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Genomic Science Program

Systems Biology for Energy and the Environment

Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

User Facilities Enabling Science

Empowering an international community of scientists with the most advanced technologies

The U.S. Department of Energy (DOE) Office of Science oversees the construction and operation of some of the nation's most advanced scientific user facilities, located at national laboratories and universities. These include particle and nuclear physics accelerators, synchrotron light sources, neutron scattering facilities, supercomputers and high-speed computer networks, nanoscale science research centers, genome sequencing facilities, and advanced resources in imaging and analysis for biological and environmental systems. Guidelines for submitting proposals for access to these facilities are available from the individual centers.

Presented below are descriptions of some of the most important facilities for the Genomic Science program.

Joint Genome Institute (JGI)

DOE Joint Genome Institute
ETOP Microfluidics Device [Roy Kaltschmidt, Berkeley Lab]

Sequencing more than one trillion DNA base pairs per year, DOE JGI in Walnut Creek, California, provides state-of-the-art capabilities for genome sequencing and analysis. With more than 1,100 worldwide collaborators on active projects, DOE JGI is the preeminent facility for sequencing plants, microbes, and microbial communities that are foundational to energy and environmental research. DOE JGI’s Community Science Program (CSP) is designed to bring high-throughput sequencing to the scientific community at large.

Environmental Molecular Sciences Laboratory (EMSL)

Penicillium spores using SEM (EMSL)
click to enlarge

Researchers are studying mineral-biological associations in the rhizosphere to better understand soil mineral weathering. Here, spores of Penicillium sp., a ubiquitous soil fungus, were imaged at EMSL. [Image available under a Creative Commons License (CC BY-NC-SA 2.0); colorization by A. Dohnalkova.]

By co-locating more than 150 premier experimental instruments and systems with supercomputing capabilities, DOE EMSL is able to make multiple types of capabilities available to single investigators or multidisciplinary teams to study environmental challenges at the molecular level. DOE EMSL, located at Pacific Northwest National Laboratory, has helped thousands of researchers use a multidisciplinary, collaborative approach to iterate between theory and experiment to solve important challenges in biogeochemistry and subsurface science, biological interactions and dynamics, and interactions at the interfaces of natural and engineered materials. EMSL’s Terrestrial and Subsurface Ecosystems (TSE) Science Theme focuses on the dynamics of nutrients, metabolites, and contaminants at biogeochemical interfaces in heterogeneous environments across multiple scales.

Facilities Integrating Collaborations for User Science (FICUS)

Facilities Integrating Collaborations for User Science (FICUS) initiative was established to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities stewarded by the Department of Energy Office of Science into their research. It current participants include the Environmental Molecular Sciences Laboratory (EMSL), the Joint Genome Institute (JGI), the Atmospheric Radiation Measurement (ARM) user facility, National Energy Research Scientific Computing Center (NERSC), and DOE Systems Biology Knowledgebase (KBase).

Biomolecular Characterization and Imaging

Structural Biology Resources

Structural biology and imaging resources—together with today’s systems biology approaches—are key capabilities for understanding the relationship between the genome, structure, function, and environmental interactions of plants and microbes important for energy and environmental missions. As part of its fundamental biology portfolio, the U.S. Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) supports a suite of experimental research technologies, methodologies, instruments, and computational capabilities at DOE facilities. The resolutions and scales provided by these resources enable studying and understanding biological structures and functional processes important to BER-funded investigators and centers. Capabilities of and contact information for each station are described at

  • Genomics-Enabled Plant Biology for Determination of Gene Function DE-FOA-0002601 [12/16/21]
  • Systems Biology-Enabled Microbiome Research to Facilitate Predictions of Interactions and Behavior in the Environment DE-FOA-0002602 [12/15/21]
  • Biosystems Design to Enable Safe Production of Next-Generation Biofuels, Bioproducts, and Biomaterials DE-FOA-0002600 [12/13/21]
  • SBIR/STTR Funding Call for Climate, Energy and Scientific R&D DE-FOA-0002555 [12/13/21]
  • Quantum-Enabled Bioimaging and Sensing Approaches for Bioenergy DE-FOA-0002603 [11/15/21]
  • NAS Report: Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology. More »
  • JBEI's Jay Keasling named Office of Science Distinguished Scientist Fellow. More »
  • DOE BER Early Career Research Funding Opportunity Preapplications due Oct. 21. More »
  • Systems Biology of Bioenergy-Relevant Microbes Projects Awarded. [7/21] More »
  • BER Bioimaging Science Program announces new awards. [7/21] More »
  • DOE BER Request for Information – Responses due by 10- 31-21. More »
  • DOE BER Awards $45.5 Million [6/21] More »
  • More News and Announcements »

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