of UC San Francisco, shown above, as well as on the UC Berkeley and UC Santa Cruz campuses. QB3 has entered into a new data management partnership with Berkeley Lab’s Biological Data Management and Technology Center. The two efforts will merge into a joint Biological Data Management Core Facility.

The joint project will bring the center’s expertise in data management to bear on the increasingly large and complex datasets being generated by some of the world’s leading biological and biomedical research centers. QB3 is a partnership of three University of California campuses — San Francisco, Berkeley and Santa Cruz. Berkeley Lab is a U.S. Department of Energy laboratory with extensive research programs in life sciences and scientific computing.

“We see this as a very promising partnership,” said Regis Kelly, executive director of QB3. “Leveraging the expertise of the two organizations will help provide new insights into preventing, treating and curing disease.”

The main goal of the core facility will be to provide data management support for academic groups affiliated with QB3 and Berkeley Lab and help these groups to share data management experience, expertise, and technology. The new core facility, which will serve academic biological and biomedical projects in the Bay Area, will be led by Victor M. Markowitz, head of the biological data center.

“As more and more biological data is generated from experiments, the demand for managing this data becomes an ever more challenging problem,” said Horst Simon, Associate Laboratory Director for Computing Sciences at Berkeley Lab. “Effectively addressing these biological data management challenges in an academic setting requires consolidating data management and system development expertise in a central core, which has led us to create the Biological Data Management Core Facility.”

The challenge is not only the amount of data, but also how the data were generated and managed. Much of the experimental data is generated using inherently imprecise tools and techniques and is stored in diverse and poorly correlated repositories.

Addressing these challenges requires expertise in several areas, such as data modeling, data integration, database administration, data sharing and security, software engineering, and software and data quality control, according to Markowitz. “Due to the complexity and cost involved, few academic institutions can afford to acquire such expertise. Therefore, a central core can provide an effective solution to this problem,” he said.

The core facility will conduct seminars in biological data management and will help students gain practical experience in large-scale biological data management and analysis.

The Biological Data Management and Technology Center, which will form the basis for the core facility, was established in January 2004 at Berkeley Lab. Over the course of its first year of existence, the center has developed the Integrated Microbial Genomes system in collaboration with the Department of Energy Joint Genome Institute, and has worked with a number of academic organizations in the Bay Area, including the Berkeley Structural Genomics Center, the Bay Area Laboratories for Integrating Nanotechnology in Cancer consortium, and the Center for Neurobiology and Psychiatry at UCSF, to assess their data management needs and help develop strategies to address them.

Berkeley Lab’s Computing Sciences organization is well known for managing large-scale computational and networking facilities such as the U.S. Department of Energy’s National Energy Research Scientific Computing Center (NERSC) and Energy Sciences Network for national user communities with thousands of scientific users.

The California Institute for Quantitative Biomedical Research (QB3) is a cooperative effort among three campuses of the University of California and private industry. The Institute builds on strengths in the engineering and physical sciences at UC Berkeley, engineering and mathematical sciences at UC Santa Cruz, and the medical sciences at UC San Francisco, as well as strong biology programs at the three campuses. QB3 harnesses the quantitative sciences to integrate our understanding of biological systems at all levels of complexity — from atoms and protein molecules to cells, tissues, organs and the entire organism. This long-sought integration allows scientists to attack problems that have been simply unapproachable before, setting the stage for fundamental new discoveries, new products and new technologies for the benefit of human health.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California. Learn more at

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