National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase

Washington, DC—The DOE Office of Science (SC) announced today the selection of a collaboration of top scientists from across the Nation to lead development of a computer-based Systems Biology Knowledgebase ( for the scientific community that is designed to advance understanding of microbes and plants for energy and environmental solutions.

"Hidden in the mountains of biology data we are accumulating today are the secrets of Nature's solutions to a broad range of challenges we face in energy and the environment," said Dr. Sharlene Weatherwax, DOE Associate Director of Science for Biological and Environmental Research. "The Knowledgebase will accelerate our ability to unlock those secrets and help take systems biology to a new level."

The Knowledgebase is designed to accelerate discovery by enabling data integration, mining, and computational analysis of the masses of information currently being produced by rapid genomic sequencing and other high-throughput techniques of contemporary systems biology. For over a decade, experts have pointed to a need for more integrated computational processing of the new biology data, which has been expanding at an increasing pace as sequencing and other technologies have advanced. Increasingly, new insights in system biology come from comparative studies across multiple genomes and organisms. The Knowledgebase will provide enhanced power to rapidly achieve such comparisons.

Leading the collaboration will be principal investigator Adam Arkin of Lawrence Berkeley National Laboratory (LBNL), with co-principal investigators Rick Stevens of Argonne National Laboratory (ANL), Robert Cottingham of Oak Ridge National Laboratory (ORNL), and Sergei Maslov of Brookhaven National Laboratory. Also participating as investigators in the multi-institutional program are Pamela Ronald of the University of California, Davis; Matthew DeJongh of Hope College in Michigan; Gary Olsen of the University of Illinois at Urbana-Champaign; Doreen Ware of the Cold Spring Harbor Laboratory; and Mark Gerstein of Yale University.

SC's Office of Biological and Environmental Research (BER) initiated the Knowledgebase effort in Fiscal Year 2009 with $3 million in seed money from the American Recovery and Reinvestment Act. The initial funds were used to map out a strategy and architecture for the Knowledgebase, as well as to support pilot software development projects and procure new hardware. SC's FY 2012 Budget Request includes $12 million for researchers to begin the build-out and development of the Knowledgebase, which will involve extensive software development, data capture, and integration. The Knowledgebase will provide unparalleled new capabilities to evaluate new data-driven theories of complex microbial and plant systems function and to extend the framework with data, protocols, algorithms, and models that may be rigorously tested.

The DOE Systems Biology Knowledgebase will leverage major existing scientific capabilities and supercomputing facilities within the DOE national laboratory complex, including the Joint Genome Institute, the DOE BioEnergy Research Centers, the Energy Sciences Network, the National Energy Research Scientific Computing Center at LBNL and the Magellan testbed, along with the DOE Leadership Computing Facilities at ORNL and ANL.

BER's Genomic Science program, which funds the Knowledgebase, supports research aimed at identifying the fundamental principles that drive biological systems relevant to DOE missions in energy and the environment. For more information on this program, please visit the Genomic Science website. To go directly to the Knowledgebase, simply click: