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38-455: The JGI advances genomics research by providing the research community with access to the latest generation of genome sequencing and analysis capabilities. It employs a staff of 250 scientists, technicians, and other personnel to support the research of the 2,180 scientific users who make use of it for their research each year. The facility sequenced 658 trillion total bases in FY 2022, and this output

76-558: A National Academy of Sciences report titled Opportunities in Chemistry . The report identified scientific challenges relating to energy and the environment that required fundamental research to achieve a solution. In response, then director of PNNL, William R. Wiley, and lab senior managers proposed a center for molecular science that would bring together researchers from the physical and life sciences and theoreticians with experience in computing and molecular process modeling. Wiley envisioned

114-899: A Web of Science search in March 2020. In June 2013, EMSL retired the Chinook computer and welcomed Cascade, a 3.4-petaflops system. EMSL celebrated its twentieth anniversary in August 2017, showcasing NWChem computational chemistry software, and advances in subsurface science and foundational biofuel production. Scientific leaders participated in the event, including internationally recognized scientists Thom Dunning, Steve Colson, and Jean Futrell. Today, EMSL focuses its scientific research in Functional and Systems Biology, Environmental Transformations and Interactions, and Computing, Analytics, and Modeling together with users from diverse scientific communities. This science

152-488: A biogeochemistry question concerning the fundamental interaction between microbes and minerals, and a study addressing the structure and function of proteins in the cell membrane. Work on these challenges led to new opportunities for the scientific community, with research campaigns designed to focus teams on a single challenge. In January 2007, EMSL celebrated its first permanent expansion: a nearly 4,000-square-foot raised floor for an 11.8-teraflop computer named Chinook, which

190-450: A facility with advanced instrumentation for the study of molecular-level chemistry in an integrated and collaborative manner. Ohio-based Battelle Memorial Institute, which operates PNNL for DOE, approved $ 8.5 million in funding over four years to build the facility; develop research programs; and obtain the equipment, facilities, scientists, and support staff. Construction began in July 1994 and

228-450: A few months to a few years. EMSL users do not have to stay on-site for the duration of their project and can visit the laboratory when needed. Much of the sample processing and analysis can be handled remotely. EMSL's user community provides the laboratory’s management team with recommendations for scientific direction and efficient operations through an elected committee of representatives. The idea that would become EMSL began in 1985 with

266-672: A single integrated communications network that became the basis for the commercial Internet . The Office of Biological and Environmental Research (BER) supports research and scientific user facilities in the biological and environmental sciences to support DOE's missions in energy, environment, and basic research. BER initiated the Human Genome Project in 1986 and has continued to support activity in genomics -based systems biology and initiatives related to biotechnology applications. The Joint Genome Institute , formed in 1997, initially conducted sequencing of human DNA in support of

304-462: Is a Department of Energy, Office of Science facility at Pacific Northwest National Laboratory in Richland, Washington , United States. EMSL scientists and collaborators perform fundamental research that focuses on the biological, biogeochemical, and physical principles to predict processes occurring at the molecular and genomics-controlled smallest scales to the environmental Earth system changes at

342-467: Is a user research facility whereby scientists, from around the world, can submit project proposals to access the laboratory’s experts and equipment at no cost. Proposals are screened through a competitive peer-review process to ensure the project is scientifically impactful and relevant to DOE's Office of Biological and Environmental Research mission. Scientists whose proposals are accepted are referred to as EMSL users. Typical user research projects can last

380-606: Is driving technology development and computational capabilities. Office of Science The Office of Science is a component of the United States Department of Energy (DOE). The Office of Science is the lead federal agency supporting fundamental scientific research for energy and the Nation’s largest supporter of basic research in the physical sciences. The Office of Science portfolio has two principal thrusts: direct support of scientific research and direct support of

418-453: Is now doubling about every two years. Research at JGI is organized into seven programs: The JGI provides users with access, at no cost, to high-throughput genomic and specialized capabilities and data analysis. Researchers submit proposals to one of the seven JGI user programs, and all proposals are reviewed for scientific merit and relevance to the DOE research mission. If the proposal is approved,

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456-406: Is provided for research activities in the national laboratories and universities. The office is the principal (or the single largest) source of U.S. federal government support for research in high-energy physics, nuclear physics, fusion energy, materials science, and chemical sciences. The Office of Science is estimated to provide 40 percent of the funding for basic research in the physical sciences in

494-589: The Energy Policy Act of 2005 . DOE lists 76 Nobel Prize winners as having been associated with Office of Science programs or facilities under DOE and its predecessor agencies. The Office of Science is led by a Presidentially-nominated, Senate-confirmed Director and three senior career federal Deputy Directors. The current acting director of the Office of Science is Harriet Kung . The current deputy directors are Principal Deputy Director Dr. J. Stephen Binkley,

532-469: The Energy Sciences Network (ESnet), which interconnects more than 40 DOE sites at speeds up to 100 gigabits per second. ESnet is a successor to a network that the Office of Science created in 1974 to connect geographically dispersed researchers through a single network. In the 1980s the Office of Science collaborated with DARPA , NSF and NASA to convert the agencies' separate networks into

570-484: The Human Genome Project —the JGI generated the complete sequences of Chromosomes 5, 16 and 19—the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the DOE's science mission. Since 2004, the JGI has been a user facility that advances genomics research in a broad range of disciplines where DNA sequence information is likely to drive scientific discoveries. In February 2004,

608-506: The Thomas Jefferson National Accelerator Facility . The Office is currently led by Acting Director Dr. Harriet Kung . The Office of Science includes six interdisciplinary science program offices: The Office of Advanced Scientific Computing Research (ASCR) supports research and development in applied mathematics , computer science , and integrated network environments. The programs it supports represent

646-632: The University of California , which manages the three national labs for the DOE, leased laboratory and office space in a light industrial park in Walnut Creek, California to consolidate genome research activities. Led by biotechnology industry veteran Nigel Mouncey, who assumed the position of Director in March 2017, the DOE JGI receives its funding from the Office of Biological and Environmental Research in DOE's Office of Science. Originally established to work on

684-679: The four DOE Bioenergy Research Centers. The Director of JGI since 2017 is Nigel Mouncey. Mouncey also serves as the President of the Society for Industrial Microbiology and Biotechnology (SIMB) The Joint Genome Institute ( JGI ) was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing , technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (Berkeley Lab), Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL).In 1999,

722-551: The 17 United States Department of Energy National Laboratories . The office is the predominant U.S. federal government sponsor for research in the physical sciences , including physics , chemistry , computer science , applied mathematics , materials science , nanoscience , and engineering , as well as systems biology and environmental sciences . The Office of Science makes extensive use of peer review and federal advisory committees to develop general directions for research investments, to identify priorities, and to determine

760-402: The DOE mission areas of bioenergy , understanding global cycles such as the carbon cycle , and biogeochemistry and are chosen primarily based on scientific merit as determined by outside review. In 2006, the JGI published the genome of the first tree sequenced—the cottonwood ( Populus trichocarpa ). In partnership with other federal institutions and universities, the JGI has also published

798-561: The Genomes OnLine Database. The Integrated Microbial Genomes System (IMG), which provides a framework for comparative analysis of primarily microbial genomes, though the system also supports eukaryotic genomes and environmental samples. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective. Environmental Molecular Sciences Laboratory The Environmental Molecular Sciences Laboratory ( EMSL , pronounced em-zul)

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836-466: The Human Genome Project. Its current focus is on sequencing the genomes of microbes , microbial communities , fungi , plants , and other organisms. Environmental efforts include research on the global carbon cycle and possible mitigation of the impacts of climate change . When it started in 1978, BER's Climate Change Research Program was the first U.S. research program to investigate

874-543: The JGI launched the Community Sequencing Program (CSP), known as the Community Science Program, which provides the scientific community at large with access to high-throughput, high-quality sequencing, DNA synthesis, metabolomics and analysis capabilities. The projects involve many important multicellular organisms, microbes and communities of microbes called metagenomes (or microbiomes) related to

912-675: The JGI provides the users a number of standard sequencing, synthesis, and metabolomics products. The JGI collaborates extensively with the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory (PNNL). The two facilities jointly manage the Facilities Integrating Collaborations for User Science (FICUS) program, designed for researchers who require the capabilities of both user facilities to perform their research. The JGI also performs extensive sequencing on behalf of

950-424: The U.S. ITER Project Office, a partnership of Oak Ridge National Laboratory and Princeton Plasma Physics Laboratory. More than 90 percent of the Office of Science budget is allocated to research and scientific facilities. The fundamental research areas in which the Office of Science has programs include physics and other basic energy sciences, biological and environmental sciences, and computational science. Support

988-610: The United States. It is also a major source of funding for government-supported research in climate change, geophysics, genomics, life sciences, and science education. In constant dollars , Office of Science annual budgets for Basic Energy Science and Advanced Scientific Computing nearly doubled between fiscal years 1996 and 2009. Budgets for High Energy Physics and Biological and Energy Research remained relatively constant through that 14-year period. Nuclear Physics and Fusion Energy Sciences budgets were relatively static through most of

1026-784: The coupling of terrestrial and atmospheric processes. Rhizosphere Function investigates interactions between genes and the environment at the molecular level to understand, predict and control plant and ecosystem traits at the systems scale. Structural Biology gains structural, biochemical, and dynamic information about proteins, protein complexes, and other biomolecules at nanoscale spatial and temporal resolutions to understand function. Systems Modeling uses computational models of protein structure and function, metabolic modeling, and machine learning approaches to associate genotype with phenotype and to understand biological processes that control nutrient flux, and enable predictive approaches to biodesign and biofuel/bioproduct production. EMSL

1064-489: The development, construction, and operation of unique, open-access scientific user facilities that are made available for use by external researchers. The Office of Science manages this research portfolio through six interdisciplinary scientific program offices: Advanced Scientific Computing Research, Basic Energy Sciences, Biological and Environmental Research, Fusion Energy Sciences, High Energy Physics and Nuclear Physics. The Office of Science also has responsibility for 10 of

1102-463: The effects of greenhouse gases on climate and environment. The Office of Science climate change research program is now the third largest in the U.S. The Fusion Energy Sciences (FES) organization supports efforts to expand the fundamental understanding of plasma physics and the knowledge needed to develop a fusion energy source. This organization supports U.S. participation in the ITER project through

1140-421: The genome sequences of sorghum, a candidate feedstock for biofuels and biomanufacturing. The JGI also supports programs dedicated to functional and evolutionary genomics related to the organisms and environments being sequenced and the development of computational and bioinformatic tools for data management and mining. These genome and metagenome/microbiome analysis systems include Genome Portal, Phytozome, IMG and

1178-745: The largest and most active computer science research effort within the U.S. federal government. Supercomputer facilities supported by ASCR include the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory in California, and the Leadership Computing Facility at Oak Ridge National Laboratory in Tennessee and Argonne National Laboratory in Illinois. The ASCR supports

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1216-423: The largest scales. The Functional and Systems Biology Science Area focuses on understanding enzymes and biochemical pathways that connect protein structures and functions to phenotypic responses and interactions within cells, among cells in communities, and between cellular membrane surfaces and their environment for microbes and plants. The Environmental Transformations and Interactions Science Area focuses on

1254-619: The mechanistic and predictive understanding of the environmental (physiochemical, hydrological, biogeochemical), microbial, plant, and ecological processes in above and belowground ecosystems, the atmosphere, and their interfaces. The Computing, Analytics, and Modeling Science Area focuses on using state-of-the-art experimental data to develop a predictive understanding of biological and environmental systems through advanced data analytics, visualization, and computational modeling and simulation. EMSL uses Integrated Research Platforms to uncover critical information for understanding and predicting

1292-896: The molecular functions of biological and ecosystem processes. Biogeochemical Transformations investigates how molecular interactions at the Earth’s land, water, and air interfaces transform and transport nutrients and contaminants within the environment. Biomolecular Pathways investigates the translation of genomic information into functional relationships among biomolecules within cells in response to changes in their internal or external environment. Cell Signaling and Communications reveals dynamic interactions and trafficking of molecular signals within and between cells, populations, and communities to understand complex inter-relationships between organisms in response to their environment. Terrestrial-Atmospheric Processes investigates molecular transformations, physical processes that control them, and

1330-512: The period, but had substantial increases in fiscal 2009. The increase in the Fusion budget reinstated the U.S. contribution to ITER, which was reduced significantly in the previous year. DOE's Office of Energy Research was a predecessor to the Office of Science. In 2006, the Office of Science was placed under the oversight of the Under Secretary of Energy for Science , a new position created by

1368-424: The very best scientific proposals to support. The 10 Office of Science national laboratories are: Ames Laboratory , Argonne National Laboratory , Brookhaven National Laboratory , Fermi National Accelerator Laboratory , Lawrence Berkeley National Laboratory , Oak Ridge National Laboratory , Pacific Northwest National Laboratory , Princeton Plasma Physics Laboratory , SLAC National Accelerator Laboratory , and

1406-678: Was completed in August 1997. EMSL opened October 1, 1997 for full operation. During its first five years, EMSL leaders built capabilities, recruited scientific leadership, and attracted users. The leaders then expanded the scientific focus to include biology, particularly the study of naturally occurring microbes for environmental cleanup, alternative energy, and carbon dioxide reduction in the atmosphere. EMSL's early user program focused on single investigator studies that crossed scientific areas and quickly reached more than 1,000 users per year, representing every state and several foreign countries. During this period, EMSL focused on two Grand Challenges:

1444-615: Was then the fifth-fastest system in the world. In April 2008, EMSL dedicated a new office pod to distinguished user J. Mike White that houses nearly 100 staff and users PNNL. In early 2012, EMSL opened its Quiet Wing housing a suite of ultrasensitive high-resolution microscopy and scanning instruments. In October 2010, EMSL’s premier computational chemistry software package, NWChem went open source, allowing computer scientists worldwide to contribute to its future development and making it available to more researchers and students. The code has been cited over 3760 times since 2010, according to

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