genomic.science@science.doe.gov
Office of Biological and Environmental Research
U.S. Department of Energy Office of Science
Susan Gregurick
Office of Biological and Environmental Research
U.S. Department of Energy Office of Science
genomic.science@science.doe.gov
Office of Biological and Environmental Research
U.S. Department of Energy Office of Science
Office of Biological and Environmental Research
U.S. Department of Energy Office of Science
The KBase User Interface will contain a rich set of modeling tools for predictive systems biology.
The new Systems Biology Knowledgebase (KBase) is a collaborative effort designed to accelerate our understanding of microbes, microbial communities, and plants. It will be a community-driven, extensible and scalable open-source software framework and application system. KBase will offer free and open access to data, models and simulations, enabling scientists and researchers to build new knowledge and share their findings.
May 2012: KBase website launches Alpha Release with draft tutorials, database loads, unified prototypes, workflow drafts, cloud and cluster services
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.
2010: BER awarded funding to 11 university-led projects for research to develop new computational biology and bioinformatic methods to enable KBase. These awards were given in response to Funding Opportunity Announcement DE-FOA-0000143. (Learn more about these university projects and the completed Recovery Act pilots.)
September 2010: DOE Systems Biology Knowledgebase Implementation Plan published.
2009: With funding from the American Recovery and Reinvestment Act, a year-long R&D project was carried out to support the conceptual design and implementation planning necessary to develop KBase. Completed in September 2010, this effort included a series of community planning workshops and five pilot projects. Together, these workshops and pilots informed the scientific objectives, software requirements, and design approaches detailed in the DOE Systems Biology Knowledgebase Implementation Plan, the final product of the R&D project.
May 2008: DOE BER holds computing workshop on GTL Systems Biology Knowledgebase. The subsequent report was published in March 2009.
