Overview of the DOE Systems Biology Knowledgebase and Related Research Activities

The Office of Biological and Environmental Research (BER) within the U.S. Department of Energy’s (DOE) Office of Science advances world-class biological and environmental research and provides scientific facilities to support DOE missions in scientific discovery and innovation, energy security, and environmental responsibility. As a leader in systems biology, BER’s Genomic Science program supports scientific research that seeks to achieve a predictive understanding of microbial and plant systems relevant to DOE missions. By revealing the genetic blueprints and fundamental principles that control the biological functions of these systems, the Genomic Science program advances the foundational knowledge underlying biological approaches to producing biofuels, sequestering carbon in terrestrial ecosystems, and cleaning up contaminated environments.

The program funds a portfolio of systems biology research that produces petabytes of data annually. Examples include genomic sequences on microbes, plants, and complex environmental samples; proteomic data; expression data; isotopic flux data for pathway analysis; protein binding data for functional annotation; data from imaging of proteins localized in subcellular compartments; and metadata associated with diverse experimental conditions and sampling techniques. Integrating and using these diverse data to develop predictive models of biological systems will require an integrated computational environment. To provide the research community with such a resource, the Genomic Science program is developing the DOE Systems Biology Knowledgebase. A knowledgebase is a cyberinfrastructure consisting of a collection of data, organizational methods, standards, analysis tools, and interfaces representing a dynamic body of knowledge.