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Sample records for genome institute jgi

  1. Joint Genome Institute (JGI)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    data (Rumen HiSeq dataset). Investigators: Edward Rubin, Victor Markowitz, Shane Canon, Jeremy Brand, (LBNL) More Information: See the JGI web site Last edited: 2012-04-12...

  2. Eukaryotic Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    From the JGI webportal users can choose Eukaryotic genomes from a photo list, access the JGI FTP directories to download data files, use the Tree of Life navigation tool, or choose a genome and go directly to a website specific to that one genome. The individual sites include direct access to download sequence files, BLAST, search, view and navigate the genomic annotations.

  3. Joint Genome Institute (JGI) | U.S. DOE Office of Science (SC)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Joint Genome Institute (JGI) Biological and Environmental Research (BER) BER Home About Research Facilities User Facilities Atmospheric Radiation Measurement Climate Research Facility (ARM) Environmental Molecular Sciences Laboratory (EMSL) Joint Genome Institute (JGI) Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) Community Resources Contact Information Biological and Environmental Research U.S. Department of Energy

  4. Microbial Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    As of March 2008, The Joint Genome Institute has released 296 Prokaryotic microbial sites, with 216 in finished status.

  5. Integrated Microbial Genomes (IMG) System from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov. [Abstract from The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions; Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova and Nikos C. Kyrpides; Nucleic Acids Research, 2008, Vol. 36. (Database Issue) See also the companion system, Integrated Microbial Genomes with Microbiome Samples.

  6. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  7. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  8. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  9. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema (OSTI)

    Miranda Harmon-Smith

    2010-09-01

    A Howard Hughes Medical Institute (HHMI) video production describing the Whole Genome Shotgun Sequencing process at the US Department of Energy's Joint Genome Institute (JGI).

  10. JGI Genomics and Bioinformatics for Undergraduate Educators Workshop

    Broader source: Energy.gov [DOE]

    The JGI will be holding the JGI Genomics and Bioinformatics for Undergraduate Educators Workshop in conjunction with the JGI User Meeting. The workshop will take place March 23-26, 2013 at the JGI.

  11. Diatom Genomics (2009 JGI User Meeting)

    SciTech Connect (OSTI)

    Ambrust, Ginger

    2009-03-26

    Ginger Armbrust from the University of Washington spoke about diatom genomics on March 26, 2009 at the DOE JGI User Meeting

  12. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Ambrust, Ginger

    2011-04-25

    Ginger Armbrust from the University of Washington spoke about diatom genomics on March 26, 2009 at the DOE JGI User Meeting

  13. Genome Improvement at JGI-HAGSC

    SciTech Connect (OSTI)

    Grimwood, Jane: Schmutz, Jeremy, J.: Myers, Richard, M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  14. Genomic Sequencing of Single Bacterial Cells (2010 JGI User Meeting)

    SciTech Connect (OSTI)

    Woyke, Tanje

    2010-03-26

    Tanja Woyke from the DOE JGI on the "Genomic Sequencing of Single Bacterial Cells" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  15. Opening Remarks from the Joint Genome Institute and Argonne Lab High Performance Computing Workshop (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Rubin, Eddy

    2010-01-25

    DOE JGI Director Eddy Rubin gives opening remarks at the JGI/Argonne High Performance Computing (HPC) Workshop on January 25, 2010.

  16. Opening Remarks from the Joint Genome Institute and Argonne Lab High Performance Computing Workshop (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-06-03

    DOE JGI Director Eddy Rubin gives opening remarks at the JGI/Argonne High Performance Computing (HPC) Workshop on January 25, 2010.

  17. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Hodges, Scott [University of California, Santa Barbara

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  18. Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Hodges, Scott [University of California, Santa Barbara] [University of California, Santa Barbara

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on "Genomic Speciation and Adaptation in Aquilegia" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  19. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Shuster, Stephen [Penn State University] [Penn State University

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  20. Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Shuster, Stephen [Penn State University

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  1. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using...

  2. Using Genomics to Dissect Seed Development (JGI Seventh Annual...

    Office of Scientific and Technical Information (OSTI)

    Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting) Citation Details In-Document Search Title: Using Genomics to Dissect Seed...

  3. Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Moose, Steve

    2011-04-25

    Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  4. Genomics Dan Rokhsar, DOE JGI/LBNL & UC Berkeley NERSC User Meeting

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for Genomics Dan Rokhsar, DOE JGI/LBNL & UC Berkeley NERSC User Meeting 4 February 2014 Computing for Genomics * The DOE Joint Genome Institute - Who we are, what we do, and why * Two computational problems in genomics - "Assembling" genomes from "shotgun" sequence - "Annotating" "metagenomic" data 2 DOE JGI- A Genomics User Facility * In 1997, as part of the ramp-up for the human genome project, the DOE Office of Biological and Environmental Research

  5. Computational Challenges for Microbial Genome and Metagenome Analysis (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Mavrommatis, Kostas

    2011-06-08

    Kostas Mavrommatis of the DOE JGI gives a presentation on "Computational Challenges for Microbial Genome & Metagenome Analysis" at the JGI/Argonne HPC Workshop on January 26, 2010.

  6. Joint Genome Institute's Automation Approach and History

    SciTech Connect (OSTI)

    Roberts, Simon

    2006-07-05

    Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.

  7. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    SciTech Connect (OSTI)

    Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge; Hua, Susan; Poliakov, Alexander; Shabalov, Igor; Smirnova, Tatyana; Grigoriev, Igor V.; Dubchak, Inna

    2013-10-10

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Here we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  8. Efficient Short-Read Assembly of Eukaryotic Genomes (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Chapman, Jarrod

    2011-06-03

    Jarrod Chapman of the DOE JGI gives a presentation on "Efficient Short-Read Assembly of Eukaryotic Genomes" at the JGI/Argonne HPC Workshop on January 25, 2010.

  9. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Zimmer, Carl [New York Times] [New York Times

    2012-03-20

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  10. Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Zimmer, Carl [New York Times

    2013-01-22

    Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  11. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Tringe, Susannah [DOE JGI

    2013-01-22

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  12. Introduction to Using NERSC for the Joint Genome Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC Introduction to Using NERSC for the Joint Genome Institute May 2, 2011 jgi logo sm NERSC Training Event 1:00-5:00 p.m. PDT May 2, 2011 Joint Genome Institute, 2800 Mitchell...

  13. A Collection of Algal Genomes from the JGI (Conference) | SciTech...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Citation Details In-Document Search Title: A Collection of Algal Genomes from the JGI Algae, defined as photosynthetic eukaryotes other than plants, constitute a major component...

  14. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Tuskan, Gerry

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  15. Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Tuskan, Gerry

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on "Resequencing in Populus: Towards Genome Wide Association Genetics" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  16. Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Kjiersten Fagnan Named NERSC/JGI Engagement Lead Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead September 1, 2014 fagnan.jpg Kjiersten Fagnan has been named the NERSC/JGI Engagement Lead for Joint Genome Institute (JGI) computational and data analysis efforts carried out at the Department of Energy's (DOE) National Energy Research Scientific Computing Center (NERSC). Fagnan, who holds a Ph.D. in Applied Mathematics from the University of Washington, started at NERSC as a petascale postdoc

  17. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology] [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

    2012-03-22

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  18. Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Benner, Stephen [Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology

    2013-01-22

    Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  19. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    SciTech Connect (OSTI)

    Goldberg, Robert [UCLA] [UCLA

    2012-03-21

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  20. Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

    ScienceCinema (OSTI)

    Goldberg, Robert [UCLA

    2013-01-22

    Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  1. Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rubin, Eddy

    2011-04-25

    Director Eddy Rubin on "Discovery of Genes and Genomes through Deep Metagenomic Sequencing of Cow Rumen" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  2. From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Hallam, Steven

    2011-04-26

    Steven Hallam of the University of British Columbia talks "From Fjords to Open Seas: Ecological Genomics of Expanding Oxygen Minimum Zones" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  3. Parallel Assembly of Large Genomes from Paired Short Reads (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Aluru, Srinivas [Iowa State University

    2011-06-08

    Srinivas Aluru from Iowa State University gives a presentation on "Parallel Assembly of Large Genomes from Paired Short Reads" at the JGI/Argonne HPC Workshop on January 25, 2010.

  4. Annotation of Plant Genomes using RNA-seq Data (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Pellegrinni, Matteo [UCLA

    2011-06-08

    Matteo Pellegrini from University of California, Los Angeles gives a presentation on "Annotation of Plant Genomes using RNA-seq Data" at the JGI/Argonne HPC Workshop on January 25, 2010.

  5. 2013 Progress Report -- DOE Joint Genome Institute None 59 BASIC...

    Office of Scientific and Technical Information (OSTI)

    bit.lyJGI-Vision for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the...

  6. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Robinson, Gene

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  7. Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Robinson, Gene

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on "Genomic and Systems Biology Analyses of Social Behavior" at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011

  8. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect (OSTI)

    Gilbert, David

    2009-03-12

    While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that dominated how sequencing was done in the last decade is being replaced by a variety of new processes and sequencing instruments. The JGI, with an increasing number of next-generation sequencers, whose throughput is 100- to 1,000-fold greater than the Sanger capillary-based sequencers, is increasingly focused in new directions on projects of scale and complexity not previously attempted. These new directions for the JGI come, in part, from the 2008 National Research Council report on the goals of the National Plant Genome Initiative as well as the 2007 National Research Council report on the New Science of Metagenomics. Both reports outline a crucial need for systematic large-scale surveys of the plant and microbial components of the biosphere as well as an increasing need for large-scale analysis capabilities to meet the challenge of converting sequence data into knowledge. The JGI is extensively discussed in both reports as vital to progress in these fields of major national interest. JGI's future plan for plants and microbes includes a systematic approach for investigation of these organisms at a scale requiring the special capabilities of the JGI to generate, manage, and analyze the datasets. JGI will generate and provide not only community access to these plant and microbial datasets, but also the tools for analyzing them. These activities will produce essential knowledge that will be needed if we are to be able to respond to the world's energy and environmental challenges. As the JGI Plant and Microbial programs advance, the JGI as a user facility is also evolving. The Institute has been highly successful in bending its technical and analytical skills to help users solve large complex problems of major importance, and that effort will continue unabated. The JGI will increasingly move from a central focus on 'one-off' user projects coming from small user communities to much larger scale projects driven by systematic and problem-focused approaches to selection of sequencing targets. Entire communities of scientists working in a particular field, such as feedstock improvement or biomass degradation, will be users of this information. Despite this new emphasis, an investigator-initiated user program will remain. This program in the future will replace small projects that increasingly can be accomplished without the involvement of JGI, with imaginative large-scale 'Grand Challenge' projects of foundational relevance to energy and the environment that require a new scale of sequencing and analysis capabilities. Close interactions with the DOE Bioenergy Research Centers, and with other DOE institutions that may follow, will also play a major role in shaping aspects of how the JGI operates as a user facility. Based on increased availability of high-throughput sequencing, the JGI will increasingly provide to users, in addition to DNA sequencing, an array of both pre- and post-sequencing value-added capabilities to accelerate their science.

  9. Genomics and Systems Biology of Tuberculosis (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Galagan, James

    2011-04-25

    James Galagan from the Broad Institute spoke about the "Genomics and Systems Biology of TB" on March 26, 2009 during the 4th Annual User Meeting

  10. New Metadata Organizer and Archive Streamlines JGI Data Management

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    New Metadata Organizer Streamlines JGI Data Management New Metadata Organizer and Archive Streamlines JGI Data Management JAMO poster to be presented December 11 at the Bay Area Scientific Computing Day December 5, 2013 Contact: Kathy Kincade, +1 510 495 2124, kkincade@lbl.gov A new centralized data management system now up and running at the Department of Energy's National Energy Research Scientific Computing (NERSC) facility is helping researchers at the Joint Genome Institute (JGI) deal more

  11. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI] [Kerfeld Lab, UC Berkeley and JGI

    2012-03-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  12. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

    2013-01-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  13. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gallivan, Justin [Emory University] [Emory University

    2012-03-21

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  14. Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gallivan, Justin [Emory University

    2013-01-22

    Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  15. Genomics on the Half Shell: So, What do Oysters Have to do with Energy? (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Hedgecock, Dennis

    2011-04-26

    Dennis Hedgecock from the University of Southern California answers the question, "Genomics on the Half Shell: So, What Do Oysters Have to Do with Energy?" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  16. 2013 Progress Report -- DOE Joint Genome Institute (Program Document) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Program Document: 2013 Progress Report -- DOE Joint Genome Institute Citation Details In-Document Search Title: 2013 Progress Report -- DOE Joint Genome Institute In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale

  17. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Muchero, Wellington [Oak Ridge National Laboratory] [Oak Ridge National Laboratory

    2012-03-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  18. Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Muchero, Wellington [Oak Ridge National Laboratory

    2013-01-22

    Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  19. JGI Fungal Genomics Program Grigoriev, Igor V. 99; BIOFUELS;...

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  20. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis....

  1. JGI Fungal Genomics Program (Technical Report) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose...

  2. Accelerating Biofuel Feedstock Crop Improvement with Miscanthus Genomics (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Swaminathan, Kankshita

    2014-03-20

    Kankshita Swaminathan of the Energy Biosciences Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  3. Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Bristow, Jim [DOE JGI Deputy Director

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011

  4. Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Bristow, Jim [DOE JGI Deputy Director] [DOE JGI Deputy Director

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011

  5. JGI Case Study (NERSC-BER Workshop, Sep 11 2012).pptx

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Institute Computing Requirements Shane Canon, Rob Egan, David Goodstein Victor M Markowitz NERSC BER Requirements for 2017 September 11-12, 2012 Established in 1999, located in Walnut Creek Supported by the DOE Office of Science. Budget of ~70 Million/ yr ~ 300 Employees Mission User facility for large scale genomics to enable bioenergy & environmental research DOE Joint Genome Institute (JGI) JGI Programs Plants Fungi Microbes Metagenomes Bioenergy Carbon Cycling Biogeochemistry

  6. Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI at LANL

    2013-01-22

    Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on "Metagenome Assembly at the DOE JGI" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Brady, Siobhan [UC Davis

    2013-01-22

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  8. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Sayre, Richard [LANL] [LANL

    2012-03-22

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  9. Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Brady, Siobhan [UC Davis] [UC Davis

    2012-03-22

    Siobhan Brady from University of California, Davis, gives a talk titled "tGetting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  10. Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Sayre, Richard [LANL

    2013-01-22

    Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  11. Fueling Future with Algal Genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing...

  12. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect (OSTI)

    Gilbert, David

    2013-01-01

    The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

  13. Introduction to Using NERSC for the Joint Genome Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC Introduction to Using NERSC for the Joint Genome Institute May 2, 2011 jgi logo sm NERSC Training Event 1:00-5:00 p.m. PDT May 2, 2011 Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA Introduction to Using NERSC Richard Gerber, NERSC User Services Group Shane Canon, NERSC Technology Integration Group This half-day training will enable new users from the Joint Genome Institute to get connected and running jobs at NERSC. We will cover NERSC computational and storage systems,

  14. Synthetic Metagenomics: Converting digital information back to Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Deutsch, Sam [DOE Joint Genome Institute

    2013-03-01

    Sam Deutsch of the DOE JGI on "Synthetic Metagenomics: Converting digital information back to Biology" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  15. Genes and Genomics for Improving Energy Crops (Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Pennell, Roger

    2011-04-28

    Roger Pennell, Vice President of Trait Development at Ceres, Inc., delivers a keynote address at the 5th Annual DOE JGI User Meeting on March 25, 2010

  16. High Performance Computing and Genomics: Overview of the Issues (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Stevens, Rick [ANL

    2011-06-08

    Rick Stevens of Argonne National Laboratory presents an overview of the issues to be covered during the JGI/Argonne HPC Workshop on January 25, 2010.

  17. Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

    SciTech Connect (OSTI)

    Tarver, Angela; Fern, Alison; Diego, Matthew San; Kennedy, Megan; Zane, Matthew; Daum, Christopher; Hack, Christopher; Tang, Eric; Deshpande, Shweta; Cheng, Jan-Fang; Roberts, Simon; Alexandre, Melanie; Harmon-Smith, Miranda; Lucas, Susan

    2010-06-18

    The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation& Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.

  18. Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2013-01-22

    After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  19. Fueling Future with Algal Genomics Grigoriev, Igor 59 BASIC BIOLOGICAL

    Office of Scientific and Technical Information (OSTI)

    play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world...

  20. An Inside Look at the JGIs Sequencing Operation

    SciTech Connect (OSTI)

    Daum, Chris

    2010-06-02

    Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  1. Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Bermingham, Eldredge

    2013-03-27

    Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  2. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Mosier, Annika [Stanford University] [Stanford University

    2012-03-22

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  3. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Glass, N Louise [UC Berkeley] [UC Berkeley

    2012-03-22

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  4. Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Glass, N Louise [UC Berkeley

    2013-01-25

    N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  5. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Mosier, Annika [Stanford University

    2013-01-22

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  6. JGI Digital Scavenger Hunt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JGI Digital Scavenger Hunt JGI Digital Scavenger Hunt The NERSC webpages are a great resource for New and Old users, so this is the first stop on the JGI Digital Scavenger Hunt....

  7. 11th Annual Energy Department Joint Genome Institute Genomics...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment Meeting 11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment ...

  8. DOE Joint Genome Institute: A DOE Office of Science User Facility...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Institute About Us Phone Book Contact Us Search Our Science Our DOE Mission Areas DOE Bioenergy Research Centers Science Programs Science Highlights Scientists at JGI Our Projects...

  9. Cassava Genomics: can genomic technology benefit smallholder farmers in Africa? (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Rounsley, Steve

    2014-03-20

    Steve Rounsley of the University of Arizona speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  10. Metagenomic and Metaproteomic Analyses of Symbioses between Bacteria and Gutless Marine Worms (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Dubilier, Nicole

    2014-03-19

    Nicole Dubilier of the Max Planck Institute speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  11. Visualizing Assembling Everything (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Jaffe, David; Gnerre, Sante

    2011-06-08

    David Jaffe and Sante Gnerre of the Broad Institute give a presentation on "Visualizing assembling everything" at the JGI/Argonne HPC Workshop on January 25, 2010.

  12. Illumina GA IIx& HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

    SciTech Connect (OSTI)

    Daum, Christopher; Zane, Matthew; Han, James; Kennedy, Megan; San Diego, Matthew; Copeland, Alex; Li, Mingkun; Lucas, Susan

    2011-01-31

    The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow, reducing operational costs and project cycle times to increases ample throughput, and improving the overall quality of the sequence generated. A sequence QC analysis pipeline has been implemented to automatically generate read and assembly level quality metrics. The foremost of these optimization projects, along with sequencing and operational strategies, throughput numbers, and sequencing quality results will be presented.

  13. Genetic Control of Mosquitoes (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Matzen, Kelly

    2014-03-19

    Kelly Matzen of OXITEC speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  14. DOE Systems Biology Knowledgebase: KBase (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Arkin, Adam

    2014-03-20

    Adam Arkin from LBNL speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  15. Genomic Analysis of Adaptation and Speciation in Mimulus guttatus (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Willis, John

    2011-04-25

    John Willis of Duke University spoke about the "Genomic Analysis of Adaptation and Speciation in Mimulus guttatus" on March 26, 2009 at the 4th Annual User Meeting

  16. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Arkin, Adam [LBNL

    2013-01-15

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  17. DOE Systems Biology Knowledgebase (KBASE) (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Arkin, Adam [LBNL] [LBNL

    2012-03-21

    Adam Arkin from Berkeley Lab on the DOE Systems Biology Knowledgebase (KBASE) at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  18. Improving biofuel feedstocks by modifying xylan biosynthesis (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Lau, Jane

    2013-03-01

    Jane Lau of the Joint BioEnergy Institute on "Improving biofuel feedstocks by modifying xylan biosynthesis" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  19. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Silver, Pam [Harvard University

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  20. Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Silver, Pam [Harvard University] [Harvard University

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  1. The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Hazen, Terry [LBNL] [LBNL

    2011-03-22

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

  2. Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Knight, Rob [University of Colorado] [University of Colorado

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  3. The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Hazen, Terry [LBNL

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

  4. Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Knight, Rob [University of Colorado

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  5. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Schmutz, Jeremy [HudsonAlpha Institute

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on "New approaches and technologies to sequence de novo plant reference genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  6. DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Copeland, Alex [DOE JGI]; Brown, C Titus [Michigan State University

    2013-01-22

    DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory] [Cold Spring Harbor Laboratory

    2012-03-21

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  8. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Rieseberg, Loren [University of British Columbia] [University of British Columbia

    2012-03-21

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  9. Entering the Era of Mega-genomics ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Schatz, Michael C [Cold Spring Harbor Laboratory

    2013-01-15

    Michael Schatz from Cold Spring Harbor Laboratory on "Entering the Era of Mega-genomics" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  10. The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Rieseberg, Loren [University of British Columbia

    2013-01-15

    Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  11. 10-Year Strategic Vision: Forging the Future of the DOE JGI

    SciTech Connect (OSTI)

    2012-09-01

    Dramatic technological advances in genomics continue to transform modern biology. The DOE Joint Genome Institute (DOE JGI) has been at the leading edge of large-scale sequence-based science from its inception. Presently our ability to generate genomic data greatly outpaces our capacity to convert these data into biological insights. Bridging the gap between a sequenced genome and understanding of organism-scale functions is a significant unsolved problem in modern biology. Consequently, as the DOE JGI plans for its future, a major objective is to couple the generation of sequence data with the development of new large-scale experimental and computational capabilities to functionally annotate DNA sequences, thereby narrowing the gap between generation and interpretation of sequence data.

  12. The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Drell, Persis [SLAC Director

    2011-06-08

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

  13. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Bork, Peer

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  14. Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties(2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Bork, Peer

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on "Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011

  15. Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Thomashow, Mike

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

  16. The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Drell, Persis [SLAC Director] [SLAC Director

    2011-03-22

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

  17. Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Thomashow, Mike

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011. «

  18. JGI Digital Scavenger Hunt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JGI Digital Scavenger Hunt JGI Digital Scavenger Hunt The NERSC webpages are a great resource for New and Old users, so this is the first stop on the JGI Digital Scavenger Hunt. Here is your first clue: 1) Log on to Genepool (ssh -Y genepool.nersc.gov) 2) Load the JAMO (dev) module (module load jamo/dev) 3) Run the following sequence of commands and answer the questions: genpool10: ~ $ jamo What is the third letter of the sixth jamo command in the help menu? genepool10: ~ $ jamo info What is the

  19. Synthetic Biology for Advanced Fuels (Opening Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Keasling, Jay

    2011-04-28

    Jay Keasling, CEO of the Joint BioEnergy Institute, delivers the opening keynote on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  20. The JGI Metagenome Program (2009 JGI User Meeting)

    SciTech Connect (OSTI)

    Tringe, Susannah Green

    2009-03-25

    Susannah Tringe discussed the DOE JGI Metagenomic Program on March 25, 2009 at the 4th Annual User Meeting.

  1. The JGI Metagenome Program (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Tringe, Susannah Green

    2011-04-25

    Susannah Tringe discussed the DOE JGI Metagenomic Program on March 25, 2009 at the 4th Annual User Meeting.

  2. Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

    SciTech Connect (OSTI)

    Ley, Ruth [Cornell University] [Cornell University

    2011-03-23

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

  3. Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

    ScienceCinema (OSTI)

    Ley, Ruth [Cornell University

    2011-06-03

    The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

  4. Today, DOE's Joint Genome Institute (a

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1 6/1/2011 6.2 Decoding the Human Genome Scientists are close to completing the genetic blueprint for a human being, thanks in large part to Office of Science funding. DOE was the first federal agency to propose that the human genome could be sequenced, and it launched the Human Genome Project in 1986. Today, DOE's Joint Genome Institute (a consortium of three laboratories) is one of the 16 institutions that constitute the Human Genome Sequencing Consortium, which recently announced completion

  5. Gerber-JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    NERSC for the Joint Genome Institute Richard Gerber NERSC User Services May 2, 2011 Joint Genome Institute, Walnut Creek, CA 2 * What is NERSC? * Computing Resources * Storage Resources * How to Get Help * Accounts and Allocations * Connecting to NERSC * Computing Environment * Compiling Code * Running Jobs Outline What is NERSC? 3 !"#$% &'% ()$% *+'% ()"% ,*'% -)"% *+'% .)/% *&'% 0/% **'% 2010 Allocations 4 * NERSC serves a large population Over 3000 users, 400 projects,

  6. Development of High-Throughput Screens to Target SAM-I Riboswitches (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Hickey, Scott [UC Berkely

    2014-03-19

    Scott Hickey of the University of California Berkeley speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  7. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Willerslev, Eske [University of Copenhagen] [University of Copenhagen

    2012-03-21

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  8. Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Willerslev, Eske [University of Copenhagen

    2013-01-15

    Eske Willerslev from the University of Copenhagen on "Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  9. The JGI Mission and Programs (2009 JGI User Meeting)

    ScienceCinema (OSTI)

    Bristow, Jim

    2011-04-25

    Deputy Director of Programs Jim Bristow spoke about the DOE JGI's mission and programs at the 4th Annual User Meeting on March 25, 2009

  10. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Sullivan, Matthew B [University of Arizona

    2013-01-15

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  11. Ocean Viruses: Tiny entities with Global Impacts ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Sullivan, Matthew B [University of Arizona] [University of Arizona

    2012-03-22

    Matt Sullivan from the University of Arizona on "Ocean Viruses: Tiny Entities with Global Impacts" at the 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif.

  12. Part Mining for Synthetic Biology (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Voigt, Chris [MIT

    2013-03-01

    Chris Voigt from MIT delivers the opening keynote on "Part Mining for Synthetic Biology" at the 8th Annual Genomics of Energy & Environment Meeting on March 26, 2013 in Walnut Creek, Calif.

  13. Synthetic Biology and Bioenergy: Helping the Good Guy and Stopping the Bad (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Mercedes-Roca, Maria [Zamorano Panamerican Agriculture School

    2014-03-19

    Maria Mercedes-Roca of the Zamorano Panamerican Agriculture School speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  14. Regulation of Flowering in Brachypodium distachyon (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Amasino, Rick [University of Wisconsin

    2013-03-01

    Rick Amasino of the University of Wisconsin on "Regulation of Flowering in Brachypodium distachyon" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  15. PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Schadt, Christopher [ORNL

    2013-03-01

    Christopher Schadt of Oak Ridge National Laboratory on "Plant-Microbe Interactions" in the context of poplar trees at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 held in Walnut Creek, Calif.

  16. Strange Tails: Viral Discovery and Deep Sequencing (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    DeRisi, Joe

    2013-03-01

    Joe DeRisi of UC San Francisco on "Strange Tails: Viral discovery & deep sequencing" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  17. OSCARS Extends JGI Network Capacity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    OSCARS & JGI Science DMZ Case Studies Multi-facility Workflow Case Study News & Publications ESnet News Publications and Presentations Galleries ESnet Awards and Honors Blog ESnet Live Home » Science Engagement » Case Studies » OSCARS Case Studies » OSCARS & JGI Science Engagement Move your data Programs & Workshops Science Requirements Reviews Case Studies OSCARS Case Studies OSCARS & JGI Science DMZ Case Studies Multi-facility Workflow Case Study Contact Us Technical

  18. OSCARS Extends JGI Network Capacity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    OSCARS & JGI Science DMZ Case Studies Multi-facility Workflow Case Study News & Publications ESnet News Publications and Presentations Galleries ESnet Awards and Honors Blog ESnet...

  19. Rob Egan JGI

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Parallelized coding (and profiling) on genepool Rob Egan JGI Types of parallelism ● Fine grained ○ Lots of communication / syncs ■ "Game of Life" ■ Climate modelling ● Coarse grained ○ Moderate communication / few syncs ■ 'Map' phase of Map-Reduce ● Embarrassingly parallel ○ Zero communication / 0 syncs ○ Deterministic partitioning ■ Read mapping to a reference ■ Mandelbrot Types of parallelism ● Process multi-tasking, pipelining ○ "for f in *.gz ; do

  20. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Overbeek, Ross

    2011-06-08

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  1. Casting Annotation as an Optimization Problem (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Overbeek, Ross

    2010-01-25

    Ross Overbeek of the Fellowship for Interpretation of Genomes gives a presentation on "Casting Annotation as an Optimization Problem" at the JGI/Argonne HPC Workshop on January 25, 2010.

  2. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Banks, Jody [Purdue University] [Purdue University

    2012-03-21

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  3. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Kaeppler, Shawn [University of Wisconsin, Madison] [University of Wisconsin, Madison

    2012-03-21

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  4. Uncovering Transcriptional Circuits in Arabidoposis by Functional Genomics (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Pruneda-Paz, Jose [UC San Diego

    2013-03-01

    Jose Pruneda-Paz of UC San Diego on "Uncovering Transcriptional Circuits in Arabidopsis by Functional Genomics" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  5. The Challenges and Opportunities for Extending Plant Genomics to Climate (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Weston, David

    2013-03-01

    David Weston of Oak Ridge National Laboratory on "The challenges and opportunities for extending plant genomics to climate" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  6. The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Banks, Jody [Purdue University

    2013-01-22

    Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

  7. Genomic Analysis of Natural Variation for Seed and Plant Size in Maize ( JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Kaeppler, Shawn [University of Wisconsin, Madison

    2013-01-15

    Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif

  8. Whole Genome Sequencing of Rice Mutants to identify Genes Controlling Cell Wall Saccharification and Response to Biotic Stress (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Ronald, Pamela [UC Davis

    2014-03-20

    Pamela Ronald of the University of California Davis speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  9. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Gmitter Jr, Fred [University of Florida

    2013-01-15

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  10. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Wullschleger, Stan [ORNL

    2013-01-22

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  11. Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Wullschleger, Stan [ORNL] [ORNL

    2012-03-22

    Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

  12. Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Gmitter Jr, Fred [University of Florida

    2012-03-21

    Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  13. Soybean (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Stacey, Gary

    2011-04-26

    Gary Stacey, associate director of the National Center for Soybean Biotechnology at the University of Missouri, gives a talk simply titled "Soybean" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

  14. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [DOE JGI

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  15. Defining Genome Project Standards in a New Era of Sequencing (GSC8 Meeting)

    ScienceCinema (OSTI)

    Chain, Patrick [DOE JGI

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego.

  16. Final Technical Report of Institute for Environmental Genomics of

    Office of Scientific and Technical Information (OSTI)

    Final Technical Report of Institute for Environmental Genomics of University of Oklahoma (DE-FG02-07ER64383) Project Title: Integrated Genome-Based Studies of Shewanella Ecophysiology Contract Number: DE-FG02-07ER64383 PI: Jizhong Zhou, Professor and Director, Institute for Environmental Genomics, The University of Oklahoma, Norman, OK73019 As a part of the Shewanella Federation project, we have used integrated genomic, proteomic and computational technologies to study various aspects of energy

  17. Joint Genome Institute Progress Report 2002-2005

    SciTech Connect (OSTI)

    Gilbert, David

    2005-10-03

    Progress report covering activities at the DOE-Joint Genome Institute in Walnut Creek, California for the period 2002-2005.

  18. Next-Generation Genetics in Plants: Evolutionary Trade-off, Immunity and Speciation (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Wiegel, Detlef

    2011-04-25

    Detlef Wiegel from the Max Planck Institute for Developmental Biology on "Next-generation genetics in plants: Evolutionary tradeoffs, immunity and speciation" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  19. Ocean Viral Metagenomics (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Rohwer, Forest

    2011-04-26

    Forest Rohwer from San Diego State University talks about "Ocean Viral Metagenomics" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  20. Evaluation of the Cow Rumen Metagenome; Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies(Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Sczyrba, Alex [DOE JGI

    2013-01-22

    DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  1. 11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment Meeting

    Broader source: Energy.gov [DOE]

    The 11th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting will be held March 21–25, 2016 in Walnut Creek, California. The meeting will gather together experts and researchers working in energy and environmental genomics and synthetic biology, and it will have a special focus on the work done at the DOE Joint Genome Institute. Bioenergy Technologies Office Technology Manager Daniel Fishman will be in attendance.

  2. 11th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting

    Broader source: Energy.gov [DOE]

    The 11th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting will be held March 21–25, 2016 in Walnut Creek, California. The meeting will gather together experts and researchers working in energy and environmental genomics and synthetic biology, and it will have a special focus on the work done at the DOE Joint Genome Institute. Bioenergy Technologies Office Technology Manager Daniel Fishman will be in attendance.

  3. Multi-kb Illumina reads Reveal Significant Strain Variation and Rare Organisms in Aquifer (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Sharon, Itai [UC Berkely

    2014-03-20

    Itai Sharon from the University of California at Berkely speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  4. Creating a Multi-functional Library of Grass Transcription Factors for the Energy Crop Model System Brachypodium Distachyon (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Coomey, Joshua [University of Massashusetts Amherst

    2014-03-20

    Joshua Coomey of the University of Massachusetts Amherst, speaks at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  5. Single Cell Isotope Probing via Raman Microspectroscopy: A New Way for Functional Analyses of Microbes in Environmental and Medical Samples (2014 DOE JGI Genomics of Energy & Environment Meeting)

    SciTech Connect (OSTI)

    Berry, David

    2014-03-20

    David Berry, University of Vienna, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif.

  6. New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Notredame, Cedric [Centre for Genomic Regulation

    2011-06-08

    Cedric Notredame from the Centre for Genomic Regulation gives a presentation on "New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era" at the JGI/Argonne HPC Workshop on January 26, 2010.

  7. Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Reeve, Wayne [Murdoch University

    2013-03-01

    Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  8. Genomics at the Ontario Institute for Cancer Research

    SciTech Connect (OSTI)

    Ali, Johar

    2010-06-02

    Johar Ali of the Ontario Institute for Cancer Research discusses genomics and next-gen applications at the OICR on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  9. Assembly-driven metagenomics of a hypersaline microbial ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Allen, Eric [Scripps and UCSD

    2013-03-01

    Eric Allen of Scripps and UC San Diego on "Assembly-driven metagenomics of a hypersaline microbial ecosystem" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  10. TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Karsenti, Eric [EMBL Heidelberg

    2013-03-01

    Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  11. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Hibbett, David [Clark University] [Clark University

    2012-03-21

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  12. Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Larsen, Peter [Argonne

    2013-03-01

    Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  13. Modulation of Root Microbiome Community Assembly by the Plant Immune Response (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Lebeis, Sarah [University of North Carolina

    2013-03-01

    Sarah Lebeis of University of North Carolina on "Modulation of root microbiome community assembly by the plant immune response" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  14. Network as Discovery Instrument: A Quick-Start Guide (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Bell, Gregory [Berkeley Lab

    2013-03-01

    Gregory Bell of Berkeley Lab on "Network as discovery instrument: a Quick-Start Guide" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  15. Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Hazen, Sam [University of Massachusetts

    2013-03-01

    Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  16. Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Gordon, Sean

    2013-03-01

    Sean Gordon of the USDA on "Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  17. Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Brodie, Eoin

    2013-03-01

    Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

  18. Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Guess, Adam

    2013-03-01

    Adam Guss of Oak Ridge National Lab on "Metabolic engineering of Clostridium thermocellum for biofuel production" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, Calif.

  19. Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Gilbert, Tom

    2013-03-01

    Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  20. Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Hibbett, David [Clark University

    2013-01-15

    David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

  1. Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Underfoot | Department of Energy Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World Underfoot Rooted in Wonder: Joint Genome Institute Study Reveals Amazing World Underfoot August 13, 2012 - 2:33pm Addthis By developing a better understanding of the microbes that affect the growth of other plants (crops like corn or wheat) researchers may be able to improve their growth -- or provide better care for them in times of drought. By developing a better understanding of the

  2. The Genomes and Metagenomes (GEM) Catalogue (first presentation) and The ISA-GCDML Workshop (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Field, Dawn [NERC Centre for Ecology and Hydrology]; Sansone, Susanna [EBI

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding ''Research Coordination Network'' from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  3. Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Khanna, Madhu

    2011-04-26

    Madhu Khanna from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  4. The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    DeLucia, Evan

    2011-04-26

    Evan DeLucia of the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute talks about "The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  5. [FIXED] JGI data loss in /projectb/sandbox area [purge

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JGI data loss in projectbsandbox area purge FIXED JGI data loss in projectbsandbox area purge August 19, 2013 by Kjiersten Fagnan We have discovered a serious bug in our...

  6. Acceleration Architectures for Bioinformatics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Gokhale, Maya

    2011-06-08

    Maya Gokhale of the Lawrence Livermore National Laboratory presents at the JGI/Argonne HPC Workshop on January 26, 2010

  7. MycoCosm portal: gearing up for 1000 fungal genomes

    SciTech Connect (OSTI)

    Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet; Kuo, Alan; Ohm, Robin; Riley, Robert; Salamov, Asaf; Zhao, Xueling; Korzeniewski, Frank; Smirnova, Tatyana; Nordberg, Henrik; Dubchak, Inna; Shabalov, Igor

    2013-10-09

    MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other omics data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

  8. Fungal Genomics Program Grigoriev, Igor 59 BASIC BIOLOGICAL SCIENCES...

    Office of Scientific and Technical Information (OSTI)

    and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world...

  9. New Metadata Organizer and Archive Streamlines JGI Data Management

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    by storing detailed metadata with each project analysts complete. We have made this project feel collaborative, which has provided momentum at JGI for doing software...

  10. JGI's Carbon Cycling Studies on Restored Marshes

    SciTech Connect (OSTI)

    Tringe, Susannah; Theroux, Susanna

    2015-06-02

    DOE Joint Genome Institute Metagenome Program Head, Susannah Tringe, and postdoc, Susie Theroux, discuss the lessons to be learned from studying the microbial diversity of marshes that have been converted to other uses, and are now being restored, as well as the potential impacts on the global carbon cycle.

  11. Phytozome System for Comparative Plant Genomics

    Energy Science and Technology Software Center (OSTI)

    2011-09-27

    Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the UC Berkeley Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release 7.0, Phytozome providesmore » access to twenty-five sequenced and annotated green plant genomes which have been clustered into gene families at eleven evolutionarily significant nodes., Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are lyper-linked and searchable.« less

  12. Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to JGI staff and users. In addition, Fagnan will be the NERSC co-chair with Shane Canon, Group Lead for NERSC's Technology Integration Group, on the JGINERSC Coordinating...

  13. Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of chemodiversity in Nature (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Noel, Joseph

    2011-04-25

    Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  14. Fueling the Future with Fungal Genomes

    SciTech Connect (OSTI)

    Grigoriev, Igor V.

    2014-10-27

    Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

  15. Phytozome: a Tool for Green Plant Comparative Genomics

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of release v4.0, Phytozome provides access to nine sequenced and annotated green plant genomes, eight of which have been clustered into gene families at six evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable. [Copied from the Overview at http://www.phytozome.net/Phytozome_info.php

  16. Critical Materials Institute uses the Materials Genome approach...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Critical Materials Institute, led by the U.S. Department of Energy's (DOE's) Ames ... When the market price of rare earth elements like europium and terbium went through the ...

  17. Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Quake, Steve [University of Stanford

    2013-01-22

    Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Pop, Mihai [University of Maryland

    2013-01-22

    University of Maryland's Mihai Pop on "Genome Assembly Forensics: Metrics for Assessing Assembly Correctness" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Standards in Genomic Science: An Open-Access Journal of the Genomic Standards Consortium (GSC8 Meeting)

    ScienceCinema (OSTI)

    Garrity, George

    2011-06-03

    George Garrity of Michigan State University talks about the GSC's open-access journal SIGS at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  20. [FIXED] JGI data loss in /projectb/sandbox area [purge]

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    JGI data loss in /projectb/sandbox area [purge] [FIXED] JGI data loss in /projectb/sandbox area [purge] August 19, 2013 by Kjiersten Fagnan We have discovered a serious bug in our purge scripts on /global/projectb. The */global/projectb/sandbox* areas are supposed to be immune from the purge (like the project directories); however, there is a bug in the purge script that caused some files to be deleted if they had not been touched for 90+ days (like data in the scratch directories). *The sandbox

  1. Fungal Genomics Program

    SciTech Connect (OSTI)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  2. USDA and DOE to Coordinate Research of Plant and Microbial Genomics...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... "The soybean represents an excellent example of how DOE JGI is playing a key role in 'translational genomics,' that is, applying the tools of DNA sequencing and molecular biology ...

  3. Solving Problems with Sequences (Closing Keynote Address - 2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Colwell, Rita

    2011-04-28

    Rita Colwell, recipient of the 2010 Stockholm Water Prize, delivers the closing keynote at the 5th Annual DOE JGI User Meeting on March 26, 2010

  4. Patterns of Nitrogen Utilization in Deep-Sea Syntrophic Consortia (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Wiegel, Detlef

    2011-04-26

    Victoria Orphan from Caltech discusses "Patterns of nitrogen utilization in deep-sea syntrophic consortia" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  5. High Performance Computational Biology: A Distributed computing Perspective (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Konerding, David [Google, Inc

    2011-06-08

    David Konerding from Google, Inc. gives a presentation on "High Performance Computational Biology: A Distributed Computing Perspective" at the JGI/Argonne HPC Workshop on January 26, 2010.

  6. 2013 | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Environmental Molecular Sciences Laboratory (EMSL) Atmospheric Radiation Measurement Climate Research Facility (ARM) Joint Genome Institute (JGI) FES User Facilities + Options ...

  7. 2011 | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Environmental Molecular Sciences Laboratory (EMSL) Atmospheric Radiation Measurement Climate Research Facility (ARM) Joint Genome Institute (JGI) FES User Facilities + Options ...

  8. 2012 | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Environmental Molecular Sciences Laboratory (EMSL) Atmospheric Radiation Measurement Climate Research Facility (ARM) Joint Genome Institute (JGI) FES User Facilities + Options ...

  9. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Simpson, Jared [Wellcome Trust Sanger Institute

    2013-01-22

    Wellcome Trust Sanger Institute's Jared Simpson on "Memory efficient sequence analysis using compressed data structures" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  10. High Performance Computing for Sequence Analysis (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Oehmen, Chris [PNNL] [PNNL

    2010-01-25

    Chris Oehmen of the Pacific Northwest National Laboratory gives a presentation on "High Performance Computing for Sequence Analysis" at the JGI/Argonne HPC Workshop on January 25, 2010.

  11. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    SciTech Connect (OSTI)

    Meyer, Folker [ANL] [ANL

    2010-01-26

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  12. Rapid Evolutionary Placement of Short Sequence Reads (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    None, None

    2011-06-08

    Alexis Stamatakis of the Technical University of Munich gives a presentation on "Rapid Evolutionary Placement of Short Sequence Reads" at the JGI/Argonne HPC Workshop on January 26, 2010.

  13. Casting a Wider Net: Distributed Resources for Metagenomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Meyer, Folker [ANL

    2011-06-08

    Folker Meyer from Argonne National Lab gives a presentation on "Casting a Wider Net: Distributed Resources for Metagenomics" at the JGI/Argonne HPC Workshop on January 26, 2010.

  14. High Performance Computing for Sequence Analysis (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Oehmen, Chris [PNNL

    2011-06-08

    Chris Oehmen of the Pacific Northwest National Laboratory gives a presentation on "High Performance Computing for Sequence Analysis" at the JGI/Argonne HPC Workshop on January 25, 2010.

  15. Next-Gen Annotation Based on Transcriptomics (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Cottingham, Bob [ORNL

    2011-06-08

    Bob Cottingham of the Oak Ridge National Laboratory gives a presentation on "Next-Gen Annotation based on Transcriptomics" at the JGI/Argonne HPC Workshop on January 25, 2010.

  16. JGI_Training_FileSystems_Feb2012.ppt

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Jason H ick Storage Systems Group Lawrence Berkeley Na:onal Lab 10 February 2012 A N ew 2 PB G PFS fi le s ystem f or the JGI "projectb" The n ew 2 PB " projectb" fi le s ystem i s a vailable o n Phoebe n ow * Some high level specs for users * 2.8 PB * Has a "per project" non--- purged, b acked---up por:on w ith s maller quota ( 1---5 T B) * And a " per u ser" p urged, not b acked---up p or:on with l arger q uota ( 10TB) File s ystems b est p rac:ces *

  17. Robotic Enrichment Processing of Roche 454 Titanium Emlusion PCR at the DOE Joint Genome Institute

    SciTech Connect (OSTI)

    Hamilton, Matthew; Wilson, Steven; Bauer, Diane; Miller, Don; Duffy-Wei, Kecia; Hammon, Nancy; Lucas, Susan; Pollard, Martin; Cheng, Jan-Fang

    2010-05-28

    Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cup samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.

  18. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    SciTech Connect (OSTI)

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  19. Visualizing Distributed Data with BigWig and BigBed at UCSC (2010 JGI/ANL HPC Workshop)

    ScienceCinema (OSTI)

    Kent, Jim [UCSC

    2011-06-08

    Jim Kent from University of California, Santa Cruz presents on "Visualizing Distributed Data with BigWig and BigBed at UCSC" at the JGI/Argonne HPC Workshop on January 26, 2010.

  20. Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Knapp, Steve

    2011-04-26

    Steve Knapp from Monsanto on "Wood-Producing Sunflower? Mining Genetic Diversity in Desert-Dwelling Wild Species" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  1. Three Non-Technical Challenges in the Development of Biomass-based Energy (2010 JGI User Meeting)

    ScienceCinema (OSTI)

    Savage, Steve

    2011-04-25

    Steve Savage from Cirrus Partners on "Three Non-Technical Challenges in the Development of Biomass-based Energy" on March 25, 2010 at the 5th Annual DOE JGI User Meeting

  2. Featured Announcements

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    October 2011 Bioinformatics Computing Consultant Position Available October 31, 2011 by Katie Antypas NERSC and the Joint Genome Institute (JGI) are searching for two individuals...

  3. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    play profound roles in the carbon cycle and are prominent candidates for biofuel production The US Department of Energy Joint Genome Institute JGI is leading the world in...

  4. Algal Functional Annotation Tool from the DOE-UCLA Institute for Genomics and Proteomics

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Lopez, David

    The Algal Functional Annotation Tool is a bioinformatics resource to visualize pathway maps, identify enriched biological terms, or convert gene identifiers to elucidate biological function in silico. These types of analysis have been catered to support lists of gene identifiers, such as those coming from transcriptome gene expression analysis. By analyzing the functional annotation of an interesting set of genes, common biological motifs may be elucidated and a first-pass analysis can point further research in the right direction. Currently, the following databases have been parsed, processed, and added to the tool: 1( Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways Database, 2) MetaCyc Encyclopedia of Metabolic Pathways, 3) Panther Pathways Database, 4) Reactome Pathways Database, 5) Gene Ontology, 6) MapMan Ontology, 7) KOG (Eukaryotic Clusters of Orthologous Groups), 5)Pfam, 6) InterPro.

  5. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    SciTech Connect (OSTI)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  6. GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

    SciTech Connect (OSTI)

    Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios; Kyrpides, Nikos C.

    2010-04-01

    We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

  7. A Collection of Algal Genomes from the JGI Kuo, Alan; Grigoriev...

    Office of Scientific and Technical Information (OSTI)

    chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all...

  8. A Collection of Algal Genomes from the JGI (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all...

  9. Overview of IMG Challenges (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Markowitz, Victor [JGI

    2013-01-22

    DOE JGI's Victor Markowitz gives an overview of IMG challenges at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  10. ZipperDB: Predictions of Fibril-forming Segments within Proteins Identified by the 3D Profile Method (from the UCLA-DOE Institute for Genomics and Proteomics)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Goldschmidt, L.; Teng, P. K.; Riek, R.; Eisenberg, D.

    ZipperDB contains predictions of fibril-forming segments within proteins identified by the 3D Profile Method. The UCLA-DOE Institute for Genomics and Proteomics has analyzed over 20,000 putative protein sequences for segments with high fibrillation propensity that could form a "steric zipper"ùtwo self-complementary beta sheets, giving rise to the spine of an amyloid fibril. The approach is unique in that structural information is used to evaluate the likelihood that a particular sequence can form fibrils. [copied with edits from http://www.doe-mbi.ucla.edu/]. In addition to searching the database, academic and non-profit users may also submit their protein sequences to the database.

  11. ZipperDB: Predictions of Fibril-forming Segments within Proteins Identified by the 3D Profile Method (from the UCLA-DOE Institute for Genomics and Proteomics)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Goldschmidt, L.; Teng, P. K.; Riek, R.; Eisenberg, D.

    ZipperDB contains predictions of fibril-forming segments within proteins identified by the 3D Profile Method. The UCLA-DOE Institute for Genomics and Proteomics has analyzed over 20,000 putative protein sequences for segments with high fibrillation propensity that could form a "steric zipper"two self-complementary beta sheets, giving rise to the spine of an amyloid fibril. The approach is unique in that structural information is used to evaluate the likelihood that a particular sequence can form fibrils. [copied with edits from http://www.doe-mbi.ucla.edu/]. In addition to searching the database, academic and non-profit users may also submit their protein sequences to the database.

  12. The Future of Microbial Genomics

    SciTech Connect (OSTI)

    Kyrpides, Nikos [Genome Biology group at the DOE Joint Genome Institute

    2010-06-02

    Nikos Kyrpides, head of the Genome Biology group at the DOE Joint Genome Institute discusses current challenges in the field of microbial genomics on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  13. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    SciTech Connect (OSTI)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  14. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    SciTech Connect (OSTI)

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at jgi.doe.gov>.

  15. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    bit ly JGI Vision for the Institute A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the...

  16. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    bit.lyJGI-Vision for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the...

  17. Directions to Berkeley Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Joint Genome Institute (JGI) San Francisco Bay Area Transit Information San Francisco Airport to the Lab by car San Francisco Airport to the Lab by BART San Francisco Airport to...

  18. Gene Calling Standards (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kyrpides, Nikos [Genome Biology Program, DOE JGI

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  19. Bioinformatics Computing Consultant Position Available

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Bioinformatics Computing Consultant Position Available Bioinformatics Computing Consultant Position Available October 31, 2011 by Katie Antypas NERSC and the Joint Genome Institute (JGI) are searching for two individuals who can help biologists exploit advanced computing platforms. JGI provides production sequencing and genomics for the Department of Energy. These activities are critical to the DOE missions in areas related to clean energy generation and environmental characterization and

  20. Oceanic Communities in a Changing Planet - The Tara Oceans Project (GSC8 Meeting)

    ScienceCinema (OSTI)

    Raes, Jeroen [University of Brussels

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Jeroen Raes of the University of Brussels discusses the Tara-Oceans expedition at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  1. Systems Biology Knowledgebase (GSC8 Meeting)

    ScienceCinema (OSTI)

    Cottingham, Robert W [ORNL

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE KnowledgeBase at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  2. Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

    ScienceCinema (OSTI)

    Jansson, Janet [LBNL

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  3. The Biocurator Society (GSC8 Meeting)

    ScienceCinema (OSTI)

    Gaudet, Pascal [Northwestern University

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009

  4. Standards and the INSDC: Submission of MIGS, MIMS, MIENS (GSC8 Meeting)

    ScienceCinema (OSTI)

    Mizrachi, Ilene [NCBI

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Ilene Mizrachi of the NCBI talks about submission of MIGS/MIMS/MIENS information at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  5. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema (OSTI)

    Tatusova, Tatiana

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  6. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  7. Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Mavrommatis, Kostas [JGI

    2013-01-22

    DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  8. Finding Fingerprints of Selection in Poplar Genomes

    ScienceCinema (OSTI)

    Tuskan, Gerald

    2014-10-28

    Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

  9. Financial Institutions

    Broader source: Energy.gov [DOE]

    A lending program begins with a financial institution that procures the funds they lend from a number of other sources.

  10. Engineering Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Institute Engineering Institute Multidisciplinary engineering research that integrates advanced modeling and simulations, novel sensing systems and new developments in information technology. May 14, 2013 Los Alamos Research Park Los Alamos Research Park, the home of Engineering Institute Contact Institute Director Charles Farrar (505) 665-0860 Email UCSD EI Director Michael Todd (858) 534-5951 Executive Administrator Ellie Vigil (505) 667-2818 Email Administrative Assistant Rebecca Duran (505)

  11. Seaborg Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Institute Seaborg Institute The institute provides a primary mechanism for fostering cooperation and collaboration in actinide science among the national laboratories, university campuses, and the national and international actinide science community. Contact Director Albert Migliori (505) 663-5627 Email Deputy Director Franz Freibert (505) 667-6879 Email Professional Staff Assistant Susan Ramsay (505) 665-0858 Email actinide The Seaborg Institute at Los Alamos integrates research programs,

  12. Flash Updates of GSC projects (GSC8 Meeting)

    SciTech Connect (OSTI)

    Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos; Meyer, Folker; Amaral-Zettler, Linda; Cole, James

    2009-09-09

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Cole (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  13. Flash Updates of GSC projects (GSC8 Meeting)

    ScienceCinema (OSTI)

    Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos; Meyer, Folker; Amaral-Zettler, Linda; Cole, James

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Cole (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  14. 2013 Science Bowl | Princeton Plasma Physics Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SciTech Connect Program Document: 2013 Progress Report -- DOE Joint Genome Institute Citation Details In-Document Search Title: 2013 Progress Report -- DOE Joint Genome Institute In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale

  15. Engineering Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    upon completion of their graduate degrees Over the last seven years, 150 students from 50 academic institutions have participated in the summer school and sixteen such TSM's have...

  16. Joint BioEnergy Institute (Other) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    JOINT BIOENERGY INSTITUTE; JBEI; GENOMICS; SYSTEMS BIOLOGY; SUGAR; FUEL SYNTHESIS; SWITCH GRASS Word Cloud More Like This Multimedia File size NAView Multimedia View Multimedia

  17. Engineering Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    EI Software Download Request EI Software Download Request Contact Institute Director Charles Farrar (505) 663-5330 Email UCSD EI Director Michael Todd (858) 534-5951 Executive Administrator Ellie Vigil (505) 667-2818 Email Administrative Assistant Rebecca Duran (505) 665-8899 Email Software Download and Data Sets First name * Last name * Email address * Institution * Software & Data Set Selection (Select one or more) SHMTools Software (0.20.0 Beta) mFUSE Interface (0.2.0 Beta) Datasets

  18. Quantum Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Quantum Institute Quantum Institute A new research frontier awaits! Our door is open and we thrive on mutually beneficial partnerships, collaborations that drive innovations and new technologies. Contact Leader Malcolm Boshier (505) 665-8892 Email Two of LANL's most successful quantum technology initiatives: quantum cryptography and the race for quantum computer The area of quantum information, science, and technology is rapidly evolving, with important applications in the areas of quantum

  19. de novo Metagenomic Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Koren, Sergey [University of Maryland

    2013-01-22

    University of Maryland's Sergey Koren on "denovo Metagenomic Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  20. Environmental Molecular Sciences Laboratory (EMSL) | U.S. DOE Office of

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science (SC) Environmental Molecular Sciences Laboratory (EMSL) Biological and Environmental Research (BER) BER Home About Research Facilities User Facilities Atmospheric Radiation Measurement Climate Research Facility (ARM) Environmental Molecular Sciences Laboratory (EMSL) Joint Genome Institute (JGI) Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) Community Resources Contact Information Biological and

  1. User Facilities | U.S. DOE Office of Science (SC)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Facilities Biological and Environmental Research (BER) BER Home About Research Facilities User Facilities Atmospheric Radiation Measurement Climate Research Facility (ARM) Environmental Molecular Sciences Laboratory (EMSL) Joint Genome Institute (JGI) Science Highlights Benefits of BER Funding Opportunities Biological & Environmental Research Advisory Committee (BERAC) Community Resources Contact Information Biological and Environmental Research U.S. Department of Energy SC-23/Germantown

  2. Genome Engineering

    SciTech Connect (OSTI)

    Voytas, Dan

    2014-03-20

    Dan Voytas, University of Minnesota, at the 9th Annual Genomics of Energy & Environment Meeting on March 20, 2014 in Walnut Creek, Calif

  3. Microbes Disprove Long-Held Assumption that All Organisms Share...

    Office of Science (SC) Website

    ... microbes whose genomes had been described through single-cell genomics and metagenomics. ... JGI researchers successfully used single-cell genomics to shed insight on a plethora of ...

  4. Exploration of Metagenome Assemblies with an Interactive Visualization Tool

    SciTech Connect (OSTI)

    Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Andersen, Evan; Tringe, Susannah; Hess, Matthias; Dubchak, Inna

    2014-07-09

    Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz

  5. Genomes to Proteomes

    SciTech Connect (OSTI)

    Panisko, Ellen A.; Grigoriev, Igor; Daly, Don S.; Webb-Robertson, Bobbie-Jo; Baker, Scott E.

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic annotation and the generation of high quality gene models, the setup and execution of global proteomics experiments that are quantitative and statistically rigorous and finally add biological context to proteomics.

  6. Genomic Science | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Genomic Science Biological and Environmental Research (BER) BER Home About Research Biological Systems Science Division (BSSD) Genomic Science DOE Bioenergy Research Centers Bioimaging Technology DOE Joint Genome Institute Structural Biology Radiochemistry & Imaging Instrumentation Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Climate and Environmental Sciences Division (CESD) Research Abstracts Searchable Archive of BER Highlights External link Facilities

  7. MIENS Minimum Information about an ENvironmental Sequence and The GSC's Not-for-Profit (GSC8 Meeting)

    ScienceCinema (OSTI)

    Yilmaz, Pelin [Max Planck Institute - Bremen]; Kolker, Eugene [Seattle Childrens Hospital

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  8. Whose genome is it, anyway?

    SciTech Connect (OSTI)

    Marshall, E.

    1996-09-27

    The genome program has issued guidelines to ensure that sequencing is done on DNA from diverse sources who have given informed consent and are anonymous. Most current sources don`t meet those criteria. It may be the first question every nonexpert asks on learning about the Human Genome Project: Whose genome are we studying, anyway? It sounds naive, says one government scientist-so naive, in fact, that {open_quotes}we chuckle as we explain that we aren`t sequencing anyone`s genome in particular; we`re sequencing a representative genome{close_quotes} made up of a mosaic of DNA from a variety of anonymous sources. And Bruce Birren, a clone-maker now at the Massachusetts Institute of Technology`s (MIT`s) Whitehead Center for Genome Research says: {open_quotes}We spent many years pooh-poohing the question{close_quotes} of whose genome would be stored in the database. But now that labs have begun working on large stretches of human DNA-aiming to identify all 3 billion base pairs in the genetic code-the question no longer seems to laughable. To the distress of program managers in Bethesda, Maryland, the initial sources of DNA are not as diverse or as anonymous as they had assumed.

  9. Microsoft PowerPoint - Microbial Genome and Metagenome Analysis Case Study (NERSC Workshop - May 7-8, 2009).ppt [Compatibility

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microbial Genome & Metagenome Analysis: Computational Challenges Natalia N. Ivanova * Nikos C. Kyrpides * Victor M. Markowitz ** * Genome Biology Program, Joint Genome Institute ** Lawrence Berkeley National Lab Microbial genome & metagenome analysis General aims Understand microbial life Apply to agriculture, bioremediation, biofuels, human health Specific aims include Specific aims include Predict biochemistry & physiology of organisms based on genome sequence Explain known

  10. Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Canon, Shane [LBNL

    2013-01-22

    DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  11. JGI Compute User Training Series

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Data Transfer and Archiving Using the Cray XE6 NERSC User Group Training Remote Setup 2010 Training Events Online Tutorials Courses NERSC Training Accounts Request Form Training Links OSF HPC Seminars Software Policies User Surveys NERSC Users Group User Announcements Help Staff Blogs Request Repository Mailing List Operations for: Passwords & Off-Hours Status 1-800-66-NERSC, option 1 or 510-486-6821 Account Support https://nim.nersc.gov accounts@nersc.gov 1-800-66-NERSC, option 2 or

  12. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) portal to the HMP (GSC8 Meeting)

    ScienceCinema (OSTI)

    Weinstock, George [Washington University School of Medicine]; Wortman, Jennifer [University of Maryland School of Medicine

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  13. The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) portal to the HMP (GSC8 Meeting)

    SciTech Connect (OSTI)

    Weinstock, George; Wortman, Jennifer

    2009-09-09

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  14. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    ScienceCinema (OSTI)

    Kolker, Eugene [Seattle Children's Hospital]; Sansone, Susanna [EBI

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  15. The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

    SciTech Connect (OSTI)

    Kolker, Eugene; Sansone, Susanna

    2011-09-11

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

  16. Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

    ScienceCinema (OSTI)

    Vaughan, Bob [EMBL]; Kaye, Jon [Gordon and Betty Moore Foundation

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009

  17. A New Arm of the GSC: the RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

    ScienceCinema (OSTI)

    Field, Dawn [NERC]; Sterk, Peter [NERC

    2011-04-29

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

  18. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOEs Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  19. Genome Analyses and Supplement Data from the International Populus Genome Consortium (IPGC)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    International Populus Genome Consortium (IPGC)

    The sequencing of the first tree genome, that of Populus, was a project initiated by the Office of Biological and Environmental Research in DOE’s Office of Science. The International Populus Genome Consortium (IPGC) was formed to help develop and guide post-sequence activities. The IPGC website, hosted at the Oak Ridge National Laboratory, provides draft sequence data as it is made available from DOE Joint Genome Institute, genome analyses for Populus, lists of related publications and resources, and the science plan. The data are available at http://www.ornl.gov/sci/ipgc/ssr_resource.htm.

  20. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Sabin Stoica, National Institute of Physics & Nuclear Engineering, Bucharest, Romania Recent Results on Neutrino Properties December 8 Mr. Changbo Fu, Cyclotron Institute, Texas ...

  1. Overview:

    Office of Scientific and Technical Information (OSTI)

    Sobecky/Taillefert Final Report April 1, 2015 Overview: In this project, experiments and research activities were conducted in collaboration between investigators at the University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3

  2. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    INSTITUTE INSTITUTE INSTITUTE INSTITUTE COLLOQUIA AND SEMINARS April 1, 2000-March 31, 2001 2000 April 4 Dr. B. Launé, Institut de Physique Nucléaire - Orsay, France GANIL: Overview and Perspectives April 11 Dr. Z. Lin, Cyclotron Institute, TAMU J/psi Absorption in Hadronic Matter April 20 Dr. R. Tribble, Texas A&M University Nuclear Astrophysics at Texas A&M April 23 Prof. S.A. Gurvitz, The Weizmann Institute of Science, Rehovot, Israel Confinement and Scaling in Deep Inelastic

  3. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    (Specialized Interface)

  4. Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Stepanauskas, Ramunas [Bigelow Laboratory

    2013-01-22

    DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  5. Genome patent fight erupts

    SciTech Connect (OSTI)

    Roberts, L.

    1991-10-11

    At a Congressional briefing while describing a new project to sequence partially every gene active in the human brain, it was made known that the National Institutes of Health was planning to file patent applications on 1,000 of these sequences a month. The scheme has engendered a firestorm of criticism from genome scientists and project officials alike. The critics argue that these sequences probably can't be patented in the first place - and even if they can, they shouldn't be. The plan would undercut patent protection for those who labor long and hard at the real task of elucidating the function of the proteins encoded by the genes, thereby driving industry away from developing inventions based on that work.

  6. The Critical Materials Institute | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Critical Materials Institute Director Alex King, Operations Manager Cynthia Feller, Jenni Brockpahler and Melinda Thach. Photo left to right: CMI Director Alex King, Operations Manager Cynthia Feller, Jenni Brockpahler and Melinda Thach. Not pictured: Carol Bergman. CMI staff phone 515-296-4500, e-mail CMIdirector@ameslab.gov The Critical Materials Institute focuses on technologies that make better use of materials and eliminate the need for materials that are subject to supply disruptions.

  7. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Bency John, Cyclotron Institute, Texas A&M University Isoscalar Giant Resonances in 12 C ... and V. E. Jacob, Cyclotron Institute, Texas A&M University Test of the Unitarity of ...

  8. Southern Research Institute Visit

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Southern Reaserch Engineering Capabilities Briefing 2010 Southern Research Institute Pharmaceutical and Biotechnology Research Briefing 2010 CAMD Introduction - Richard Kurtz Mary ...

  9. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    5-March 31, 2006 2005 April 1 Dr. Ralf Rapp, Cyclotron Institute, Texas A&M University, College Station, Texas Thermal Field Theory and Instantons II April 8 Mr. Deqiang Sun, Cyclotron Institute, Texas A&M University, College Station, Texas Bottomonium in QGP and Heavy-Ion Collisions April 22 Dr. Ralf Rapp, Cyclotron Institute, Texas A&M University, College Station, Texas Thermal Field Theory and Instantons III May 6 Dr. Massimo Mannarelli, Massachusetts Institute of Technology,

  10. Genomic Advances to Improve Biomass for Biofuels (LBNL Science at the Theater)

    ScienceCinema (OSTI)

    Rokhsar, Daniel

    2011-04-28

    Lawrence Berkeley National Lab bioscientist Daniel Rokhsar discusses genomic advances to improve biomass for biofuels. He presented his talk Feb. 11, 2008 in Berkeley, California as part of Berkeley Lab's community lecture series. Rokhsar works with the U.S. Department of Energy's Joint Genome Institute and Berkeley Lab's Genomics Division.

  11. U.S. Department of Energy Joint Genome Institute

    Office of Scientific and Technical Information (OSTI)

    ... "Many bacteria and archaea in these communities are novel at the phylum level or belong ... Barcoding: The practice of appending known unique synthetic DNA sequences to sequencing ...

  12. Rooted in Wonder: Joint Genome Institute Study Reveals Amazing...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ... investments in science and innovation, please visit the Office of Science website. ... will broaden our understanding of the biogeochemistry of plant-microbe-soil interactions. ...

  13. Department of Energy Joint Genome Institute, Walnut Creek, CA...

    Office of Scientific and Technical Information (OSTI)

    plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple...

  14. Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Dehal, Paramvir [LBNL

    2013-01-22

    Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  15. Metagenome Data Integration, Data Storage, and Retrieval (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    White, Owen [University of Maryland

    2013-01-22

    University of Maryland's Owen White on "Metagenome Data Integration, Data Storage and Retrieval" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. Scaling MG-RAST to Terabases (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Desai, Narayan [ANL

    2013-01-22

    Argonne National Lab's Narayan Desai on "Scaling MG-RAST to Terabases" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. A Collaborative Ecosystem Model for Metagenomics Data Preservation (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Cochrane, Guy [EMBL-EBI

    2013-01-22

    EMBL-EBI's Guy Cochrane on "A Collaborative Ecosystem Model for Metagenomics Data Preservation" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Marriage or Civil Unions for Single Cells and Metagenomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Rusch, Doug [J. Craig Venter Institute

    2013-01-22

    JCVI's Doug Rusch on "Marriage or Civil Unions for Single Cells and Metagenomes" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Meta-IDBA: A de novo Assembler for Metagenomic Data (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Chin, Francis [University of Hong Kong

    2013-01-22

    University of Hong Kong's Francis Chin on "Meta-­?IDBA: A de novo Assembler for Metagenomic Data" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  20. Institute for Advanced Studies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Video Collaboration » Education Opportunities » Institute for Advanced Studies Institute for Advanced Studies NMC leverages the strengths of three research universities to build joint programs, develop strategic partnerships, provide common organization and facilities. Contact Leader TBD LANL Program Administrator Pam Hundley (505) 663-5453 Email Building regional partnerships in education, leveraging strengths of three research universities The Institute for Advanced Studies (IAS) works with

  1. Graduate Studies - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Students wishing to carry out their dissertation research at the Cyclotron Institute must be formally enrolled in the graduate program of either the Department of Physics or the Department of Chemistry, but may elect to work with any Institute faculty research advisor, irrespective of that advisor's departmental affiliation. Research programs at the Cyclotron Institute are funded by the U.S. Department of Energy, the National Science Foundation, and the Robert A. Welch Foundation. Application

  2. Facilities - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Cyclotron Institute has expanded steadily since commissioning the original cyclotron in 1967 and is currently upgrading again. The diagram to the left shows the variety of...

  3. Edison Electric Institute Update

    Broader source: Energy.gov [DOE]

    Presentation—given at the Fall 2011 Federal Utility Partnership Working Group (FUPWG) meeting—discusses the Edison Electric Institute (EEI) and the current electricity landscape.

  4. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Emeritus Institute for Theoretical Condensed Matter Physics (KIT) The Exotic World of Quantum Matter: Novel States Induced by Fluctuations Tuesday, June 30, 2015 2 - 3pm MSL...

  5. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    professor in the Woodruff School of Mechanical Engineering at Georgia Institute of Technology. She was previously a postdoctoral research fellow at the Center for Integrated...

  6. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    SciTech Connect (OSTI)

    Tringe, Susannah

    2012-01-01

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

  7. Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

    ScienceCinema (OSTI)

    Tringe, Susannah

    2013-05-29

    Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

  8. Department of Energy - Chromosomes News Release 4/13/2000

    Office of Scientific and Technical Information (OSTI)

    FOR IMMEDIATE RELEASE April 13, 2000 NEWS MEDIA CONTACT: Jeff Sherwood, 202/586-5806 Ron Kolb (JGI), 510/486-7586 Researchers Decode Three Human Chromosomes Information May Lead to Treatments for Kidney Disease, Diabetes and Prostate and Colorectal Cancer U.S. Secretary of Energy Bill Richardson announced today that researchers at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, have decoded in draft form the genetic information on human chromosomes 5, 16 and 19.

  9. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    JGI Its key project the Genomics Encyclopedia of Fungi targets fungi related to plant health symbionts pathogens and biocontrol agents and biorefinery processes cellulose...

  10. "Title","Creator/Author","Publication Date","OSTI Identifier...

    Office of Scientific and Technical Information (OSTI)

    and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world...

  11. TITLE AUTHORS SUBJECT SUBJECT RELATED DESCRIPTION PUBLISHER AVAILABILI...

    Office of Scientific and Technical Information (OSTI)

    energy and the environment and to promote functional studies on a system level Combining new sequencing technologies and comparative genomics tools JGI is now leading the world in...

  12. Building international genomics collaboration for global health security

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cui, Helen H.; Erkkila, Tracy; Chain, Patrick S. G.; Vuyisich, Momchilo

    2015-12-07

    Genome science and technologies are transforming life sciences globally in many ways and becoming a highly desirable area for international collaboration to strengthen global health. The Genome Science Program at the Los Alamos National Laboratory is leveraging a long history of expertise in genomics research to assist multiple partner nations in advancing their genomics and bioinformatics capabilities. The capability development objectives focus on providing a molecular genomics-based scientific approach for pathogen detection, characterization, and biosurveillance applications. The general approaches include introduction of basic principles in genomics technologies, training on laboratory methodologies and bioinformatic analysis of resulting data, procurement, and installationmore » of next-generation sequencing instruments, establishing bioinformatics software capabilities, and exploring collaborative applications of the genomics capabilities in public health. Genome centers have been established with public health and research institutions in the Republic of Georgia, Kingdom of Jordan, Uganda, and Gabon; broader collaborations in genomics applications have also been developed with research institutions in many other countries.« less

  13. Cyclotron Institute Upgrade Project - Facilities - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Upgrade Overview / K150 Cyclotron / Light Ion Guide / Heavy Ion Guide / Negative Ion Source / CB-ECRIS Facility Upgrade White Paper Overview Picture of the experimental set up to measure beta-decay half-lives. On January 3, 2005 the Cyclotron Institute Upgrade Project (CIUP) began with the approval of the CIUP management plan by the Department of Energy Nuclear Physics Office. The project will extend to the first quarter of calendar year 2011. When completed, the upgraded facility will provide

  14. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology Genomics and Systems Biology Los Alamos scientists perform research in functional genomics and structural genomics, and applications for such work cover diverse fields such as energy, agriculture, and environmental cleanup. Contact Us Babetta Marrone Biofuels Program Manager Email Cheryl Kuske DOE BER Biological System Science Division Program Manager Email Kirsten McCabe Emerging Threats Program Manager Email Rebecca McDonald Bioscience Communications Email "We

  15. Genome Science/Technologies

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genome Genome Science/Technologies Los Alamos using cutting-edge sequencing, finishing, and analysis, impact valuable genomic data. Srinivas Iyer Bioscience Group Leader Email Get Expertise David Bruce Bioscience Deputy Group Leader Email Momchilo Vuyisich Scientist Email Rebecca McDonald Bioscience Communications Email State-of-the art technology and extensive genomics expertise Protein research Read caption + Los Alamos National Laboratory graduate student, Patricia Langan, changes the

  16. The human genome project

    SciTech Connect (OSTI)

    Yager, T.D.; Zewert, T.E.; Hood, L.E. )

    1994-04-01

    The Human Genome Project (HGP) is a coordinated worldwide effort to precisely map the human genome and the genomes of selected model organisms. The first explicit proposal for this project dates from 1985 although its foundations (both conceptual and technological) can be traced back many years in genetics, molecular biology, and biotechnology. The HGP has matured rapidly and is producing results of great significance.

  17. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2-March 31, 2003 2002 April 2 Dr. Bency John, Cyclotron Institute, Texas A&M University Isoscalar Giant Resonances in 12 C April 9 Professor J. Rapaport, Ohio University, Athens, Ohio Charge Exchange Reactions and Spin Transfer Measurements April 16 M. Sanchez-Vega and V. E. Jacob, Cyclotron Institute, Texas A&M University Test of the Unitarity of the CKM Matrix via Superallowed β + decay. April 23 Dr. Subrata Pal, Cyclotron Institute, Texas A&M University Strange Particle

  18. Contact - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Contact Website Manager Bruce Hyman Email: hyman@comp.tamu.edu Mailing Address Cyclotron Institute Texas A&M University 3366 TAMU College Station, TX, 77843-3366 Campus Location...

  19. Cyclotron Institute REU Program

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    led by Institute faculty. Students will have the opportunity to share their work via an oral presentation and virtual poster session. Gopal Subedi at the TAMU REU poster session....

  20. Critical Materials Institute

    ScienceCinema (OSTI)

    Alex King

    2013-06-05

    Ames Laboratory Director Alex King talks about the goals of the Critical Materials Institute in diversifying the supply of critical materials, developing substitute materials, developing tools and techniques for recycling critical materials, and forecasting materials needs to avoid future shortages.

  1. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    5-March 31, 2006 2005 April 1 Dr. Ralf Rapp, Cyclotron Institute, Texas A&M University, College Station, Texas Thermal Field Theory and Instantons II April 8 Mr. Deqiang Sun, ...

  2. About - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    About The Texas A&M University Cyclotron Institute, a Department of Energy University Facility, is jointly supported by DOE and the State of Texas and is a major technical and ...

  3. UNCLASSIFIED Institute for Materials ...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    PSI: the X-ray free electron laser SwissFEL and its future experimental capabilities. Biography: Prof. Dr. Jol Mesot is, since 2008, director of the Paul Scherrer Institute...

  4. Classification Training Institute Catalog | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Classification Training Institute Catalog Classification Training Institute Catalog Classification Training Institute (CTI) Catalog

  5. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    INSTITUTE COLLOQUIA AND SEMINARS April 1, 2010-March 31, 2011 2010 May 11 Dr. J. J. Ressler, Lawrence Livermore National Laboratory, Livermore, California Surrogate Reactions for Nuclear Energy Application May 12 Professor Lie-Wen Chen, Institute of Nuclear, Particle Astronomy and Cosmology (INPAC) and Department of Physics, Shanghai Jiao Tong University, Shanghai, China Probing the Nuclear Symmetry Energy with Heavy-Ion Reactions and Neutron Skin Thickness of Heavy Nuclei May 13 Professor A. R.

  6. People - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Overview Dr. Ralf Rapp meets with his research group. At the Institute we focus on conducting basic research, educating students in accelerator-based science and technology, and providing technical capabilities for a wide variety of applications in space science, materials science, analytical procedures and nuclear medicine. Approximately 100 Institute members - scientists, engineers, technicians, support staff, graduate students and undergraduate students - are involved in these programs.

  7. Resources | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Resources The Critical Materials Institute offers connections to resources, including: List of resources U.S. Rare Earth Magnet Patents Table Government agency contacts CMI unique facilities CMI recent presentations Photographs via Flick'r: Critical Materials Institute, The Ames Laboratory Videos from The Ames Laboratory Webinars from Colorado School of Mines To offer comments on the CMI website or to ask questions, please contact us via e-mail at CMIdirector@ameslab.gov or call 515-296-4500.

  8. Site Map - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Site Map Cyclotron Institute About K500 Beam Schedule Recent News Seminars and Colloquia Cyclotron Institute Safety (limited access) Radiation Effects Facility REU Program Research Heavy Ion Reactions Fundamental Interactions Nuclear Astrophysics Interactions of Highly Charged Ions With Matter Theoretical Nuclear Physics Nuclear Structure External Collaborations Publications Research Groups Facilities K500 Cyclotron ECR Ion Sources MARS Big Sol MDM Spectrometer NIMROD Precision On-Line Decay

  9. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    SciTech Connect (OSTI)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  10. A Taste of Algal Genomes from the Joint Genome Institute Kuo...

    Office of Scientific and Technical Information (OSTI)

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis,...

  11. A Taste of Algal Genomes from the Joint Genome Institute (Conference...

    Office of Scientific and Technical Information (OSTI)

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis,...

  12. A Taste of Algal Genomes from the Joint Genome Institute (Conference...

    Office of Scientific and Technical Information (OSTI)

    from the National Technical Information Service, Springfield, VA at www.ntis.gov. Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and...

  13. IMG/M: A data management and analysis system for metagenomes

    SciTech Connect (OSTI)

    Markowitz, Victor M.; Ivanova, Natalia N.; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel; Chen, I-Min A.; Grechkin,Yuri; Dubchak,Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis,Konstantinos; Hug enholtz, Phil; Kyrpides, Nikos C.

    2007-08-01

    IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome data collected from multiple sources, while taking into account the iterative nature of sequence data generation and processing. IMG/M aims at providing support for comparative metagenome analysis in the integrated context of microbial genome and metagenome data generated with diverse sequencing technology platforms and data processing methods.

  14. Achievements of structural genomics (Conference) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Conference: Achievements of structural genomics Citation Details In-Document Search Title: Achievements of structural genomics Authors: Terwilliger, Thomas C [1] + Show Author Affiliations Los Alamos National Laboratory Publication Date: 2012-03-08 OSTI Identifier: 1170663 Report Number(s): LA-UR-12-01239; LA-UR-12-1239 DOE Contract Number: AC52-06NA25396 Resource Type: Conference Resource Relation: Conference: Institute of biological chemistry, academia sinica Taiwan ; March 21, 2012 ; Taipai,

  15. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Sakakibara, Yasumbumi [Keio University

    2013-01-22

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  16. Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Hugenholtz, Phil [University of Queensland

    2013-01-22

    University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  17. Using Soir Lucene for Large-Scale Metagenomics Data Retrieval and Analysis (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Goll, Johannes [JCVI

    2013-01-22

    JCVI's Johannes Goll on "Using Solr/Lucene for Large-Scale Metagenomics Data Retrieval and Analysis" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  18. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema (OSTI)

    Li, Weizhong [San Diego Supercomputer Center

    2013-01-22

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  19. Genomics and Systems Biology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Genomics and Systems Biology LANL leads the world in computational finishing of microbial genomes Read caption + In 2013, Los Alamos scientist Richard Sayre and his team genetically modified the organisms to harvest light more efficiently for maximum production. Overview of Research and Highlights Researchers at Los Alamos National Laboratory are using their renowned expertise in genomics, computation, and experimental biology as the foundation of a dynamic systems biology capability. Systems

  20. Ecologic Institute | Open Energy Information

    Open Energy Info (EERE)

    Institute Name: Ecologic Institute Address: Pfalzburger Strasse 4344 Place: Berlin, Germany Year Founded: 1995 Phone Number: +49 (30) 86880-0 Website: ecologic.eu...

  1. Institutional Change Process for Sustainability

    Broader source: Energy.gov [DOE]

    For establishing institutional change in a federal agency to achieve sustainability or other energy efficiency goals, follow the five-step institutional change process.

  2. Strategies for Achieving Institutional Change

    Broader source: Energy.gov [DOE]

    Many strategies—including those derived from Institutional Change Principles–may be used to effect institutional change in support of energy and sustainability objectives.

  3. Rahus Institute | Open Energy Information

    Open Energy Info (EERE)

    article is a stub. You can help OpenEI by expanding it. Rahus Institute is a policy organization located in Martinez, California. References About Rahus Institute Retrieved...

  4. Policies - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Policies Policies Web Accessibility Privacy and Security Policy Use of Information Resources Contact Information Texas A&M University College of Science Department of Chemistry Department of Physics and Astronomy Cyclotron Institute Additional Links University Rules Texas A&M System Policies

  5. Commitment Institutional Change Principle

    Broader source: Energy.gov [DOE]

    Commitment can be a crucial element that helps federal agencies inject and emphasize sustainability in their organizational culture. Institutions and people change when they have made definite commitments to change, especially when those commitments relate to future conditions. Research shows that explicit commitments improve the rate at which people adopt energy-efficient behaviors.

  6. Use of Institutional Controls

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-04-09

    The Policy ensures that the Department of Energy will use institutional controls in the management of resources, facilities and properties under its control, and in implementing its programmatic responsibilities. Certified 1-28-11. Supersedes DOE P 454.1, dated 4-9-03.

  7. Use of Institutional Controls

    Broader source: Directives, Delegations, and Requirements [Office of Management (MA)]

    2003-04-09

    The Policy ensures that the Department of Energy will use institutional controls in the management of resources, facilities and properties under its control, and in implementing its programmatic responsibilities. Certified 1-28-11. Superseded by Chg 1 (Admin Chg), dated 12-7-15.

  8. Genomics Division Home

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the most primitive soil microbe represent a watershed opportunity for biology. The Genomics Division is taking advantage of this wealth of new information. While it is well...

  9. Human Genome: DOE Origins

    Office of Scientific and Technical Information (OSTI)

    of the Department of Energy; DOE Technical Report; 1988 Mapping and Sequencing the Human Genome; DOE Technical Report; 1988 Understanding our Genetic Inheritance: The U.S....

  10. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1-March 31, 2002 2001 April 10 Dr. Massimo Di Toro, LNS/INFN and the University of Catania, Italy Isospin Effects on Nuclear Dynamics April 12 Dr. C. Lewis, U.S. Environmental Protection Agency, Research Triangle, North Carolina Air Pollution Research Using Radiocarbon Measurements April 17 Professor Olga Kocharovskaya, Department of Physics, Texas A&M University, College Station, Texas Laser Control of Mossbauer Nuclear Transitions May 1 Dr. Bency John, Cyclotron Institute, Texas A&M

  11. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    6-March 31, 2007 2006 April 6 Dr. Jamal Jalilian-Marian, Institute for Nuclear Theory, University of Washington, Seattle, Washington An Introduction to Particle Production in High Energy Nuclear Collisions April 7 Professor Taka Kajino, National Astronomical Observatory, University of Tokyo, Tokyo, Japan A Frontier of Nuclear Astrophysics: Big-Bang Cosmology and Supernova Nucleosynthesis April 19 Dr. Anna Stasto, Brookhaven National Laboratory, Upton, New York High Energy Limit and Parton

  12. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    7-March 31, 2008 2007 April 5 Dr. Nigel Orr, Laboratoire de Physique Corpusculaire, Universite de Caen Basse-Normandie, France Probing Nuclear Structure Far from Stability: from Breakup to Knockout April 10 Dr. Lie-wen Chen, Institute of Theoretical Physics, Shanghai Jiao Tong University, Shanghai, China Probing the Nuclear Symmetry Energy with Heavy-Ion Reactions Induced by Neutron- Rich Nuclei April 11 Dr. Nigel Orr, Laboratoire de Physique Corpusculaire, Universite de Caen Basse-Normandie,

  13. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    09-March 31, 2010 2009 April 17 Professor Jian-Wei Qiu, Department of Physics and Astronomy, Iowa State University, Ames, Iowa and Brookhaven National Laboratory, Upton, New York QCD and High Energy Nuclear Collisions April 21 Dr. Peter Levai, KFKI Research Institute for Particle and Nuclear Physics, Budapest, Hungary Can We Find Quark-Gluon Plasma in pp Collision at LHC? April 28 Professor Wolfgang Mittig, NSCL, Michigan State University, East Lansing, Michigan Nuclear Power and Global Energy

  14. Publications - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Publications "Progress in Research", Cyclotron Institute Annual Reports View individual articles: 2015 / 2014 / 2013 / 2012 / 2011 / 2010 / 2009 / 2008 / 2007 / 2006 / 2005 / 2004 / 2003 / 2002 / 2001 / 2000 / 1999 Download complete documents: 2015 / 2014 / 2013 / 2012 / 2011 / 2010 / 2009 / 2008 / 2007 / 2006 / 2005 / 2004 / 2003 List of Papers Published by Year 2012 / 2011 / 2010 / 2009 / 2008 / 2007/ 2006 / 2005 / 2004 / 2003 / 2002 / 2001 / 2000 / 1999 / 1998 / 1997 / 1996 / 1995 /

  15. Research - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Overview Viewing gamma ray spectra. The Institute research program focuses on the atomic nucleus, a many-body system of strongly interacting constituents bound together by the strongest forces known in nature. The properties investigated often can be described in terms of the motions of single nucleons (neutrons and protons), the correlated motions of several nucleons, and the collective motions of many nucleons. On a finer scale, they can be understood in terms of the degrees of freedom of

  16. Research | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research Four Research Thrusts organizational chart of four research thrusts (A click on the org chart image will lead to a pdf version that includes hotlinks for the e-mail addresses for leaders.) CMI has more than 30 projects focused in four areas. Project titles are available in a table, which can be sorted by project leader, location of project leader, project title or project number. CMI research is conducted at partner institutions, including national laboratories, universities and

  17. SRF Institute | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SRF Institute Jefferson Lab is recognized as a world leader in accelerator science. This expertise comes from the planning, building, maintaining and operating of the Continuous Electron Beam Accelerator Facility (CEBAF) - the lab's particle accelerator. CEBAF is based on superconducting radiofrequency (SRF) technology and produces a stream of charged electrons that scientists use to probe the nucleus of the atom. CEBAF was the first large-scale application of SRF technology in the U.S., and it

  18. ORGANIZATIONAL CHART - CYCLOTRON INSTITUTE

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    INSTITUTE April 1, 2000 - March 31, 2001 Health Physics Rodriguez DIRECTOR Natowitz SEE Line Proj. Manager Clark Horvat Hyman Utley Senior ME Derrig Graduate Students Research Associates Research Scientists Research Group Leaders Administration Harris Wellmann Batson Valerian Deason Computer Syst. Hagel Burch Student Wkrs Senior Acc. Phys. May Acc. Phys. Kim Clark Operations Chief Abegglen Target Maker Utley Building Maintenance Mynar Gallegos Kingsbury Shumbera Electrical Shop Cowden Haisler

  19. Careers | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Careers The Critical Materials Institute at the The Ames Laboratory, a Department of Energy national laboratory affiliated with Iowa State University, offers a variety of career opportunities. These include: Postdoctoral Research Associate Also, The Ames Laboratory participates in federal programs that help develop the research workforce. These include the following programs with the U.S. Department of Energy: Graduate Student Research Program (new in 2014) Science Undergraduate Laboratory

  20. Advanced Studies Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Nuclear Security Administration Programs Advanced Simulation and Computing and Institutional R&D Programs The Advanced Simulation and Computing (ASC) Program supports the Department of Energy's National Nuclear Security Administration (DOE/NNSA) Defense Programs' use of simulation-based evaluation of the nation's nuclear weapons stockpile. The ASC Program is responsible for providing the simulation tools and computing environments required to qualify and certify the nation's nuclear

  1. SciTech Connect: genomics

    Office of Scientific and Technical Information (OSTI)

    genomics Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: genomics Semantic Semantic Term Title: Full Text: Bibliographic Data: Creator Author:...

  2. Towards the Perfect Genome Sequence (Opening Keynote) ( 7th Annual SFAF Meeting, 2012)

    ScienceCinema (OSTI)

    Weinstock, George [Washington University

    2013-03-22

    George Weinstock, associate director at the Genome Institute at Washington University, delivered the opening keynote "Towards the Perfect Genome Sequence" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  3. Ethiopian Development Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Ethiopian Development Research Institute Jump to: navigation, search Logo: Ethiopian Development Research Institute Name: Ethiopian Development Research Institute Address: Ethiopia...

  4. CMI Social Media | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Social Media Facebook: Critical Materials Institute Twitter: CMI_hub LinkedIn: Critical Materials Institute Flickr: Critical Materials Institute

  5. Utilization Technology Institute | Open Energy Information

    Open Energy Info (EERE)

    Utilization Technology Institute Jump to: navigation, search Name: Utilization Technology Institute Place: Des Plaines, IL References: Utilization Technology Institute1...

  6. MASSACHUSETTS INSTITUTE OF TECHNOLOGY | Princeton Plasma Physics...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    MASSACHUSETTS INSTITUTE OF TECHNOLOGY American Fusion News Category: Massachusetts Institute of Technology (MIT) Link: MASSACHUSETTS INSTITUTE OF TECHNOLOGY...

  7. Genome Project Standards in a New Era of Sequencing

    SciTech Connect (OSTI)

    GSC Consortia; HMP Jumpstart Consortia; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G.; Hostetler, J.; Muzny, D.; Detter, J. C.; Ali, J.; Birren, B.; Bruce, D. C.; Buhay, C.; Cole, J. R.; Ding, Y.; Dugan, S.; Field, D.; Garrity, G. M.; Gibbs, R.; Graves, T.; Han, C. S.; Harrison, S. H.; Highlander, S.; Hugenholtz, P.; Khouri, H. M.; Kodira, C. D.; Kolker, E.; Kyrpides, N. C.; Lang, D.; Lapidus, A.; Malfatti, S. A.; Markowitz, V.; Metha, T.; Nelson, K. E.; Parkhill, J.; Pitluck, S.; Qin, X.; Read, T. D.; Schmutz, J.; Sozhamannan, S.; Strausberg, R.; Sutton, G.; Thomson, N. R.; Tiedje, J. M.; Weinstock, G.; Wollam, A.

    2009-06-01

    For over a decade, genome 43 sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole genome sequencing that requires a careful reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker 'draft', however these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better reflect the quality of the genome sequence, based on our collective understanding of the different technologies, available assemblers, and the varied efforts to improve upon drafted genomes. Due to the increasingly rapid pace of genomics we avoided the use of rigid numerical thresholds in our definitions to take into account the types of products achieved by any combination of technology, chemistry, assembler, or improvement/finishing process.

  8. INSTITUTE COLLOQUIA AND SEMINARS

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4-March 31, 2005 2004 April 8 Dr. Jeffrey W. Martin, Kellogg Radiation Laboratory, California Institute of Technology, Pasadena, California Ultracold Neutrons April 20 Professor J. W. Watson, Department of Physics, Kent State University, Kent, Ohio Short-range Correlations in Nuclei from (p,2p+n) and (e,e'p+N) Measurements May 10 Mr. Sean Liddick, NSCL- Michigan State University, East Lansing, Michigan The Evolution of Shell Structure in the A~60 Mass Region May 25 Dr. Juha Ärje, Department of

  9. Massachusetts Institute of Technology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    05/2010 Teppei Katori, MIT 1 Teppei Katori for the MiniBooNE collaboration Massachusetts Institute of Technology U-Maryland Nuclear/HEP seminar, College Park, October, 5, 2010 MiniBooNE, a neutrino oscillation experiment at Fermilab 10/05/2010 Teppei Katori, MIT 2 Outline 1. Introduction 2. Neutrino beam 3. Events in the detector 4. Cross section model 5. Oscillation analysis and result 6. New Low energy excess result 7. Anti-neutrino oscillation result 8. Neutrino disappearance result 9.

  10. LIG - Facilities - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Light Ion Guide Light Ion Guide. Texas A&M University is currently configuring a scheme for the production of radioactive-ion beams that incorporates a light-ion guide (LIG) coupled with an ECRIS constructed for charge-boosting (CB-ECRIS). This scheme is part of an upgrade to the Cyclotron Institute and is intended to produce radioactive beams suitable for injection into the K500 superconducting cyclotron. The Light-Ion Guide (LIG) will produce radioactive species mainly from (p,n)

  11. Human Genome Program

    SciTech Connect (OSTI)

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  12. Genomic definition of species

    SciTech Connect (OSTI)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  13. Genomic library construction

    DOE Patents [OSTI]

    Church, George M.; Zhang, Kun

    2011-07-26

    Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.

  14. Integrative Genomics Building

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Integrative Genomics Building Community Berkeley Global Campus Environmental Documents Tours Community Programs Friends of Berkeley Lab ⇒ Navigate Section Community Berkeley Global Campus Environmental Documents Tours Community Programs Friends of Berkeley Lab Project Description The Integrative Genomics Building (IGB) is proposed to be an approximately 77,000 gsf, four-story research and office building constructed in the former Bevatron area - a fully developed site in the geographic

  15. The MicrobesOnline Web site for comparative genomics

    SciTech Connect (OSTI)

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche,Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    2004-11-05

    At present, hundreds of microbial genomes have been sequenced, and hundreds more are currently in the pipeline. The Virtual Institute for Microbial Stress and Survival has developed a publicly available suite of Web-based comparative genomic tools (http://www.microbesonline.org) designed to facilitate multispecies comparison among prokaryotes. Highlights of the Microbes Online Web site include operon and regulon predictions, a multispecies genome browser, a multispecies Gene Ontology browser, a comparative KEGG metabolic pathway viewer, a Bioinformatics Workbench for in-depth sequence analysis, and Gene Carts that allow users to save genes of interest for further study while they browse. In addition, we provide an interface for genome annotation, which like all of the tools reported here, is freely available to the scientific community.

  16. Cyclotron Institute Upgrade Project

    SciTech Connect (OSTI)

    Clark, Henry; Yennello, Sherry; Tribble, Robert

    2014-08-26

    The Cyclotron Institute at Texas A&M University has upgraded its accelerator facilities to extend research capabilities with both stable and radioactive beams. The upgrade is divided into three major tasks: (1) re-commission the K-150 (88”) cyclotron, couple it to existing beam lines to provide intense stable beams into the K-500 experimental areas and use it as a driver to produce radioactive beams; (2) develop light ion and heavy ion guides for stopping radioactive ions created with the K-150 beams; and (3) transport 1+ ions from the ion guides into a charge-breeding electron-cyclotron-resonance ion source (CB-ECR) to produce highly-charged radioactive ions for acceleration in the K-500 cyclotron. When completed, the upgraded facility will provide high-quality re-accelerated secondary beams in a unique energy range in the world.

  17. GenomeVista

    Energy Science and Technology Software Center (OSTI)

    2002-11-04

    Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suitemore » of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program to find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

  18. Integrative Bioengineering Institute

    SciTech Connect (OSTI)

    Eddington, David; Magin,L,Richard; Hetling, John; Cho, Michael

    2009-01-09

    Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the design philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.

  19. Link Alpha J

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    j A B C D E F G H I J K L M N O P Q R S T V W Y Z Filter by alpha... A B C D E F G H I J K L M N O P Q R S T U V W Y Z JBEI: Joint BioEnergy Institute JCAP: Joint Center for Artificial Photosynthesis JDEM: The Joint Dark Energy Mission JGI: Joint Genome Institute Job Descriptions Job Hazards Analysis (JHA Help Center) Job Hazards Analysis (JHA Login page) Job Opening Request Jobs

  20. Berkeley Quantitative Genome Browser

    Energy Science and Technology Software Center (OSTI)

    2008-02-29

    The Berkeley Quantitative Genome Browser provides graphical browsing functionality for genomic data organized, at a minimum, by sequence and position. While supporting the annotation browsing features typical of many other genomic browsers, additional emphasis is placed on viewing and utilizing quantitative data. Data may be read from GFF, SGR, FASTA or any column delimited format. Once the data has been read into the browser's buffer, it may be searched. filtered or subjected to mathematical transformation.more » The browser also supplies some graphical design manipulation functionality geared towards preparing figures for presentations or publication. A plug-in mechanism enables development outside the core functionality that adds more advanced or esoteric analysis capabilities. BBrowse's development and distribution is open-source and has been built to run on Linux, OSX and MS Windows operating systems.« less

  1. Human Genome: DOE Origins

    Office of Scientific and Technical Information (OSTI)

    DOE Origins Resources with Additional Information Charles DeLisi Charles DeLisi The genesis of the Department of Energy (DOE) human genome project took place when "Charles DeLisi ... conceived of a concerted effort to sequence the human genome under the aegis of the ... DOE. ... In 1985, DeLisi took the reins of DOE's Office of Health and Environmental Research [OHER], the program that supported most Biology in the Department. The origins of DOE's biology program traced to the Manhattan

  2. Latest News | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    News News releases CMI in the news News archive CMI social media Latest News News about CMI: Critical Materials Institute gains ten industrial and research affiliates, April 11, 2016 On energy.gov: Critical Materials Institute Gains Ten Industrial and Research Affiliates How true is conventional wisdon about price volatility of tech metals?, Feb. 11, 2016 Need rare-earths know-how? The Critical Materials Institute offers lower-cost access to experts and research, Dec. 1, 2015 Get schooled in

  3. Los Alamos National Laboratory Institutes

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Los Alamos National Laboratory Institutes The National Security Education Center has formed several institutes, each with a partner university or consortia of universities. The formation of these institutes serves the need for LANL to recruit new staff and provide educational opportunities that will enhance retention at the Laboratory. This is accomplished by:  Developing long-term collaborative relationships with universities whose research interests are important to the Laboratory. 

  4. Nuclear Structure - Research - Cyclotron Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Nuclear Structure depiction of giant resonance modes (ref. Xinfeng Chen, "Giant Resonance Study By 6Li Scattering" Nuclear structure studies at the Institute explore a wide range...

  5. Continuous Change Institutional Change Principle

    Broader source: Energy.gov [DOE]

    ecause it takes time to establish institutional change, federal agencies need multiyear plans that continuously work to achieve, reinforce, and improve significant and persistent sustainability goals.

  6. Institutional Change Basics for Sustainability

    Broader source: Energy.gov [DOE]

    Institutional change integrates technology, policy, and behavior to make new sustainability practices and perspectives become a typical part of how an agency operates.

  7. Financial Institution Lending Program Webinars

    Broader source: Energy.gov [DOE]

    Provides a listing of past Financial Institution Lending Program webinars and associated files. Author: U. S. Department of Energy, Energy Efficiency & Renewable Energy

  8. CASL - Massachusetts Institute of Technology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Massachusetts Institute of Technology Cambridge, MA The Department of Nuclear Science and Engineering at MIT has been a leader in the development of the nuclear engineering...

  9. invention disclosures | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Critical Materials Institute will be defined by how well it meets its mission to assure supply chains of materials critical to clean energy technologies. To enable innovation in...

  10. Research and Institutional Integrity Office

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    about any of these ethics policies and related procedures, please contact Meredith Montgomery, Director of Institutional Assurance and Integrity, at 510-486-4453 or...

  11. Izabela Stroe: Worcester Polytechnic Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Izabela Stroe: Worcester Polytechnic Institute Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues submit...

  12. Hitachi Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Institute Jump to: navigation, search Name: Hitachi Research Institute Place: Tokyo, Japan Zip: 101-8010 Product: Hitachi Research Institute is the think tank of the Hitachi...

  13. GHG Management Institute | Open Energy Information

    Open Energy Info (EERE)

    GHG Management Institute Jump to: navigation, search Name: GHG Management Institute Address: Greenhouse Gas Management Institute 9215 View Avenue NW Seattle, WA USA 98117 Place:...

  14. Cornell Fuel Cell Institute | Open Energy Information

    Open Energy Info (EERE)

    Cornell Fuel Cell Institute Jump to: navigation, search Name: Cornell Fuel Cell Institute Place: Ithaca, New York Zip: 14850 Product: The Cornell Fuel Cell Institute (CFCI)...

  15. Form:Research Institution | Open Energy Information

    Open Energy Info (EERE)

    Research Institution Jump to: navigation, search Add a Research or Development Institution Input your research or development institution name below to add to the registry. If your...

  16. UC Berkeley- Energy Institute | Open Energy Information

    Open Energy Info (EERE)

    Berkeley- Energy Institute Jump to: navigation, search Logo: UC Berkeley- Energy Institute Name: UC Berkeley- Energy Institute Address: 2547 Channing Way Place: Berkeley,...

  17. Honda Research Institute | Open Energy Information

    Open Energy Info (EERE)

    search Name: Honda Research Institute Place: Mountain View, California Sector: Biofuels, Solar Product: California-based research institute of Honda. The institute conducts...

  18. Sustainable Europe Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Europe Research Institute Jump to: navigation, search Logo: Sustainable Europe Research Institute Name: Sustainable Europe Research Institute Address: Garnisongasse 721 A -1090...

  19. Industrial Technology Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Technology Research Institute Jump to: navigation, search Logo: Industrial Technology Research Institute Name: Industrial Technology Research Institute Address: Rm. 112, Bldg. 24,...

  20. Low Carbon Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Research Institute Jump to: navigation, search Logo: Low Carbon Research Institute Name: Low Carbon Research Institute Address: King Edward VII Avenue CF10 3NB Place: Cardiff,...

  1. Rocky Mountain Institute | Open Energy Information

    Open Energy Info (EERE)

    Rocky Mountain Institute Jump to: navigation, search Logo: Rocky Mountain Institute Name: Rocky Mountain Institute Address: 1820 Folsom Street Place: Boulder, Colorado Zip: 80302...

  2. Determine Institutional Change Sustainability Goals

    Office of Energy Efficiency and Renewable Energy (EERE)

    The first step in the institutional change process is defining your federal agency's sustainability goals. That is, decide what outcomes are desired (or required) over what period of time. Behavioral, organizational, and institutional changes typically are means to achieve desired energy, resource, or greenhouse gas emission outcomes. They are not ends in and of themselves.

  3. Plumbing Manufacturer's Institute Ex Parte Communication Regarding...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Plumbing Manufacturer's Institute Ex Parte Communication Regarding Showerheads Plumbing Manufacturer's Institute Ex Parte Communication Regarding Showerheads Letter to Department ...

  4. Clean Energy Manufacturing Innovation Institute for Composites...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Clean Energy Manufacturing Innovation Institute for Composites Materials and Structures Clean Energy Manufacturing Innovation Institute for Composites Materials and Structures ...

  5. Manufacturing Innovation Institute for Smart Manufacturing: Advanced...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Manufacturing Innovation Institute for Smart Manufacturing: Advanced Sensors, Controls, Platforms, and Modeling for Manufacturing Manufacturing Innovation Institute for Smart ...

  6. Denver University - International Institute for Environment and...

    Open Energy Info (EERE)

    - International Institute for Environment and Enterprise Name: Denver University - International Institute for Environment and Enterprise Address: 2199 S. University Blvd....

  7. Project Management Institute Highlights Savannah River Nuclear...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Project Management Institute Highlights Savannah River Nuclear Solutions in Publication Project Management Institute Highlights Savannah River Nuclear Solutions in Publication ...

  8. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. .........32 Comprehensive Legacy Management and Institutional Controls ...

  9. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. .........49 Comprehensive Legacy Management and Institutional Controls ...

  10. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. .........52 Comprehensive Legacy Management and Institutional Controls ...

  11. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. .........33 Comprehensive Legacy Management and Institutional Controls ...

  12. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. .........34 Comprehensive Legacy Management and Institutional Controls ...

  13. Gas Technology Institute (Partnership for Advanced Residential...

    Open Energy Info (EERE)

    Technology Institute (Partnership for Advanced Residential Retrofit) Jump to: navigation, search Name: Gas Technology Institute Place: Des Plaines, IL Website:...

  14. Performance Assessment Institute-NV

    SciTech Connect (OSTI)

    Lombardo, Joesph

    2012-12-31

    The National Supercomputing Center for Energy and the Environment’s intention is to purchase a multi-purpose computer cluster in support of the Performance Assessment Institute (PA Institute). The PA Institute will serve as a research consortium located in Las Vegas Nevada with membership that includes: national laboratories, universities, industry partners, and domestic and international governments. This center will provide a one-of-a-kind centralized facility for the accumulation of information for use by Institutions of Higher Learning, the U.S. Government, and Regulatory Agencies and approved users. This initiative will enhance and extend High Performance Computing (HPC) resources in Nevada to support critical national and international needs in "scientific confirmation". The PA Institute will be promoted as the leading Modeling, Learning and Research Center worldwide. The program proposes to utilize the existing supercomputing capabilities and alliances of the University of Nevada Las Vegas as a base, and to extend these resource and capabilities through a collaborative relationship with its membership. The PA Institute will provide an academic setting for interactive sharing, learning, mentoring and monitoring of multi-disciplinary performance assessment and performance confirmation information. The role of the PA Institute is to facilitate research, knowledge-increase, and knowledge-sharing among users.

  15. Institutional computing (IC) information session

    SciTech Connect (OSTI)

    Koch, Kenneth R; Lally, Bryan R

    2011-01-19

    The LANL Institutional Computing Program (IC) will host an information session about the current state of unclassified Institutional Computing at Los Alamos, exciting plans for the future, and the current call for proposals for science and engineering projects requiring computing. Program representatives will give short presentations and field questions about the call for proposals and future planned machines, and discuss technical support available to existing and future projects. Los Alamos has started making a serious institutional investment in open computing available to our science projects, and that investment is expected to increase even more.

  16. Facility Upgrade - Cyclotron Institute - TAMU

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    the Cyclotron Institute Facility Upgrade White Paper Follow the links below to open the files, or right click and select "Save Target As..." to save the file to your computer. File...

  17. My Account | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    My Account Primary tabs Log in(active tab) Request new password Username * Enter your Critical Materials Institute username. Password * Enter the password that accompanies your username. Log in

  18. Multiple Motivations Institutional Change Principle

    Broader source: Energy.gov [DOE]

    The multiple motivations principle suggests that a portfolio approach—rather than a single strategy—may be required to achieve change. Research demonstrates that people and institutions adopt new...

  19. Hydraulic Institute Mission and Vision:

    Energy Savers [EERE]

    Institute Mission and Vision: Vision: To be a global authority on pumps and pumping systems. Mission: To be a value-adding resource to member companies and pump users worldwide by: * Developing and delivering comprehensive industry standards. * Expanding knowledge by providing education and tools for the effective application, testing, installation, operation and maintenance of pumps and pumping systems. * Serving as a forum for the exchange of industry information. The Hydraulic Institute is a

  20. News Releases | Critical Materials Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Releases Critical Materials Institute gains ten industrial and research affiliates, April 11, 2016 How true is conventional wisdom about price volatility of tech metals?, Feb. 11, 2016 Ames Laboratory scientist named to National Academy of Inventors, Jan. 11, 2016 Need rare-earths know-how? The Critical Materials Institute offers lower-cost access to experts and research, December 1, 2015 Get schooled in rare-earth metals: CMI, Iowa State to offer unique materials science class, November 30,

  1. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Doethideomycetes Fungi

    SciTech Connect (OSTI)

    Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabien; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.

    2012-03-13

    The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related species can have very diverse host plants. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.

  2. *** CANCELED *** SCIENCE ON SATURDAY- "Finding a Needle in A (Genomic)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Haystack or How Can Computers Help Cure Cancer" | Princeton Plasma Physics Lab February 9, 2013, 9:30am Science On Saturday MBG Auditorium *** CANCELED *** SCIENCE ON SATURDAY- "Finding a Needle in A (Genomic) Haystack or How Can Computers Help Cure Cancer" Professor Olga G. Troyanskaya Lewis-Sigler Institute for Integrative Genomics & Department of Computer Science, Princeton University Science on Saturday is a series of lectures given by scientists, mathematicians, and

  3. Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

    ScienceCinema (OSTI)

    Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

    2011-04-28

    Science at the Theater: From the sun to your gas tank: A new breed of biofuels may help solve the global energy challenge and reduce the impact of fossil fuels on global warming. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who are developing ways to convert the solar energy stored in plants into liquid fuels. Jay Keasling is one of the foremost authorities in the ?eld of synthetic biology. He is applying this research toward the production of advanced carbon-neutral biofuels that can replace gasoline on a gallon-for-gallon basis. Keasling is Berkeley Labs Acting Deputy Director and the Chief Executive Of?cer of the U.S. Department of Energys Joint BioEnergy Institute. Jim Bristow is deputy director of programs for the U.S. Department of Energy Joint Genome Institute (JGI), a national user facility in Walnut Creek, CA. He developed and implemented JGIs Community Sequencing Program, which provides large-scale DNA sequencing and analysis to advance genomics related to bioenergy and environmental characterization and cleanup. Susanna Green Tringe is a computational biologist with the U.S. Department of Energy Joint Genome Institute (JGI). She helped pioneer the ?eld of metagenomics, a new strategy for isolating, sequencing, and characterizing DNA extracted directly from environmental samples, such as the contents of the termite gut, which yielded enzymes responsible for breakdown of wood into fuel.

  4. Fungal Genome Sequencing and Bioenergy

    SciTech Connect (OSTI)

    Schadt, Christopher Warren; Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Rizvi, L; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions.

  5. Fungal Genome Sequencing and Bioenergy

    SciTech Connect (OSTI)

    Baker, Scott; Thykaer, Jette; Adney, William S; Brettin, Tom; Brockman, Fred; Dhaeseleer, Patrick; Martinez, A diego; Miller, R michael; Rokhsar, Daniel; Schadt, Christopher Warren; Torok, Tamas; Tuskan, Gerald A; Bennett, Joan; Berka, Randy; Briggs, Steven; Heitman, Joseph; Taylor, John; Turgeon, Gillian; Werner-Washburne, Maggie; Himmel, Michael E

    2008-01-01

    To date, the number of ongoing filamentous fungal genome sequencing projects is almost tenfold fewer than those of bacterial and archaeal genome projects. The fungi chosen for sequencing represent narrow kingdom diversity; most are pathogens or models. We advocate an ambitious, forward-looking phylogenetic-based genome sequencing program, designed to capture metabolic diversity within the fungal kingdom, thereby enhancing research into alternative bioenergy sources, bioremediation, and fungal-environment interactions. Published by Elsevier Ltd on behalf of The British Mycological Society.

  6. Institutional

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Expand Utility Resources News & Events Expand News & Events Skip navigation links Marketing Resources Reports, Publications, and Research Agricultural Commercial Consumer...

  7. The Petascale Data Storage Institute

    SciTech Connect (OSTI)

    Gibson, Garth; Long, Darrell; Honeyman, Peter; Grider, Gary; Kramer, William; Shalf, John; Roth, Philip; Felix, Evan; Ward, Lee

    2013-07-01

    Petascale computing infrastructures for scientific discovery make petascale demands on information storage capacity, performance, concurrency, reliability, availability, and manageability.The Petascale Data Storage Institute focuses on the data storage problems found in petascale scientific computing environments, with special attention to community issues such as interoperability, community buy-in, and shared tools.The Petascale Data Storage Institute is a collaboration between researchers at Carnegie Mellon University, National Energy Research Scientific Computing Center, Pacific Northwest National Laboratory, Oak Ridge National Laboratory, Sandia National Laboratory, Los Alamos National Laboratory, University of Michigan, and the University of California at Santa Cruz.

  8. Category:Academic Institutions | Open Energy Information

    Open Energy Info (EERE)

    title"Alternative Energy Institute">Alternative Energy Institute","title":"Alternative Energy Institute","link":null,"lat":34.9848017,"lon":-101.9100121,"alt":0,"add...

  9. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    This collection contains approximately 240 images from the genome programs of DOE's Office of Science. The images are divided into galleries related to biofuels research, systems biology, and basic genomics. Each image has a title, a basic citation, and a credit or source. Most of the images are original graphics created by the Genome Management Information System (GMIS). GMIS images are recognizable by their credit line. Permission to use these graphics is not needed, but please credit the U.S. Department of Energy Genome Programs and provide the website http://genomics.energy.gov. Other images were provided by third parties and not created by the U.S. Department of Energy. Users must contact the person listed in the credit line before using those images. The high-resolution images can be downloaded.

  10. Southface Energy Institute: Advanced Commercial Buildings Initiative...

    Broader source: Energy.gov (indexed) [DOE]

    Southface Energy Institute: Advanced Commercial Buildings Initiative Lead Performer: Southface Energy Institute - Atlanta, GA Partners: - City of Atlanta - Atlanta, GA - Georgia ...

  11. Australian Solar Institute | Open Energy Information

    Open Energy Info (EERE)

    search Name: Australian Solar Institute Place: Newcastle, New South Wales, Australia Zip: 2300 Sector: Solar Product: New South Wales-based institute providing support...

  12. Paul Scherrer Institut | Open Energy Information

    Open Energy Info (EERE)

    Paul Scherrer Institut Jump to: navigation, search Name: Paul Scherrer Institut Place: Aargau, Villigen Zip: 5232 Number of Employees: 1001-5000 Website: www.psi.ch Coordinates:...

  13. Institute for Environmental Solutions | Open Energy Information

    Open Energy Info (EERE)

    Environmental Solutions Jump to: navigation, search Logo: Institute for Environmental Solutions Name: Institute for Environmental Solutions Address: 761 Newport St. Place: Denver,...

  14. Tokyo Institute of Technology | Open Energy Information

    Open Energy Info (EERE)

    Jump to: navigation, search Name: Tokyo Institute of Technology Place: Tokyo, Tokyo, Japan Zip: 152-8550 Product: The Tokyo Institute of Technology runs collaboration programmes...

  15. Demand Management Institute (DMI) | Open Energy Information

    Open Energy Info (EERE)

    Demand Management Institute (DMI) Jump to: navigation, search Name: Demand Management Institute (DMI) Address: 35 Walnut Street Place: Wellesley, Massachusetts Zip: 02481 Region:...

  16. Victoria Transport Policy Institute | Open Energy Information

    Open Energy Info (EERE)

    Transport Policy Institute Jump to: navigation, search Name: Victoria Transport Policy Institute Address: 1250 Rudlin Street, Place: Victoria, British Columbia Website:...

  17. Manufacturing Institutes Exhibit American Innovation at Hannover...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Manufacturing Institutes Exhibit American Innovation at Hannover Messe Manufacturing Institutes Exhibit American Innovation at Hannover Messe April 25, 2016 - 4:30pm Addthis The ...

  18. Resources on Institutional Change for Sustainability | Department...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Publications These publications offer information about institutional change programs. Communities of Practice: A Tool for Creating Institutional Change in Support of the Mission ...

  19. Hahn Meitner Institute | Open Energy Information

    Open Energy Info (EERE)

    Meitner Institute Jump to: navigation, search Name: Hahn-Meitner-Institute Place: Berlin, Germany Zip: 14109 Product: Berlin-based, scientific research centre. Coordinates:...

  20. National Environmental Research Institute | Open Energy Information

    Open Energy Info (EERE)

    Research Institute Jump to: navigation, search Name: National Environmental Research Institute Address: Box. 358 Frederiksborgvej 399 DK 4000 Place: Roskilde, Denmark Phone Number:...

  1. Stockholm Environment Institute (SEI) | Open Energy Information

    Open Energy Info (EERE)

    The Stockholm Environment Institute, located in Stockholm, Sweden, is an independent international research institute. The SEI is dedicated to bringing scientific insights to...

  2. Institute for Energy Research | Open Energy Information

    Open Energy Info (EERE)

    Energy Research Jump to: navigation, search Logo: Institute for Energy Research Name: Institute for Energy Research Address: 1415 S. Voss Rd. Place: Houston, Texas Zip: 77057...

  3. Shaoxing Jinggong Mechanical and Electrical Research Institute...

    Open Energy Info (EERE)

    Shaoxing Jinggong Mechanical and Electrical Research Institute Company SJMERI Jump to: navigation, search Name: Shaoxing Jinggong Mechanical and Electrical Research Institute...

  4. EMei Semiconductor Materials Plant Research Institute | Open...

    Open Energy Info (EERE)

    EMei Semiconductor Materials Plant Research Institute Jump to: navigation, search Name: EMei Semiconductor Materials Plant & Research Institute Place: Emei, Sichuan Province, China...

  5. Electronics and Telecommunications Research Institute ETRI |...

    Open Energy Info (EERE)

    and Telecommunications Research Institute ETRI Jump to: navigation, search Name: Electronics and Telecommunications Research Institute (ETRI) Place: Daejeon, Korea (Republic) Zip:...

  6. Solar Living Institute | Open Energy Information

    Open Energy Info (EERE)

    Living Institute Jump to: navigation, search Name: Solar Living Institute Address: 13771 S. Hwy. 101 Place: Hopland, California Zip: 95449 Region: Bay Area Website:...

  7. Energy Biosciences Institute EBI | Open Energy Information

    Open Energy Info (EERE)

    EBI Jump to: navigation, search Name: Energy Biosciences Institute (EBI) Place: Berkeley, California Zip: 94720 Sector: Biofuels Product: US-based research institution...

  8. Institutional Research & Development Reports | National Nuclear...

    National Nuclear Security Administration (NNSA)

    Home About Us Our Programs Defense Programs Future Science & Technology Programs Advanced Simulation and Computing and Institutional R&D Programs Institutional Research ...

  9. Edison Welding Institute | Open Energy Information

    Open Energy Info (EERE)

    Welding Institute Jump to: navigation, search Name: Edison Welding Institute Address: 1250 Arthur E. Adams Drive Place: Columbus, Ohio Zip: 43221-3585 Sector: Efficiency, Services...

  10. ORISE: Oak Ridge Sitewide Institutional Review Board

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Oak Ridge Sitewide Institutional Review Board The Federal Policy for the Protection of Human Subjects, also known as the Common Rule, requires that each institution that engages in...

  11. Global Climate Change Institute | Open Energy Information

    Open Energy Info (EERE)

    Change Institute Jump to: navigation, search Name: Global Climate Change Institute Place: Tsinghua University, Beijing Municipality, China Zip: 100084 Product: Global Climate...

  12. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Department of Energy Comprehensive Legacy Management and Institutional Controls Plan Doc. ... Appendix A Contact List Comprehensive Legacy Management and Institutional Controls ...

  13. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Fernald Preserve, Fernald, Ohio Comprehensive Legacy Management and Institutional Controls ... blank LMSFERS03496-9.0 Comprehensive Legacy Management and Institutional Controls ...

  14. Contacts: Alex King, Director, Critical Materials Institute,...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Institute researchers named Most Influential Scientific Minds of 2014 Contacts: Alex King, Director, Critical Materials Institute, (515) 296-4505 Laura Millsaps, Public Affairs,...

  15. International Institute for Sustainable Development (IISD) |...

    Open Energy Info (EERE)

    by working collaboratively with other institutions -building long term strategic alliances, while retaining the institutional agility necessary to confront the challenges of...

  16. Alternative Energy Institute | Open Energy Information

    Open Energy Info (EERE)

    Alternative Energy Institute Name: Alternative Energy Institute Address: 2402 russell long blvd Place: Canyon, Texas Zip: 79016 Region: Texas Area Number of Employees: 11-50 Year...

  17. Category:Public Institutions | Open Energy Information

    Open Energy Info (EERE)

    :,"polygons":,"circles":,"rectangles":,"locations":"text":"Institute" title"Alternative Energy Institute">Alternative Energy...

  18. Institute of Geophysics, Planetary Physics, and Signatures

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Institute of Geophysics, Planetary Physics, and Signatures Institute of Geophysics, Planetary Physics, and Signatures Promoting and supporting high-quality, cutting-edge science in...

  19. Renewable Energy Institute International | Open Energy Information

    Open Energy Info (EERE)

    International Jump to: navigation, search Logo: Renewable Energy Institute International Name: Renewable Energy Institute International Address: 5022 Bailey Loop Place: McClellan,...

  20. Joint BioEnergy Institute

    SciTech Connect (OSTI)

    Keasling, Jay; Simmons, Blake; Tartaglino, Virginia; Baidoo, Edward; Kothari, Ankita

    2015-06-15

    The Joint BioEnergy Institute (JBEI) is a U.S. Department of Energy (DOE) Bioenergy Research Center dedicated to developing advanced biofuelsliquid fuels derived from the solar energy stored in plant biomass that can replace gasoline, diesel and jet fuels.

  1. The genome of Eucalyptus grandis

    SciTech Connect (OSTI)

    Myburg, Alexander A; Grattapaglia, Dario; Tuskan, Gerald A; Yang, Xiaohan; Priya, Ranjan; Tschaplinski, Timothy J; Ye, Chuyu; Li, Ting

    2014-01-01

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  2. Saint Joseph's University Institute for Environmental Stewardship

    SciTech Connect (OSTI)

    McCann, Michael; Springer, Clint

    2014-06-18

    Task A: Examination of the physiological, morphological, and reproductive responses of Panicum virgatum (switchgrass) cultivars identified as potential biofuel producing cultivars as well as naturally-occurring varieties of switchgrass to projected changes in climate for the central portion of the United States. This project was a multi-year project set in a field site located at the Konza Prairie Biological Station near Manhattan, KS USA. The major objective of the study was to understand the physiological and growth responses of the important biofuel grass species, Panicum virgatum (switch grass) to simulated changes in precipitation expected for the Central Plains region of the United States. Population level adaptation to broad-scale regional climates or within-population variation in genome size of this genetically and phenotypically diverse C4 grass species may influence the responses to future precipitation variability associated with climate change. Therefore, we investigated switchgrass responses to water variability between natural populations collected across latitudinal gradient and populations. P. virgatum plants from natural populations originating from Kansas, Oklahoma, and Texas received frequent, small precipitation events (“ambient’) or infrequent, large precipitation events (‘altered”) to simulate contrasting rainfall variability expected from this region. We measured leaf-level physiology, aboveground biomass varied significantly by population origin but did not differ by genome size. Our results suggest that trait variation in P. virgatum is primarily attributed to population-level adaptation across latitudinal gradient, not genome size, and that neither population-level adaptation nor genome size may be important predictors of P. virgatum responses to future climatic conditions. Based solely on the data presented here, the most important consideration when deciding what varieties of switchgrass to cultivate for biofuel feedstocks under future climate scenarios is local adaptation and not necessarily genome size as has been hypothesized in the literature. Task B: Installation of an extensive green roof system on the Science Center at Saint Joseph's University for research, research-training and educational outreach activities. An experimental green roof system was designed and installed by an outside contractor (Roofmeadows) on the roof of the Science Center at Saint Joseph's University. The roof system includes four test plots, each with a different drainage system, instrumentation to monitor storm water retention, roof deck temperature, heat flux into and out of the building, rain fall, wind speed and direction, relative humidity and heat emission from the roof system. The vegetative roof was planted with 26 species of plants, distributed throughout the roof area, to assess species/variety growth and coverage characteristics, both in terms of the different drain layer systems, and in terms of the different exposures along the north to south axis of the building. Analysis of the drain layer performance, in terms of storm water retention, shows that the aggregate (stone) drainage layer system performed the best, with the moisture management mat system second, and the geotextile drain layer and reservoir sheet layer systems coming in last. This information is of value in the planning and design of vegetative roof systems since the different types of drainage layer systems have different installation costs and different weights. The different drainage layer systems also seem to be having an impact on plant growth and spread with the test plot with the reservoir sheet layer actually having the poorest plant coverage and plant spread of all areas of the roof studied. Plant growth performance analysis is ongoing, but significant differences have been observed in the third growing season ('13) along the north to south axis, with most species doing better towards the northern end of the roof (in terms of percent ground coverage and plant spread and reproduction). Interestingly, plant growth in all four of the test plots was reduced relative to the lower areas of the roof (the lower area was ca. 2 inches lower than the test plots, due to the space needed for sensors under the plots. The lower roof area uses an aggregate drain layer comparable to that in the third test plot), even when accounting for the north to south differences. The reasons for these differences are not clear and studies are underway to examine the impact of wind scour, drainage rates, temperature, and other factors. This information will be of value to planners of extensive vegetative roof systems in the Philadelphia (and broader) region, since plant growth and roof system overall performance is influenced by local climate, making broad generalizations of performance difficult. Task C: Education and community outreach efforts by the IES involving conferences at SJU, presentations by faculty and students off campus, and educational signage. The Institute for Environmental Stewardship hosted three storm water management workshops on the SJU campus in Philadelphia, in collaboration with the Lower Merion Conservancy, a not-for-profit organization located in Montgomery County, PA. These workshops were free and open to the public. The three workshops (held each year in March) drew more than 200 participants total. The presenters included local and state government agencies, not for profit organizations involved in storm water and open space preservation, designers, engineers, planners and others. Feedback was uniformly positive and we plan to continue the workshops for the foreseeable future. Educational signage has been installed at four locations on campus to explain campus infrastructure related to storm water (rain gardens, vegetative roof and green facades), as well as detailed signage installed on the Science Center roof for the vegetative roof system. More than 100 people (from in and outside of SJU) have thus far participated in tours of the roof system. A digital signage system has been installed in the adjacent library and this system provides information about the vegetative roof project and other efforts. A web camera system for the roof has also been installed and the video will be simulcast to the digital signage and with web site (www.sju.edu/ies) in the near future.

  3. Saint Joseph's University Institute for Environmental Stewardship

    SciTech Connect (OSTI)

    McCann, Micahel P.; Springer, Clint J.

    2014-06-03

    Task A: Examination of the physiological, morphological, and reproductive responses of Panicum virgatum (switchgrass) cultivars identified as potential biofuel producing cultivars as well as naturally-occurring varieties of switchgrass to projected changes in climate for the central portion of the United States. This project was a multi-year project set in a field site located at the Konza Prairie Biological Station near Manhattan, KS USA. The major objective of the study was to understand the physiological and growth responses of the important biofuel grass species, Panicum virgatum (switch grass) to simulated changes in precipitation expected for the Central Plains region of the United States. Population level adaptation to broad-scale regional climates or within-population variation in genome size of this genetically and phenotypically diverse C4 grass species may influence the responses to future precipitation variability associated with climate change. Therefore, we investigated switchgrass responses to water variability between natural populations collected across latitudinal gradient and populations. P. virgatum plants from natural populations originating from Kansas, Oklahoma, and Texas received frequent, small precipitation events (“ambient’) or infrequent, large precipitation events (‘altered”) to simulate contrasting rainfall variability expected from this region. We measured leaf-level physiology, aboveground biomass varied significantly by population origin but did not differ by genome size. Our results suggest that trait variation in P. virgatum is primarily attributed to population-level adaptation across latitudinal gradient, not genome size, and that neither population-level adaptation nor genome size may be important predictors of P. virgatum responses to future climatic conditions. Based solely on the data presented here, the most important consideration when deciding what varieties of switchgrass to cultivate for biofuel feedstocks under future climate scenarios is local adaptation and not necessarily genome size as has been hypothesized in the literature. Task B: Installation of an extensive green roof system on the Science Center at Saint Joseph's University for research, research-training and educational outreach activities. An experimental green roof system was designed and installed by an outside contractor (Roofmeadows) on the roof of the Science Center at Saint Joseph's University. The roof system includes four test plots, each with a different drainage system, instrumentation to monitor storm water retention, roof deck temperature, heat flux into and out of the building, rain fall, wind speed and direction, relative humidity and heat emission from the roof system. The vegetative roof was planted with 26 species of plants, distributed throughout the roof area, to assess species/variety growth and coverage characteristics, both in terms of the different drain layer systems, and in terms of the different exposures along the north to south axis of the building. Analysis of the drain layer performance, in terms of storm water retention, shows that the aggregate (stone) drainage layer system performed the best, with the moisture management mat system second, and the geotextile drain layer and reservoir sheet layer systems coming in last. This information is of value in the planning and design of vegetative roof systems since the different types of drainage layer systems have different installation costs and different weights. The different drainage layer systems also seem to be having an impact on plant growth and spread with the test plot with the reservoir sheet layer actually having the poorest plant coverage and plant spread of all areas of the roof studied. Plant growth performance analysis is ongoing, but significant differences have been observed in the third growing season ('13) along the north to south axis, with most species doing better towards the northern end of the roof (in terms of percent ground coverage and plant spread and reproduction). Interestingly, plant growth in all four of the test plots was reduced relative to the lower areas of the roof (the lower area was ca. 2 inches lower than the test plots, due to the space needed for sensors under the plots. The lower roof area uses an aggregate drain layer comparable to that in the third test plot), even when accounting for the north to south differences. The reasons for these differences are not clear and studies are underway to examine the impact of wind scour, drainage rates, temperature, and other factors. This information will be of value to planners of extensive vegetative roof systems in the Philadelphia (and broader) region, since plant growth and roof system overall performance is influenced by local climate, making broad generalizations of performance difficult. Task C: Education and community outreach efforts by the IES involving conferences at SJU, presentations by faculty and students off campus, and educational signage. The Institute for Environmental Stewardship hosted three storm water management workshops on the SJU campus in Philadelphia, in collaboration with the Lower Merion Conservancy, a not-for-profit organization located in Montgomery County, PA. These workshops were free and open to the public. The three workshops (held each year in March) drew more than 200 participants total. The presenters included local and state government agencies, not for profit organizations involved in storm water and open space preservation, designers, engineers, planners and others. Feedback was uniformly positive and we plan to continue the workshops for the foreseeable future. Educational signage has been installed at four locations on campus to explain campus infrastructure related to storm water (rain gardens, vegetative roof and green facades), as well as detailed signage installed on the Science Center roof for the vegetative roof system. More than 100 people (from in and outside of SJU) have thus far participated in tours of the roof system. A digital signage system has been installed in the adjacent library and this system provides information about the vegetative roof project and other efforts. A web camera system for the roof has also been installed and the video will be simulcast to the digital signage and with web site (www.sju.edu/ies) in the near future.

  4. Saint Joseph's University Institute for Environmental Stewardship

    SciTech Connect (OSTI)

    McCann, Michael P.; Springer, Clint J.

    2014-06-05

    Task A: Examination of the physiological, morphological, and reproductive responses of Panicum virgatum (switchgrass) cultivars identified as potential biofuel producing cultivars as well as naturally-occurring varieties of switchgrass to projected changes in climate for the central portion of the United States. This project was a multi-year project set in a field site located at the Konza Prairie Biological Station near Manhattan, KS USA. The major objective of the study was to understand the physiological and growth responses of the important biofuel grass species, Panicum virgatum (switch grass) to simulated changes in precipitation expected for the Central Plains region of the United States. Population level adaptation to broad-scale regional climates or within-population variation in genome size of this genetically and phenotypically diverse C4 grass species may influence the responses to future precipitation variability associated with climate change. Therefore, we investigated switchgrass responses to water variability between natural populations collected across latitudinal gradient and populations. P. virgatum plants from natural populations originating from Kansas, Oklahoma, and Texas received frequent, small precipitation events (“ambient’) or infrequent, large precipitation events (‘altered”) to simulate contrasting rainfall variability expected from this region. We measured leaf-level physiology, aboveground biomass varied significantly by population origin but did not differ by genome size. Our results suggest that trait variation in P. virgatum is primarily attributed to population-level adaptation across latitudinal gradient, not genome size, and that neither population-level adaptation nor genome size may be important predictors of P. virgatum responses to future climatic conditions. Based solely on the data presented here, the most important consideration when deciding what varieties of switchgrass to cultivate for biofuel feedstocks under future climate scenarios is local adaptation and not necessarily genome size as has been hypothesized in the literature. Task B: Installation of an extensive green roof system on the Science Center at Saint Joseph's University for research, research-training and educational outreach activities. An experimental green roof system was designed and installed by an outside contractor (Roofmeadows) on the roof of the Science Center at Saint Joseph's University. The roof system includes four test plots, each with a different drainage system, instrumentation to monitor storm water retention, roof deck temperature, heat flux into and out of the building, rain fall, wind speed and direction, relative humidity and heat emission from the roof system. The vegetative roof was planted with 26 species of plants, distributed throughout the roof area, to assess species/variety growth and coverage characteristics, both in terms of the different drain layer systems, and in terms of the different exposures along the north to south axis of the building. Analysis of the drain layer performance, in terms of storm water retention, shows that the aggregate (stone) drainage layer system performed the best, with the moisture management mat system second, and the geotextile drain layer and reservoir sheet layer systems coming in last. This information is of value in the planning and design of vegetative roof systems since the different types of drainage layer systems have different installation costs and different weights. The different drainage layer systems also seem to be having an impact on plant growth and spread with the test plot with the reservoir sheet layer actually having the poorest plant coverage and plant spread of all areas of the roof studied. Plant growth performance analysis is ongoing, but significant differences have been observed in the third growing season ('13) along the north to south axis, with most species doing better towards the northern end of the roof (in terms of percent ground coverage and plant spread and reproduction). Interestingly, plant growth in all four of the test plots was reduced relative to the lower areas of the roof (the lower area was ca. 2 inches lower than the test plots, due to the space needed for sensors under the plots. The lower roof area uses an aggregate drain layer comparable to that in the third test plot), even when accounting for the north to south differences. The reasons for these differences are not clear and studies are underway to examine the impact of wind scour, drainage rates, temperature, and other factors. This information will be of value to planners of extensive vegetative roof systems in the Philadelphia (and broader) region, since plant growth and roof system overall performance is influenced by local climate, making broad generalizations of performance difficult. Task C: Education and community outreach efforts by the IES involving conferences at SJU, presentations by faculty and students off campus, and educational signage. The Institute for Environmental Stewardship hosted three storm water management workshops on the SJU campus in Philadelphia, in collaboration with the Lower Merion Conservancy, a not-for-profit organization located in Montgomery County, PA. These workshops were free and open to the public. The three workshops (held each year in March) drew more than 200 participants total. The presenters included local and state government agencies, not for profit organizations involved in storm water and open space preservation, designers, engineers, planners and others. Feedback was uniformly positive and we plan to continue the workshops for the foreseeable future. Educational signage has been installed at four locations on campus to explain campus infrastructure related to storm water (rain gardens, vegetative roof and green facades), as well as detailed signage installed on the Science Center roof for the vegetative roof system. More than 100 people (from in and outside of SJU) have thus far participated in tours of the roof system. A digital signage system has been installed in the adjacent library and this system provides information about the vegetative roof project and other efforts. A web camera system for the roof has also been installed and the video will be simulcast to the digital signage and with web site (www.sju.edu/ies) in the near future.

  5. PNNL: About PNNL - Institutional Partnerships

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Research, Development, and Deployment Collaborations See what we offer universities, other research institutions, and private industry. We look forward to working with you! For Universities Here's what we offer our university partners: Paloma Borque and Andrea Neumann Paloma Borque of McGill University and Andrea Neumann of the University of North Dakota monitor sophisticated instruments onboard an atmospheric research aircraft as part of a climate field study. It's part of a national,

  6. University of Delaware Energy Institute

    SciTech Connect (OSTI)

    Klein, Michael T

    2012-09-30

    The main goal of this project funded through this DOE grant is to help in the establishment of the University of Delaware Energy Institute (UDEI) which is designed to be a long-term, on-going project. The broad mission of UDEI is to develop collaborative programs encouraging research activities in the new and emerging energy technologies and to partner with industry and government in meeting the challenges posed by the nationâ??s pressing energy needs.

  7. PNNL: About PNNL - Institutional Partnerships

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Collaborate to Address Complex, National Challenges By working with other experts and sharing information, we can make significant advances in science and in technological solutions for the nation. See what we offer universities, other research institutions, and private industry. Why Collaborate With Us? Tap into unique capabilities and expertise. For example: Dr. Jonas Warneke Jonas Warneke received the Feodor Lynen Research Fellowship to advance catalysis research at PNNL. Image copyright:

  8. Information Science & Technology Institute

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Opportunities » ISTI Information Science & Technology Institute Providing connection to program management for capability needs, as well as IS&T integration and support for mission-critical centers and activities. Contact Leader Francis Alexander (505) 665-4518 Email Deputy Carolyn Connor (505) 665-9891 Email Professional Staff Assistant Josephine Olivas (505) 663-5725 Email Enhancing capabilities in information science and technology by fostering science, technology, and engineering to

  9. Human genome. 1993 Program report

    SciTech Connect (OSTI)

    Not Available

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  10. Microbial Dark Matter & Beyond

    SciTech Connect (OSTI)

    Rubin, Eddy [DOE JGI Director

    2014-03-19

    Eddy Rubin, DOE JGI Director, at the 9th Annual Genomics of Energy & Environment Meeting on March 19, 2014 in Walnut Creek, Calif. The talk is related to a study published in the journal Science

  11. Genomic Aspects of Research Involving Polyploid Plants

    SciTech Connect (OSTI)

    Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tschaplinski, Timothy J [ORNL; Wullschleger, Stan D [ORNL; Tuskan, Gerald A [ORNL

    2011-01-01

    Almost all extant plant species have spontaneously doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been created during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize the recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomics diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. It is anticipated that polyploids will be a regular subject of genomics research in the foreseeable future as the rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes in polyploid plants. The fast accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  12. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

    Decoding DNA Resources with Additional Information Charles DeLisi As head of DOE's Office of Health and Environmental Research, Charles DeLisi played a pivotal role in proposing and initiating the Human Genome Program in 1986. The U.S. Department of Energy (DOE) has historically been active in supporting human genome research. On September 10, 2003, Secretary of Energy Spencer Abraham presented the Secretary's Gold Award to Aristides Patrinos and Francis Collins for their leadership of the

  13. Structural Genomics: Expectations and Reality

    Office of Scientific and Technical Information (OSTI)

    Impact of Structural Genomics: Expectations and Outcomes Running head: Same Authors: John-Marc Chandonia 1 and Steven E. Brenner 1,2 Address for correspondence: Steven E. Brenner Department of Plant and Microbial Biology 461A Koshland Hall University of California Berkeley, CA 94720-3102 email: brenner@compbio.berkeley.edu fax: (413) 280-7813 Affiliations: 1 - Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 2 -

  14. WIPP - Passive Institutional Controls (PICs)

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The U.S. Department of Energy has developed a program for the development of Passive Institutional Controls to alert future generations to the potential hazards of intersecting the Waste Isolation Pilot Plant (WIPP) repository. These controls are required by U.S. Environmental Protection Agency [Title 40 CFR, Sections 191.14 and 194.43]. The purpose of a passive control, or a PIC, is to indicate the location of the repository and to convey the dangers associated with human exposure to the

  15. Critical Materials Institute Affiliates Program

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    4 Critical Materials Institute Affiliates Program MEMBER AGREEMENT ("Agreement") WHEREAS, The Ames Laboratory ("AMES"), a U.S. Department of Energy ("DOE") National Laboratory operated by Iowa State University of Science and Technology ("ISU") under the authority of its Contract DE-AC02-07CH11358, with administrative offices at 311 TASF, Ames, IA 50011-3020, is the recipient of funding from the U.S. Department of Energy's Office of Energy Efficiency and

  16. PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Lukjancenko, Oksana [Technical University of Denmark

    2013-01-25

    Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect (OSTI)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual annotators from Europe and the USA). Olivier Vallon has been most active in continued input of annotation information.

  18. The mouse genome informatics and the mouse genome database

    SciTech Connect (OSTI)

    Maltais, L.J.; Blackburn, R.E.; Bradt, D.W.

    1994-09-01

    The Mouse Genome Database (MGD) is a centralized, comprehensive database of the mouse genome that includes genetic mapping data, comparative mapping data, gene descriptions, mutant phenotype descriptions, strains and allelic polymorphism data, inbred strain characteristics, physical mapping data, and molecular probes and clones data. Data in MGD are obtained from the published literature and by electronic transfer from laboratories working on large backcross panels of mice. MGD provides tools that enable the user to search the database, retrieve data, generate reports, analyze data, annotate records, and build genetic maps. The Encyclopedia of the Mouse Genome provides a graphic user interface to mouse genome data. It consists of software tools including: LinkMap, a graphic display of genetic linkage maps with the ability to magnify regions of high locus density: CytoMap, a graphic display of cytogenetic maps showing banded chromosomes with cytogenetic locations of genes and chromosomal aberrations; CATS, a catalog searching tool for text retrieval of mouse locus descriptions. These software tools provide access to the following data sets: Chromosome Committee Reports, MIT Genome Center data, GBASE reports, Mouse Locus Catalog (MLC), and Mouse Cytogenetic Mapping Data. The MGD is available to the scientific community through the World Wide Web (WWW) and Gopher. In addition GBASE can be accessed via the Internet.

  19. The Energy Institute | Open Energy Information

    Open Energy Info (EERE)

    The Energy Institute (EI), located in London, United Kingdom, is a professional support body for nearly 13,500 professionals worldwide. The Energy Institute is a tool for society...

  20. Energy & Geoscience Institute | Open Energy Information

    Open Energy Info (EERE)

    Institute Name: Energy & Geoscience Institute Address: 423 Wakara way, Suite 300 Place: Salt Lake City, Utah Zip: 84108 Region: Utah Number of Employees: 51-200 Year Founded: 1972...

  1. Institutional Plan FY 2003 - 2007

    SciTech Connect (OSTI)

    Chartock, Michael; Hansen, Todd

    2003-01-27

    The Fiscal Year (FY) 2003-2007 Institutional Plan describes the strategic directions and key issues that Lawrence Berkeley National Laboratory management must address with the Department of Energy (DOE) in charting its future as a multiprogram national laboratory. The Plan provides an overview of the Laboratory's mission, strategic plan, initiatives, and the resources required to fulfill its role in support of national needs in fundamental science and technology, energy resources, and environmental quality. The Plan facilitates the Department of Energy's ongoing efforts to strengthen the Integrated Laboratory System. Preparation and review of the Institutional Plan is one element of the Department of Energy's strategic management planning activities, implemented through an annual planning process. The Plan supports the President's Management Agenda and the Government Performance and Results Act of 1993. The Plan complements the current performance-based contract between the Department of Energy and the Regents of the University of California, and summarizes Best Management Practices for a potential future results-based contract as a basis for achieving DOE goals and the Laboratory's scientific and operations objectives. It identifies technical and administrative directions in the context of national energy policy and research needs and the Department of Energy's program planning initiatives. Preparation of the Plan is coordinated by the Planning and Strategic Development Office from information contributed by Berkeley Lab's scientific and support divisions and DOE comments on prior years' plans. The Laboratory Mission section identifies the specific strengths of Berkeley Lab that contribute to the mission in general and the Integrated Laboratory System in particular. The Laboratory Strategic Plan section identifies the existing activities in support of DOE Office of Science and other sponsors; support for DOE goals; and the Laboratory Scientific Vision and operations goals. The Initiatives section describes some of the specific new research programs representing major long-term opportunities for the Department of Energy and Berkeley Lab. The Operations Strategic Planning section describes our strategic thinking in the areas of human resources; site and cyber security; workforce diversity; communications and trust; integrated safety management; and technology transfer activities. The Infrastructure Strategic Planning section describes Berkeley Lab's facilities planning process and our site and facility needs. The Summary of Major Issues section provides context for discussions at the Institutional Planning On-Site Review. The Resource Projections are estimates of required budgetary authority for Berkeley Lab's research programs.

  2. Minority Serving Institutions | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Serving Institutions Minority Serving Institutions Map by Matt Loveless, Department of Energy. Our Office of Minority Economic Impact works daily to tap into the talents of students and faculty attending our nation's Minority Serving Institutions. To accomplish the mission of the Department of Energy, we need the best and brightest individuals to work at and partner with the Department. We're proud of the work of our Minority Educational Institution partners, and we work to advance our

  3. Biomass IBR Fact Sheet: Gas Technology Institute

    Broader source: Energy.gov [DOE]

    Gas Technology Institute will conduct research and development on hydropyrolysis and hydroconversion processes to make gasoline and diesel.

  4. White House Announces Eighth Manufacturing Innovation Institute |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy White House Announces Eighth Manufacturing Innovation Institute White House Announces Eighth Manufacturing Innovation Institute April 6, 2016 - 4:49pm Addthis On Thursday, April 1, the White House announced a new institute which will focus on revolutionary fibers and textile manufacturing. This new institute is the eighth manufacturing hub to be awarded as part of the National Network for Manufacturing Innovation (NNMI). Collectively, the federal government's commitment

  5. Financial Institution Lending Programs | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Financial Institution Lending Programs Financial Institution Lending Programs Financial institution loans for clean energy projects are originated and serviced through an entity other than the government, typically banks. In this case, a state or local government is not the finance program administrator, but may still play a role through credit enhancement or providing capital for the loan pool or both. Loans from financial institutions can be structured in many different ways and often look

  6. Resources on Institutional Change for Sustainability

    Broader source: Energy.gov [DOE]

    The Federal Energy Management Program (FEMP) offers resources to help agencies achieve institutional change in their organizations.

  7. Local Information - Radiation Effects Facility / Cyclotron Institute...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    These pages provide visitor and travel information for the cyclotron institute and College Station, texas. Quick Links Parking Map

  8. Francesco Grilli: Karlsruhe Institute of Technology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Francesco Grilli: Karlsruhe Institute of Technology Alumni Link: Opportunities, News and Resources for Former Employees Latest Issue:September 2015 all issues All Issues » submit Francesco Grilli: Karlsruhe Institute of Technology High-temperature superconductors January 1, 2015 Francesco Grilli Francesco Grilli Contact Linda Anderman Email Peter Hosemann Francesco Grilli now at Karlsruhe Institute of Technology After graduating with his Ph.D. from the Swiss Federal Institute of Technology in

  9. Minority Educational Institution Student Partnership Program (MEISPP) |

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Department of Energy Development » Minority Educational Institution Student Partnership Program (MEISPP) Minority Educational Institution Student Partnership Program (MEISPP) Our Minority Educational Institution Student Partnership Program (MEISPP) offers talented undergraduate and graduate students summer internship positions with the Department of Energy and our National Laboratories, with the goal of reaching underrepresented students in STEM fields, such as women and girls. Positions

  10. Geophysical Institute. Biennial report, 1993-1994

    SciTech Connect (OSTI)

    1996-01-01

    The 1993-1994 Geophysical Institute Biennial Report was published in November 1995 by the Geophysical Institute of the University of Alaska Fairbanks. It contains an overview of the Geophysical Institute, the Director`s Note, and research presentations concerning the following subjects: Scientific Predictions, Space Physics, Atmospheric Sciences, Snow, Ice and Permafrost, Tectonics and Sedimentation, Seismology, Volcanology, Remote Sensing, and other projects.

  11. Expanding genomics of mycorrhizal symbiosis

    SciTech Connect (OSTI)

    Kuo, Alan; Kohler, Annegret; Martin, Francis M.; Grigoriev, Igor V.

    2014-11-04

    The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.

  12. DOE Joint Genome Institute | U.S. DOE Office of Science (SC)

    Office of Science (SC) Website

    Radiobiology: Low Dose Radiation Research DOE Human Subjects Protection Program Climate and Environmental Sciences Division (CESD) Research Abstracts Searchable Archive of ...

  13. Human Genome Education Program

    SciTech Connect (OSTI)

    Richard Myers; Lane Conn

    2000-05-01

    The funds from the DOE Human Genome Program, for the project period 2/1/96 through 1/31/98, have provided major support for the curriculum development and field testing efforts for two high school level instructional units: Unit 1, ''Exploring Genetic Conditions: Genes, Culture and Choices''; and Unit 2, ''DNA Snapshots: Peaking at Your DNA''. In the original proposal, they requested DOE support for the partial salary and benefits of a Field Test Coordinator position to: (1) complete the field testing and revision of two high school curriculum units, and (2) initiate the education of teachers using these units. During the project period of this two-year DOE grant, a part-time Field-Test Coordinator was hired (Ms. Geraldine Horsma) and significant progress has been made in both of the original proposal objectives. Field testing for Unit 1 has occurred in over 12 schools (local and non-local sites with diverse student populations). Field testing for Unit 2 has occurred in over 15 schools (local and non-local sites) and will continue in 12-15 schools during the 96-97 school year. For both curricula, field-test sites and site teachers were selected for their interest in genetics education and in hands-on science education. Many of the site teachers had no previous experience with HGEP or the unit under development. Both of these first-year biology curriculum units, which contain genetics, biotechnology, societal, ethical and cultural issues related to HGP, are being implemented in many local and non-local schools (SF Bay Area, Southern California, Nebraska, Hawaii, and Texas) and in programs for teachers. These units will reach over 10,000 students in the SF Bay Area and continues to receive support from local corporate and private philanthropic organizations. Although HGEP unit development is nearing completion for both units, data is still being gathered and analyzed on unit effectiveness and student learning. The final field testing result from this analysis will contribute to the final revisions of each unit during the second-year of this grant.

  14. Enhancer Identification through Comparative Genomics

    SciTech Connect (OSTI)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  15. Strategies and tools for whole genome alignments

    SciTech Connect (OSTI)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  16. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  17. Complete genome sequences for the anaerobic, extremely thermophilic...

    Office of Scientific and Technical Information (OSTI)

    Complete genome sequences for the anaerobic, extremely thermophilic plant ... Title: Complete genome sequences for the anaerobic, extremely thermophilic plant ...

  18. Genome informatics: Requirements and challenges

    SciTech Connect (OSTI)

    Robbins, R.J.

    1993-12-31

    Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP); data acquisition, data analysis, data exchange, data publication, and data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be failure of genome informatics and ultimately failure of the genome project itself. Scientists need good designs to deliver the tools necessary for acquiring and analyzing DNA sequences. As these tools become more efficient, they will need new tools for comparative genomic analyses. To make the tools work, the scientists will need to address and solve nomenclature issues that are essential, if also tedious. They must devise systems that will scale gracefully with the increasing flow of data. The scientists must be able to move data easily from one system to another, with no loss of content. As scientists, they will have failed in their responsibility to share results, should repeating experiments ever become preferable to searching the literature. Their databases must become a new kind of scientific literature and the scientists must develop ways to make electronic data publishing as routine as traditional journal publishing. Ultimately, they must build systems so advanced that they are virtually invisible. In summary, the HGP can be considered the most ambitious, most audacious information-management project ever undertaken. In the HGP, computers will not merely serve as tools for cataloging existing knowledge. Rather, they will serve as instruments, helping to create new knowledge by changing the way the scientists see the biological world. Computers will allow them to see genomes, just as radio telescopes let them see quasars and electron microscopes let them see viruses.

  19. Battelle Memorial Institute Technology Marketing Summaries - Energy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Innovation Portal Battelle Memorial Institute Technology Marketing Summaries Here you'll find marketing summaries for technologies available for licensing from the Battelle Memorial Institute (BMI). The summaries provide descriptions of the technologies including their benefits, applications and industries, and development stage. Battelle Memorial Institute 24 Technology Marketing Summaries Category Title and Abstract Laboratories Date Energy Analysis Find More Like This HELM(tm) Flow

  20. Classification Training Institute | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Classification Training Institute Classification Training Institute Welcome to the Classification Training Institute (CTI) Webpage. This page provides information for Department of Energy (DOE) and non-DOE personnel concerning courses offered by the CTI, the current course schedule, and provides training and resources (reference materials and links to web pages with additional information) concerning information classified and controlled information within the DOE. This page also contains short