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Sample records for genome institute jgi

  1. Joint Genome Institute (JGI)

    U.S. Department of Energy (DOE) - all 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. Microbial Genomics Data from the DOE Joint Genome Institute (JGI)

    DOE Data Explorer

    The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project -- generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While NIH-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane. [Excerpt from the JGI page "Who We Are" at http://www.jgi.doe.gov/whoweare/whoweare.html] From the JGI webportal users can view a photo grid of organisims, check assemblies for status, access the Integrated Microbial Genomes (IMG) system to do comparative analysis of publicly available

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

    DOE Data Explorer

    The JGI makes high-quality genome sequencing data freely available to the greater scientific community through its web portal. Having played a significant role in the federally funded Human Genome Project -- generating the complete sequences of Chromosomes 5, 16, and 19--the JGI has now moved on to contributing in other critical areas of genomics research. While NIH-funded genome sequencing activities continue to emphasize human biomedical targets and applications, the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the science mission of the Department of Energy. With efficiencies of scale established at the PGF, and capacity now exceeding three billion bases generated on a monthly basis, the JGI has tackled scores of additional genomes. These include more than 60 microbial genomes and many important multicellular organisms and communities of microbes. In partnership with other federal institutions and universities, the JGI is in the process of sequencing a frog (Xenopus tropicalis), a green alga (Chlamydomonas reinhardtii), a diatom (Thalassiosira pseudonana) , the cottonwood tree (Populus trichocarpa), and a host of agriculturally important plants and plant pathogens. Microorganisms, for example those that thrive under extreme conditions such as high acidity, radiation, and metal contamination, are of particular interest to the DOE and JGI. Investigations by JGI and its partners are shedding light on the cellular machinery of microbes and how they can be harnessed to clean up contaminated soil or water, capture carbon from the atmosphere, and produce potentially important sources of energy such as hydrogen and methane. [Excerpt from the JGI page "Who We Are" at http://www.jgi.doe.gov/whoweare/whoweare.html] 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

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

    DOE Data Explorer

    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.

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

    U.S. Department of Energy (DOE) - all 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

  6. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 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 leads 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

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

    DOE Data Explorer

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

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

    DOE Data Explorer

    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.

  9. DOE JGI Whole Genome Shotgun Sequencing, part 1

    ScienceCinema

    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. DOE JGI Whole Genome Shotgun Sequencing, part 2

    ScienceCinema

    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).

  11. DOE JGI Whole Genome Shotgun Sequencing, part 3

    ScienceCinema

    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).

  12. Genome Improvement at JGI-HAGSC

    SciTech Connect

    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.

  13. JGI Genomics and Bioinformatics for Undergraduate Educators Workshop

    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.

  14. Diatom Genomics (2009 JGI User Meeting)

    SciTech Connect

    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

  15. Diatom Genomics (2009 JGI User Meeting)

    ScienceCinema

    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

  16. Genome Improvement at JGI-HAGSC

    SciTech Connect

    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.

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

    SciTech Connect

    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

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

    ScienceCinema

    Rubin, Eddy

    2016-07-12

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

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

    SciTech Connect

    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.

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

    ScienceCinema

    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

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

    ScienceCinema

    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

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

    SciTech Connect

    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

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

    SciTech Connect

    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

  4. 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...

  5. 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...

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

    ScienceCinema

    Moose, Steve

    2016-07-12

    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

  7. JGI Plant Genomics Gene Annotation Pipeline

    SciTech Connect

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

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

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    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.

  10. Joint Genome Institute's Automation Approach and History

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Chapman, Jarrod

    2016-07-12

    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.

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

    ScienceCinema

    Zimmer, Carl [New York Times

    2016-07-12

    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

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

    SciTech Connect

    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

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

    ScienceCinema

    Tringe, Susannah [DOE JGI

    2016-07-12

    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

  16. Introduction to Using NERSC for the Joint Genome Institute

    U.S. Department of Energy (DOE) - all 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...

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

    U.S. Department of Energy (DOE) - all 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...

  18. JGI Genomic Single-cell Assembly Workflow

    Energy Science and Technology Software Center

    2011-09-16

    JIGSAW is a software package disigned to quality control and assemble genomic DNA sequences from single-cell bacterial and archaeal genomes. Amplification of singel-cell genomes using multiple displacement amplification technology presents challenges that magnify the amount of contaminants in the sample and produce non uniform depth of sequence coverage. these factors pose problems whan assembling the genomic data using currently availible short read assembles. The software addresses these problems by removing contaminants and normalizing the sequencemore » read coverage prior to assemble. A hybrid assembly approach using two different open source genome assembly tools is then applied to piece together the DNA fragments. Additional reporting of QC metrics for the input sample and the genome assembly is provided for further analysis.« less

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

    ScienceCinema

    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

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

    SciTech Connect

    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

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

    ScienceCinema

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

    2016-07-12

    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.

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

    SciTech Connect

    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.

  3. Kjiersten Fagnan Appointed NERSC/JGI Engagement Lead

    U.S. Department of Energy (DOE) - all 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

  4. 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...

  5. A Taste of Algal Genomes from the Joint Genome Institute

    SciTech Connect

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    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, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

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

    ScienceCinema

    Goldberg, Robert [UCLA

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Hallam, Steven

    2016-07-12

    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

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

    ScienceCinema

    Pellegrinni, Matteo [UCLA

    2016-07-12

    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.

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

    ScienceCinema

    Aluru, Srinivas [Iowa State University

    2016-07-12

    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.

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

    ScienceCinema

    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

  12. 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

    Robinson, Gene

    2016-07-12

    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

  13. 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

    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

  14. DOE Joint Genome Institute 2008 Progress Report

    SciTech Connect

    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

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

    ScienceCinema

    Galagan, James

    2016-07-12

    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

  16. 2013 Progress Report -- DOE Joint Genome Institute

    SciTech Connect

    2013-11-01

    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 generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.

  17. New Metadata Organizer and Archive Streamlines JGI Data Management

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    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.

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

    SciTech Connect

    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.

  20. 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

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

    ScienceCinema

    Gallivan, Justin [Emory University

    2016-07-12

    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

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

    ScienceCinema

    Hedgecock, Dennis

    2016-07-12

    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

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

    SciTech Connect

    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

  4. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

    SciTech Connect

    Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

    2015-10-26

    The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

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

    ScienceCinema

    Muchero, Wellington [Oak Ridge National Laboratory

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  8. 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...

  9. 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...

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

    ScienceCinema

    Bristow, Jim [DOE JGI Deputy Director

    2016-07-12

    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

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

    SciTech Connect

    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

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

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Joint 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

  13. 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...

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

    ScienceCinema

    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.

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

    ScienceCinema

    Brady, Siobhan [UC Davis

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Sayre, Richard [LANL

    2016-07-12

    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.

  19. Introduction to Using NERSC for the Joint Genome Institute

    U.S. Department of Energy (DOE) - all 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,

  20. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  2. Assembling Complex Plant Genomes | U.S. DOE Office of Science...

    Office of Science (SC)

    Scientists from the Department of Energy's (DOE) Joint Genome Institute (JGI) teamed with other researchers to develop and test the POPSEQ approach on the barley genome. The plant ...

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

    ScienceCinema

    Stevens, Rick [ANL

    2016-07-12

    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.

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

    ScienceCinema

    Pennell, Roger

    2016-07-12

    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

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

    SciTech Connect

    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.

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

    ScienceCinema

    Kyrpides, Nikos [DOE JGI

    2016-07-12

    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

  7. 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...

  8. An Inside Look at the JGIs Sequencing Operation

    SciTech Connect

    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

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

    SciTech Connect

    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.

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

    ScienceCinema

    Glass, N Louise [UC Berkeley

    2016-07-12

    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.

  11. 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

    Mosier, Annika [Stanford University

    2016-07-12

    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

  12. 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

    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

  13. 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

    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.

  14. JGI Computing 5-Year Strategic Plan

    SciTech Connect

    Bader, D A; Brettin, T S; Cottingham, R W; Folta, P A; Golder, Y; Gregurick, S K; Himmel, M E; Mann, R C; Remington, K A; Slezak, T R

    2008-10-01

    depending on the specific user base, and the JGI has several distinct classes of users it must enable to be successful. For some, rapid and convenient dissemination of the sequence data will be sufficient to enable their external research. For others, JGI hosted analysis tools and collaborative environments will be required to catalyze individual or team research. Finally, and significantly, there are genomic scientists within the JGI, often working closely with external collaborators, who rely on the ability to devise project-dependent and often very large scale customized analyses that result in publicly available tools. A successful strategy will require effort to satisfy each of these user classes, and careful attention to economies of software reuse and extensibility. There are only a handful of sequencing facilities worldwide that operate at the scale of the JGI's Production Genomics Facility, and these are devoted almost entirely to sequencing driven by biomedical applications. The PGF therefore fulfills a unique and vital role as a resource for genomic studies of DOE relevance. Like the other large-scale facilities, JGI has been carefully following the development of 'next-generation' sequencing technologies, and clearly must continue to refresh its instrumentation as advances are made. Critical to advances in sequencing technology are the computational infrastructure advances that are required to turn raw sequence into quality data. This is one area where JGI can leverage the broader sequencing community's investment in technology development, adopting the best practices and software for sequence processing and assembly. JGI can add unique value by further developing annotation pipelines and tools that serve to build an integrated framework where the Institute's complementary science components can be viewed in a larger 'systems' perspective than is currently possible. As technology, tools, and infrastructure advance, JGI is uniquely positioned in its ability

  15. 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 ...

  16. JGI Digital Scavenger Hunt

    U.S. Department of Energy (DOE) - all 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....

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

    U.S. Department of Energy (DOE) - all 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...

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Jaffe, David; Gnerre, Sante

    2016-07-12

    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.

  1. The Genome Portal of the Department of Energy Joint Genome Institute

    SciTech Connect

    Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge; Hua, Susan; Poliakov, Alexander; Smirnova, Tatyana; Dubchak, Inna

    2014-03-14

    The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. 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. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases of inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Willis, John

    2016-07-12

    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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  7. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  8. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 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 leads 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.

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

    ScienceCinema

    Arkin, Adam [LBNL

    2016-07-12

    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

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

    SciTech Connect

    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

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

    ScienceCinema

    Silver, Pam [Harvard University

    2016-07-12

    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

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

    ScienceCinema

    Hazen, Terry [LBNL

    2016-07-12

    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.

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

    ScienceCinema

    Knight, Rob [University of Colorado

    2016-07-12

    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

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

    SciTech Connect

    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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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

  17. 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

    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.

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

    ScienceCinema

    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.

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

    ScienceCinema

    Rieseberg, Loren [University of British Columbia

    2016-07-12

    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.

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

    ScienceCinema

    Schatz, Michael C [Cold Spring Harbor Laboratory

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  3. 10-Year Strategic Vision: Forging the Future of the DOE JGI

    SciTech Connect

    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.

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

    ScienceCinema

    Thomashow, Mike

    2016-07-12

    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. «

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

    ScienceCinema

    Drell, Persis [SLAC Director

    2016-07-12

    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

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

    ScienceCinema

    Bork, Peer

    2016-07-12

    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

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

    SciTech Connect

    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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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

  10. JGI Digital Scavenger Hunt

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    Keasling, Jay

    2016-07-12

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

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

    SciTech Connect

    Tringe, Susannah Green

    2009-03-25

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

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

    ScienceCinema

    Tringe, Susannah Green

    2011-04-25

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

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

    SciTech Connect

    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.

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

    ScienceCinema

    Ley, Ruth [Cornell University

    2016-07-12

    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.

  16. Gerber-JGI

    U.S. Department of Energy (DOE) - all 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,

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

    SciTech Connect

    Hickey, Scott

    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.

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

    ScienceCinema

    Willerslev, Eske [University of Copenhagen

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Sullivan, Matthew B [University of Arizona

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    Voigt, Chris

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    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

  8. OSCARS Extends JGI Network Capacity

    U.S. Department of Energy (DOE) - all 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

  9. OSCARS Extends JGI Network Capacity

    U.S. Department of Energy (DOE) - all 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...

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

    ScienceCinema

    Kaeppler, Shawn [University of Wisconsin, Madison

    2016-07-12

    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

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

    ScienceCinema

    Banks, Jody [Purdue University

    2016-07-12

    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.

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

    SciTech Connect

    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.

  13. 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

    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.

  14. 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

    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

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

    SciTech Connect

    Pruneda-Paz, Jose

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    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.

  18. 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

    Ronald, Pamela

    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.

  19. 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

    Wullschleger, Stan [ORNL

    2016-07-12

    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.

  20. 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

    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.

  1. 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

    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.

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

    ScienceCinema

    Gmitter Jr, Fred [University of Florida

    2016-07-12

    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.

  3. Soybean (2010 JGI User Meeting)

    ScienceCinema

    Stacey, Gary

    2016-07-12

    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

  4. A GSC Global Genome Census (GSC8 Meeting)

    ScienceCinema

    Kyrpides, Nikos [DOE JGI

    2016-07-12

    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.

  5. A GSC Global Genome Census (GSC8 Meeting)

    SciTech Connect

    Kyrpides, Nikos

    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. 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.

  6. Joint Genome Institute Progress Report 2002-2005

    SciTech Connect

    Gilbert, David

    2005-10-03

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

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

    ScienceCinema

    Chain, Patrick [DOE JGI

    2016-07-12

    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.

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

    ScienceCinema

    Wiegel, Detlef

    2016-07-12

    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

  9. New Metadata Organizer and Archive Streamlines JGI Data Management

    U.S. Department of Energy (DOE) - all 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 ...

  10. Ocean Viral Metagenomics (2010 JGI User Meeting)

    ScienceCinema

    Rohwer, Forest

    2016-07-12

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

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

    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.

  12. 11th Annual Energy Department Joint Genome Institute Genomics of Energy & Environment Meeting

    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.

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

    SciTech Connect

    Sharon, Itai

    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.

  14. 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

    Coomey, Joshua

    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.

  15. 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

    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.

  16. Genomics at the Ontario Institute for Cancer Research

    SciTech Connect

    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

  17. Final Technical Report of Institute for Environmental Genomics...

    Office of Scientific and Technical Information (OSTI)

    Project Title: Integrated Genome-Based Studies of Shewanella Ecophysiology Contract Number: DE-FG02-07ER64383 PI: Jizhong Zhou, Professor and Director, Institute for Environmental ...

  18. 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

  19. 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

    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.

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

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    1 612011 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 ...

  1. 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

    Reeve, Wayne

    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.

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

    ScienceCinema

    Hibbett, David [Clark University

    2016-07-12

    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.

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

    SciTech Connect

    Allen, Eric

    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.

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

    SciTech Connect

    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.

  5. 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

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  8. 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

    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.

  9. 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

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    Notredame, Cedric [Centre for Genomic Regulation

    2016-07-12

    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.

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

    ScienceCinema

    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.

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

    ScienceCinema

    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

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

    ScienceCinema

    Khanna, Madhu

    2016-07-12

    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

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

    U.S. Department of Energy (DOE) - all 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...

  19. MycoCosm portal: gearing up for 1000 fungal genomes

    SciTech Connect

    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.

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

    ScienceCinema

    Gokhale, Maya

    2011-06-08

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

  1. 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...

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

    Office of Science (SC)

    DOE Joint Genome Institute 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

  3. JGI's Carbon Cycling Studies on Restored Marshes

    SciTech Connect

    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.

  4. Phytozome System for Comparative Plant Genomics

    Energy Science and Technology Software Center

    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

  5. 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

    Noel, Joseph

    2016-07-12

    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

  6. Critical Materials Institute uses the Materials Genome approach to

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Department of Energy Critical Materials Institute Gains Ten Industrial and Research Affiliates Critical Materials Institute Gains Ten Industrial and Research Affiliates April 12, 2016 - 10:32am Addthis News release from the Ames Laboratory, April 11, 2016. The Critical Materials Institute, a U.S. Department of Energy Innovation Hub led by the Ames Laboratory, has gained ten new affiliates to its research program, seeking ways to eliminate and reduce reliance on rare-earth metals and other

  7. Fueling the Future with Fungal Genomes

    SciTech Connect

    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.

  8. Phytozome: a Tool for Green Plant Comparative Genomics

    DOE Data Explorer

    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

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

    ScienceCinema

    Pop, Mihai [University of Maryland

    2016-07-12

    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.

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

    ScienceCinema

    Garrity, George

    2016-07-12

    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.

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

    ScienceCinema

    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.

  12. Fungal Genomics Program

    SciTech Connect

    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.

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

    ScienceCinema

    Konerding, David [Google, Inc

    2016-07-12

    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.

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

    ScienceCinema

    Colwell, Rita

    2016-07-12

    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

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

    ScienceCinema

    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

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

    ScienceCinema

    Simpson, Jared [Wellcome Trust Sanger Institute

    2016-07-12

    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

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

    ScienceCinema

    Cottingham, Bob [ORNL

    2016-07-12

    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.

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

    ScienceCinema

    Oehmen, Chris [PNNL

    2016-07-12

    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.

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

    ScienceCinema

    Meyer, Folker [ANL

    2016-07-12

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

    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.

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

    SciTech Connect

    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.

  3. JGI_Training_FileSystems_Feb2012.ppt

    U.S. Department of Energy (DOE) - all 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 *

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

    SciTech Connect

    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.

  5. About | U.S. DOE Office of Science (SC)

    Office of Science (SC)

    biology. Today, with its Genomic Sciences Program and the DOE Joint Genome Institute (JGI), BER researchers are using powerful tools of plant and microbial systems biology to ...

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

    SciTech Connect

    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.

  7. Link Alpha J

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    JBEI: Joint BioEnergy Institute JCAP: Joint Center for Artificial Photosynthesis JDEM: The Joint Dark Energy Mission JGI: Joint Genome Institute Job Descriptions Job Hazards ...

  8. Bonus Organisms in High-Throughput Eukaryotic Whole-Genome Shorgun Assembly

    SciTech Connect

    Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank; Platt, Darren

    2006-02-06

    The DOE Joint Genome Institute has sequenced over 50 eukaryotic genomes, ranging in size from 15 MB to 1.6 GB, over a wide range of organism types. In the course of doing so, it has become clear that a substantial fraction of these data sets contains bonus organisms, usually prokaryotes, in addition to the desired genome. While some of these additional organisms are extraneous contamination, they are sometimes symbionts, and so can be of biological interest. Therefore, it is desirable to assemble the bonus organisms along with the main genome. This transforms the problem into one of metagenomic assembly, which is considerably more challenging than traditional whole-genome shotgun (WGS) assembly. The different organisms will usually be present at different sequence depths, which is difficult to handle in most WGS assemblers. In addition, with multiple distinct genomes present, chimerism can produce cross-organism combinations. Finally, there is no guarantee that only a single bonus organism will be present. For example, one JGI project contained at least two different prokaryotic contaminants, plus a 145 KB plasmid of unknown origin. We have developed techniques to routinely identify and handle such bonus organisms in a high-throughput sequencing environment. Approaches include screening and partitioning the unassembled data, and iterative subassemblies. These methods are applicable not only to bonus organisms, but also to desired components such as organelles. These procedures have the additional benefit of identifying, and allowing for the removal of, cloning artifacts such as E.coli and spurious vector inclusions.

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

    ScienceCinema

    Savage, Steve

    2016-07-12

    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

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

    ScienceCinema

    Knapp, Steve

    2016-07-12

    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

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

    ScienceCinema

    Kent, Jim [UCSC

    2016-07-12

    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.

  12. Overview:

    Office of Scientific and Technical Information (OSTI)

    Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface ...

  13. 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...

  14. Featured Announcements

    U.S. Department of Energy (DOE) - all 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...

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

    DOE Data Explorer

    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.

  16. Joint Facilities User Forum on Data Intensive Computing Lessons Learned

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    User Forum on Data Intensive Computing Lessons Learned - NERSC/JGI Partnership Kjiersten Fagnan, NERSC User Services/JGI --- 1 --- June 1 7, 2 013 Outline * Overview o f N ERSC/JGI P artnership - DOE J GI b ackground - Team o verview - Compute r esources * CompuBng S trategic P lan - JGI G oals - NERSC G oals * Lessons Learned --- 2 --- DOE Joint Genome Institute 3 DOE JGI, Serving as a genomic user facility in support of the DOE missions: * Walnut Creek, CA facility opened in 1999 * 250

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

  19. 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...

  20. 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...

  1. Human Genome Research: Decoding DNA

    Office of Scientific and Technical Information (OSTI)

    ... Speeding Up the Process of Gene Discovery Engineered Enzyme Accelerates DNA Sequencing Putting a Virus to Practical Use DOE Joint Genome Institute The Human Genome Project: ...

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

    ScienceCinema

    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.

  3. 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

    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.

  4. 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

    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.

  5. The Future of Microbial Genomics

    SciTech Connect

    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

  6. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    SciTech Connect

    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

    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.

  7. 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...

  8. "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...

  9. Directions to Berkeley Lab

    U.S. Department of Energy (DOE) - all 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...

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

    SciTech Connect

    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>.

  11. Gene Calling Standards (GSC8 Meeting)

    ScienceCinema

    Kyrpides, Nikos [Genome Biology Program, DOE JGI

    2016-07-12

    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.

  12. Bioinformatics Computing Consultant Position Available

    U.S. Department of Energy (DOE) - all 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

  13. Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274

    SciTech Connect

    Steindorff, Andrei S.; Noronha, Elilane F.; Ulhoa, Cirano J.; Kuo, Alan; Salamov, Asaf A.; Haridas, Sajeet; Riley, Robert W.; Druzhinina, Irina S.; Kubicek, Christian P.; Grigoriev, Igor V.

    2015-03-17

    Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline we predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared with the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.

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

    ScienceCinema

    Raes, Jeroen [University of Brussels

    2016-07-12

    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

  15. Systems Biology Knowledgebase (GSC8 Meeting)

    ScienceCinema

    Cottingham, Robert W [ORNL

    2016-07-12

    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.

  16. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema

    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.

  17. The Biocurator Society (GSC8 Meeting)

    ScienceCinema

    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

  18. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema

    White, Owen [University of Maryland

    2016-07-12

    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

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

    ScienceCinema

    Jansson, Janet [LBNL

    2016-07-12

    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

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

    ScienceCinema

    Mizrachi, Ilene [NCBI

    2016-07-12

    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.

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

    ScienceCinema

    Mavrommatis, Kostas [JGI

    2016-07-12

    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.

  2. Engineering Institute

    U.S. Department of Energy (DOE) - all 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)

  3. Seaborg Institute

    U.S. Department of Energy (DOE) - all 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,

  4. Financial Institutions

    Energy.gov [DOE]

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

  5. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  6. 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

  7. Engineering Institute

    U.S. Department of Energy (DOE) - all 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...

  8. Finding Fingerprints of Selection in Poplar Genomes

    SciTech Connect

    Tuskan, Gerald

    2014-10-02

    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. Finding Fingerprints of Selection in Poplar Genomes

    ScienceCinema

    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.

  10. Rob Egan JGI

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Fine grained Lots of communication syncs "Game of Life" Climate modelling Coarse grained Moderate communication few syncs 'Map' phase of ...

  11. Flash Updates of GSC projects (GSC8 Meeting)

    SciTech Connect

    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.

  12. Flash Updates of GSC projects (GSC8 Meeting)

    ScienceCinema

    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.

  13. Engineering Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Education Opportunities » Engineering Institute Engineering Institute Engineering dynamics that include flight, vibration isolation for precision manufacturing, earthquake engineering, blast loading, signal processing, and experimental model analysis. Contact Leader, Los Alamos Charles Farrar Email Leader, UCSD Michael Todd Email Los Alamos Program Administrator Jutta Kayser (505) 663-5649 Email Administrative Assistant Stacy Baker (505) 663-5233 Email Collaboration for conducting

  14. Engineering Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    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 ...

  15. Quantum Institute

    U.S. Department of Energy (DOE) - all 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

  16. Engineering Institute

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    Koren, Sergey [University of Maryland

    2016-07-12

    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.

  18. Expanding genomics of mycorrhizal symbiosis

    Office of Scientific and Technical Information (OSTI)

    taonfcr® Don MICROBIOLOGY MINI REVIEW ARTICLE published: 04 November 2014 doi: 10.3389/fmicb.2014.00582 Expanding genomics of mycorrhizal symbiosis Alan Kuo1, Annegret Kohler2, Francis M. Martin2* and Igor V Grigoriev1* 1 United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA 2 UMR, Lab of Excellence forAdvanced Research on the Biology ofTReeand Forest Ecosystems, Tree-Microbe Interactions, Institut National de la Recherche Agronomique, Universite de Lorraine, Nancy,

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

    U.S. Department of Energy (DOE) - all 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

  20. Genome Engineering

    SciTech Connect

    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

  1. Building international genomics collaboration for global health security

    SciTech Connect

    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 installation 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.

  2. PNNL: IDREAM - Partnering Institutions

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Partnering Institutions Washington State University University of Washington Oak Ridge National Laboratory University of Notre Dame Georgia Institute of Technology

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

    Office of Science (SC)

    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

  4. Exploration of Metagenome Assemblies with an Interactive Visualization Tool

    SciTech Connect

    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

    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

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

    ScienceCinema

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

    2016-07-12

    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

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

    U.S. Department of Energy (DOE) - all 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

  8. Whose genome is it, anyway?

    SciTech Connect

    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. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    S.A. Gurvitz, The Weizmann Institute of Science, Rehovot, Israel Confinement and Scaling ... S.A. Gurvitz, The Weizmann Institute of Science, Rehovot, Israel Confinement and Scaling ...

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

    ScienceCinema

    Canon, Shane [LBNL

    2016-07-12

    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. Institutional Change Process Step 2: Assess Institutional Rules...

    Office of Environmental Management (EM)

    2: Assess Institutional Rules, Roles, and Tools Institutional Change Process Step 2: Assess Institutional Rules, Roles, and Tools Graphic of the Institutional Change Continuous ...

  12. JGI Compute User Training Series

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    List Need Help? Out-of-hours Status and Password help Call operations: 1-800-66-NERSC, ... Learn how to change your password, set your security questions, change your shell, and ...

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

    DOE Data Explorer

    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.

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

    DOE Data Explorer

    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.

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

    ScienceCinema

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

    2016-07-12

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

    ScienceCinema

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

    2016-07-12

    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.

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

    ScienceCinema

    Field, Dawn [NERC; Sterk, Peter [NERC

    2016-07-12

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    ScienceCinema

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

    2016-07-12

    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

  1. The evolution of microbial species - a view through the genomic lens

    SciTech Connect

    Varghese, Neha; Mukherjee, Supratim; ivanova, Natalia; Mavromatis, Konstantinos; Konstantinidis, Konstantinos; Kyrpides, Nikos; Pati, Amrita

    2014-03-17

    For a long time prokaryotic species definition has been under debate and a constant source of turmoil in microbiology. This has recently prompted the ASM to call for a scalable and reproducible technique, which uses meaningful commonalities to cluster microorganisms into groups corresponding to prokaryotic species. Whole-genome Average Nucleotide Identity (gANI) was previously suggested as a measure of genetic distance that generally agrees with prokaryotic species assignments based on the accepted best practices (DNA-DNA hybridization and 16S rDNA similarity). In this work, we prove that gANI is indeed the meaningful commonality based on which microorganisms can be grouped into the aforementioned clusters. By analyzing 1.76 million pairs of genomes we find that identification of the closest relatives of an organism via gANI is precise, scalable, reproducible, and reflects the evolutionary dynamics of microbes. We model the previously unexplored statistical properties of gANI using 6,000 microbial genomes and apply species-specific gANI cutoffs to reveal anomalies in the current taxonomic species definitions for almost 50percent of the species with multiple genome sequences. We also provide evidence of speciation events and genetic continuums in 17.8percent of those species. We consider disagreements between gANI-based groupings and named species and demonstrate that the former have all the desired features to serve as the much-needed natural groups for moving forward with taxonomy. Further, the groupings identified are presented in detail at http://ani.jgi-psf.org to facilitate comprehensive downstream analysis for researchers across different disciplines

  2. A Celebration of The Genome, 1953-2003

    Office of Scientific and Technical Information (OSTI)

    Celebration of The Genome, 1953-2003 This April Join the National Institutes of Health and the Department of Energy in a month-long series of scientific, educational, cultural and ...

  3. Genome patent fight erupts

    SciTech Connect

    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.

  4. GOLD: The Genomes Online Database

    DOE Data Explorer

    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:

  1. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Jeffrey W. Martin, Kellogg Radiation Laboratory, California Institute of Technology, Pasadena, California Ultracold Neutrons April 20 Professor J. W. Watson, Department of Physics, ...

  2. People - Cyclotron Institute

    U.S. Department of Energy (DOE) - all 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 ...

  3. Facilities - Cyclotron Institute

    U.S. Department of Energy (DOE) - all 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...

  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. U.S. Department of Energy Joint Genome Institute

    Office of Scientific and Technical Information (OSTI)

    ... benefit growers in the not-too-distant future," Jones said. ... extract cellulosic ethanol and higher-energy-content fuels. ... and Wayne Hurlbert (Storage Systems). "NERSC has a ...

  6. 2013 Progress Report -- DOE Joint Genome Institute (Program Document...

    Office of Scientific and Technical Information (OSTI)

    Close Cite: Bibtex Format Close 0 pages in this document matching the terms "" Search For Terms: Enter terms in the toolbar above to search the full text of this document for ...

  7. 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...

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

    Office of Environmental Management (EM)

    microbes that affect the growth of other plants (crops like corn or wheat) researchers ... microbes that affect the growth of other plants (crops like corn or wheat) researchers ...

  9. Building international genomics collaboration for global health security

    DOE PAGES [OSTI]

    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

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

    SciTech Connect

    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.

  11. William Arndt

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    William Arndt William Arndt 11214167 10103524655099960 4159392778273133987 n William (Bill) Arndt Ph.D. Post Doc HPC optimization of Bioinformatics applications warndt@lbl.gov Berkeley Lab Berkeley, CA US William Arndt is a post doctoral software developer at NERSC. His focus is the targeted optimization of bioinformatics applications for use on HPC resources supported by NERSC. He is partially funded by the Joint Genome Institute and focuses on improving software heavily used by JGI

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

    ScienceCinema

    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.

  13. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    Chin, Francis [University of Hong Kong

    2016-07-14

    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.

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

    ScienceCinema

    Cochrane, Guy [EMBL-EBI

    2016-07-12

    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.

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

    SciTech Connect

    Cochrane, Guy

    2011-10-12

    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.

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

    ScienceCinema

    White, Owen [University of Maryland

    2016-07-12

    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.

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

    ScienceCinema

    Dehal, Paramvir [LBNL

    2016-07-12

    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.

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

    ScienceCinema

    Rusch, Doug [J. Craig Venter Institute

    2016-07-12

    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.

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

    ScienceCinema

    Desai, Narayan [ANL

    2016-07-12

    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.

  1. Cyclotron Institute REU Program

    U.S. Department of Energy (DOE) - all 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....

  2. Financial Institution Lending Programs

    Energy.gov [DOE]

    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...

  3. Contact - Cyclotron Institute

    U.S. Department of Energy (DOE) - all 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...

  4. Critical Materials Institute

    ScienceCinema

    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.

  5. New England Fuel Institute

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    and CEO of the New England Fuel Institute Before the U.S. Department of Energy and the Quadrennial Energy Review Task Force Public Hearing on "New England Regional ...

  6. UNCLASSIFIED Institute for Materials ...

    U.S. Department of Energy (DOE) - all 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...

  7. Genomic Data and Annotation from the SEED

    DOE Data Explorer

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  8. Resources | Critical Materials Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Resources The Critical Materials Institute offers connections to resources, including: CMI Annual Report (page includes link pdf of 20-page report) 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

  9. Great Lakes Energy Institute

    SciTech Connect

    Alexander, J. Iwan

    2012-11-18

    The vision of the Great Lakes Energy Institute is to enable the transition to advanced, sustainable energy generation, storage, distribution and utilization through coordinated research, development, and education. The Institute will place emphasis on translating leading edge research into next generation energy technology. The Institute’s research thrusts focus on coordinated research in decentralized power generation devices (e.g. fuel cells, wind turbines, solar photovoltaic devices), management of electrical power transmission and distribution, energy storage, and energy efficiency.

  10. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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.

  11. 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...

  12. "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...

  13. 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...

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

    SciTech Connect

    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.

  15. Human Genome: DOE Origins

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Human Genome Research: DOE Origins Resources with Additional Information Charles DeLisi Charles DeLisi The genesis of the Department of Energy (DOE) human genome project took place ...

  16. Ecologic Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  17. Institutional Change Process for Sustainability

    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.

  18. Strategies for Achieving Institutional Change

    Office of Energy Efficiency and Renewable Energy (EERE)

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

  19. Rahus Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  20. Genome Science/Technologies

    U.S. Department of Energy (DOE) - all 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

  1. Exploiting the genome

    SciTech Connect

    Block, S.; Cornwall, J.; Dyson, F.; Koonin, S.; Lewis, N.; Schwitters, R.

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  2. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all 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

  3. The human genome project

    SciTech Connect

    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.

  4. Ethiopian Development Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  5. Utilization Technology Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  7. CMI Social Media | Critical Materials Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

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

  8. Institutional Change Process Step 2: Assess Institutional Rules, Roles, and

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Tools | Department of Energy 2: Assess Institutional Rules, Roles, and Tools Institutional Change Process Step 2: Assess Institutional Rules, Roles, and Tools Graphic of the Institutional Change Continuous Improvement Process gear. The steps begin with Determine Goals and move to Assess Institutional Rules, Roles and Tools then to Develop Action Plan then to Implement Plan then finally to Measure and Evaluate. The process begins again with Determine Goals. Determine Goals Develop Action Plan

  9. Commitment Institutional Change Principle

    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.

  10. Use of Institutional Controls

    Directives, Delegations, and Other 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.

  11. Use of Institutional Controls

    Directives, Delegations, and Other 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.

  12. 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,...

  13. 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,...

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

    SciTech Connect

    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

  15. Cyclotron Institute » Education

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Education The Cyclotron Institute provides education and training in nuclear science at the undergraduate, graduate, and postdoctoral levels. Faculty teach a variety of courses in nuclear chemistry and nuclear physics. Research is emphasized at the graduate and postdoctoral levels, although we also have a Research Experience for Undergraduates Program each summer. Finally, we also participate in the Saturday Morning Physics program for high school students each spring.

  16. Cyclotron Institute » Research

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Research Student Analyzing Data 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 quarks

  17. Research | Critical Materials Institute

    U.S. Department of Energy (DOE) - all 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

  18. ORGANIZATIONAL CHART - CYCLOTRON INSTITUTE

    U.S. Department of Energy (DOE) - all 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. Nuclear Energy Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    (NEI) Summit Presentation University-Industry- Laboratory Partnerships: Gauging Effectiveness Douglas Kothe, CASL Director Oak Ridge National Laboratory February 26, 2014 CASL-U-2014-0355-000 CASL-U-2014-0355-000 University-Industry-Laboratory Partnerships Gauging Effectiveness CASL: The Consortium for Advanced Simulation of Light Water Reactors A DOE Energy Innovation Hub Douglas B. Kothe Oak Ridge National Laboratory Director, CASL 9 th Nuclear Energy R&D Summit Nuclear Energy Institute

  20. Careers | Critical Materials Institute

    U.S. Department of Energy (DOE) - all 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

  1. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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

  2. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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

  3. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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,

  4. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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

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

    ScienceCinema

    Weinstock, George [Washington University

    2016-07-12

    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.

  6. Genomics and Systems Biology

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Genomics and Systems Biology Los Alamos National Laboratory 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

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

    ScienceCinema

    Goll, Johannes [JCVI

    2016-07-12

    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.

  8. 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

    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.

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

    ScienceCinema

    Hugenholtz, Phil [University of Queensland

    2016-07-12

    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.

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

    ScienceCinema

    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.

  11. 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....

  12. Genomics Division Home

    U.S. Department of Energy (DOE) - all 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...

  13. Cyclotron Institute REU Program

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    NOW TAKING APPLICATIONS FOR SUMMER 2017 REU! "Texas A&M Science - Labors of Lab." REU student Kassie Marble featured in TAMU College of Science Video The Texas A&M Cyclotron Institute, with support from the National Science Foundation, serves as a Research Experiences for Undergraduates site during the summer of each year. Alysssa Dibidad in the K150 control room. This REU site focuses on research in nuclear and particle science. Students will have the opportunity to work

  14. Cyclotron Institute » Publications

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Publications Cyclotron Institute Upgrade White Paper Annual Reports 2015-2016 (full report) 2014-2015 (full report) 2013-2014 (full report) 2012-2013 (full report) 2011-2012 (full report) 2010-2011 (full report) 2009-2010 (full report) 2008-2009 (full report) 2007-2008 (full report) 2006-2007 (full report) 2005-2006 (full report) 2004-2005 (full report) 2003-2004 (full report) 2002-2003 (full report) 2001-2002 2000-2001 1999-2000 1998-1999

  15. Cyclotron Institute » Tours

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Tours We do offer tours of our facility to educational groups on a limited basis. Visitors will learn how a cyclotron works and get to see the ion source, control room, and one of the experimental halls. Unfortunately, access to the cyclotron itself is dictated by operational constraints which cannot be predicted in advance. If you would like to schedule a tour of the Cyclotron Institute, please contact Julie Anderson at unulldnulle TOD umat nullTnullOD pmnulloc TA nosrednullnnullAJnull or

  16. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    INSPECTION REPORT: INS-O-15-02 INSPECTION REPORT: INS-O-15-02 April 2, 2015 Allegation Regarding Human Reliability Program Unsuitable Reportable Behaviors at the Office of Secure Transportation Publically available version of the OUO report issued in November 2014. FREQUENTLY REQUESTED FOIA: Inspection Report: INS-O-15-02 (1008.14 KB) More Documents & Publications Inspection Report: INS-O-15-02 FIA-15-0058 - In the Matter of Bradley P. Jones Inspection Report: DOE/IG-0921

    INSTITUTE

  17. INSTITUTE COLLOQUIA AND SEMINARS

    U.S. Department of Energy (DOE) - all 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

  18. Genome Project Standards in a New Era of Sequencing

    SciTech Connect

    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

  19. 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:...

  20. Cyclotron Institute Upgrade Project

    SciTech Connect

    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.

  1. Form:Research Institution | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  2. Industrial Technology Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  3. Cornell Fuel Cell Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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)...

  4. Hitachi Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  5. GHG Management Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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:...

  6. Honda Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  7. Rocky Mountain Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Rocky Mountain Institute Jump to: navigation, search Logo: Rocky Mountain Institute Name: Rocky Mountain Institute Address: 1820 Folsom Street Place: Boulder, Colorado Zip: 80302...

  8. Sustainable Europe Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  9. Low Carbon Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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,...

  10. UC Berkeley- Energy Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

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

  11. The MicrobesOnline Web site for comparative genomics

    SciTech Connect

    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.

  12. Complete genome sequence of Arthrobacter sp. strain FB24

    SciTech Connect

    Nakatsu, C. H.; Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, T.; Han, Cliff F.; Beasley, Federico; Chen, Weimin; Konopka, Allan; Xie, Gary

    2013-09-30

    Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program.

  13. Human Genome Program

    SciTech Connect

    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.

  14. COLLEGE OF SCIENCE CYCLOTRON INSTITUTE Cyclotron Institute, Texas...

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Candidates must have experience with modern nuclear instrumentation and data analysis ... The position will be based at the Institute in College Station, Texas, USA. The Cyclotron ...

  15. Genomes to Life Diversity Initiative

    SciTech Connect

    McClure, Thomas

    2010-03-15

    This was a collaborative initiative between Western Carolina University, Furman University and the University of North Carolina-Asheville. At each of the institutions, funds from the grant award were used for the acquisition of mostly microscopy laboratory equipment, supporting supplies and necessary training as appropriate. The distribution of funds was: $495,000 Western Carolina University; $130,000 Furman University; $100,000 University of North Carolina-Asheville for a total of $725,000 total award from DOE. Western Carolina University purchased significant instrumentation with funds from this award that included among others, fermenters, a Confocal microscope, and an automated sequencer. The fermenters have been used in research and courses and to prepare biochemical materials for research and courses. The Confocal microscope has provided Western students and faculty with unique imaging opportunities not generally available except in medical schools. Unlike regular optical microscopy, confocal microscopy offers a three-dimensional image that can be viewed from different angles. In addition, the device has been set up to be controlled from remote locations, providing high school and institutions of higher education students across Western North Carolina with the opportunity to use state-of-the-art instrumentation from their location. One of the goals of this collaboration was to get more high school students interested in science. The automated sequencer has become a very significant instructional and research tool. It has been widely used for characterizing the oak genome, which has very significant implications for Western North Carolina. More recently, it has been used for groundbreaking forensic science research. This device has been used to create a database to identify unidentified persons. The instrument has also been used in several undergraduate and graduate courses, where students learn the principles and operation of this very important instrument

  16. Genomic definition of species

    SciTech Connect

    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.

  17. Genomic library construction

    DOEpatents

    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.

  18. Cyclotron Institute » Graduate Studies

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Graduate Studies Students wishing to carry out their dissertation research at the Cyclotron Institute must be formally enrolled in the graduate program in the departments of Physics, Chemistry, or Nuclear Engineering, 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 generally funded by the U.S. Department of Energy, the National Science Foundation, and the Robert A. Welch

  19. Los Alamos National Laboratory Institutes

    U.S. Department of Energy (DOE) - all 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. 

  20. Molluscan Evolutionary Genomics

    SciTech Connect

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  1. Integrative Genomics Building

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Integrative Genomics Building Community Environmental Documents Tours Community Programs Friends of Berkeley Lab ⇒ Navigate Section Community 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 interior of the Berkeley Lab. The IGB is intended to

  2. Integrative Bioengineering Institute

    SciTech Connect

    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.

  3. Atlanta Community Leaders’ Institute Conference

    Energy.gov [DOE]

    The Atlanta Community Leaders Institute (CLI) held a conference on February 8 and 9 at Morehouse School of Medicine, in Atlanta, Georgia.

  4. Bolton Community Leaders’ Institute Conference

    Energy.gov [DOE]

    The Bolton Community Leaders Institute (CLI) held a conference on February 22 and 23 at the Southeastern Community College in Whiteville, North Carolina.

  5. Institutional Change Basics for Sustainability

    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.

  6. Continuous Change Institutional Change Principle

    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.

  7. Nuclear Structure - Research - Cyclotron Institute

    U.S. Department of Energy (DOE) - all 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 ...

  8. CASL - Massachusetts Institute of Technology

    U.S. Department of Energy (DOE) - all 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. Research and Institutional Integrity Office

    U.S. Department of Energy (DOE) - all 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...

  10. Izabela Stroe: Worcester Polytechnic Institute

    U.S. Department of Energy (DOE) - all 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...

  11. My Account | Critical Materials Institute

    U.S. Department of Energy (DOE) - all 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 ...

  12. Ebolavirus comparative genomics

    DOE PAGES [OSTI]

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; et al

    2015-07-14

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of themore » same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.« less

  13. Gas Technology Institute (Partnership for Advanced Residential...

    OpenEI (Open Energy Information) [EERE & EIA]

    Technology Institute (Partnership for Advanced Residential Retrofit) Jump to: navigation, search Name: Gas Technology Institute Place: Des Plaines, IL Website:...

  14. Denver University - International Institute for Environment and...

    OpenEI (Open Energy Information) [EERE & EIA]

    - International Institute for Environment and Enterprise Name: Denver University - International Institute for Environment and Enterprise Address: 2199 S. University Blvd....

  15. 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 ...

  16. Institute for Advanced Composites Manufacturing Innovation Holds...

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Institute for Advanced Composites Manufacturing Innovation Holds Second Membership Meeting Institute for Advanced Composites Manufacturing Innovation Holds Second Membership Meeting ...

  17. 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 ...

  18. 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 ...

  19. 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 ...

  20. 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 ...

  1. 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 ...

  2. GenomeVista

    Energy Science and Technology Software Center

    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

  3. Cyclotron Institute » Facilities Overview

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Facilities Overview Facility Layout 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 sophisticated detectors and spectrometers that enhance the Institute's capacity for nuclear research. Follow the links in the menu for more detailed information about our facilities

  4. 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.

  5. Berkeley Quantitative Genome Browser

    Energy Science and Technology Software Center

    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

  6. Performance Assessment Institute-NV

    SciTech Connect

    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.

  7. Institutional computing (IC) information session

    SciTech Connect

    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.

  8. Multiple Motivations Institutional Change Principle

    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...

  9. Facility Upgrade - Cyclotron Institute - TAMU

    U.S. Department of Energy (DOE) - all 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...

  10. Cyclotron Institute » External Collaborations

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    External Collaborations High Energy Physics Instrumentation A number of research projects involving Institute scientists are carried out at other large national and international accelerator facilities in collaboration with groups from other universities and laboratories worldwide. Many of these are directly complementary to the local experimental program but others, as described below, explore other frontiers. Cyclotron Institute scientists carry out research within the BRAHMS and STAR

  11. Cyclotron Institute » Journal Links

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Journal Links Acta Physica Polonica A Acta Physica Polonica B LANL e-Print Archive Nuclear Experiment Nuclear Theory Accelerator Physics Atomic Physics American Physical Society Physical Review A Physical Review C Physical Review D Physical Review Letters Reviews of Modern Physics Institute of Physics Journal of Physics B: Atomic, Molecular and Optical Physics Journal of Physics G: Nuclear and Particle Physics American Institute of Physics Applied Physics Letters Physics Today Nuclear Physics A

  12. Hydraulic Institute Mission and Vision:

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    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

  13. Southface Energy Institute: Advanced Commercial Buildings Initiative |

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Department of Energy Southface Energy Institute: Advanced Commercial Buildings Initiative Southface Energy Institute: Advanced Commercial Buildings Initiative Southface Energy Institute: Advanced Commercial Buildings Initiative Lead Performer: Southface Energy Institute - Atlanta, GA Partners: - City of Atlanta - Atlanta, GA - Georgia Institute of Technology - Atlanta, GA - Kendeda Fund - Atlanta, GA - Oak Ridge National Laboratory - Oak Ridge, TN - Acuity Brands Lighting - Atlanta, GA -

  14. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Doethideomycetes Fungi

    SciTech Connect

    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.

  15. *** CANCELED *** SCIENCE ON SATURDAY- "Finding a Needle in A (Genomic)

    U.S. Department of Energy (DOE) - all 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

  16. Category:Academic Institutions | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    title"Alternative Energy Institute">Alternative Energy Institute","title":"Alternative Energy Institute","link":null,"lat":34.9848017,"lon":-101.9100121,"alt":0,"add...

  17. Institute for Energy Research | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  18. Shaoxing Jinggong Mechanical and Electrical Research Institute...

    OpenEI (Open Energy Information) [EERE & EIA]

    Shaoxing Jinggong Mechanical and Electrical Research Institute Company SJMERI Jump to: navigation, search Name: Shaoxing Jinggong Mechanical and Electrical Research Institute...

  19. EMei Semiconductor Materials Plant Research Institute | Open...

    OpenEI (Open Energy Information) [EERE & EIA]

    EMei Semiconductor Materials Plant Research Institute Jump to: navigation, search Name: EMei Semiconductor Materials Plant & Research Institute Place: Emei, Sichuan Province, China...

  20. Electronics and Telecommunications Research Institute ETRI |...

    OpenEI (Open Energy Information) [EERE & EIA]

    and Telecommunications Research Institute ETRI Jump to: navigation, search Name: Electronics and Telecommunications Research Institute (ETRI) Place: Daejeon, Korea (Republic) Zip:...

  1. NREL: Energy Executive Leadership Academy - Leadership Institute

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Leadership Institute Participants in NREL's Executive Energy Leadership Institute learn about renewable energy and energy efficiency from the experts through this accelerated...

  2. National Environmental Research Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Research Institute Jump to: navigation, search Name: National Environmental Research Institute Address: Box. 358 Frederiksborgvej 399 DK 4000 Place: Roskilde, Denmark Phone Number:...

  3. Stockholm Environment Institute (SEI) | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    The Stockholm Environment Institute, located in Stockholm, Sweden, is an independent international research institute. The SEI is dedicated to bringing scientific insights to...

  4. Finnish Meteorological Institute Doppler Lidar (Dataset) | Data...

    Office of Scientific and Technical Information (OSTI)

    Finnish Meteorological Institute Doppler Lidar Title: Finnish Meteorological Institute Doppler Lidar This doppler lidar system provides co-polar and cross polar attenuated ...

  5. Tokyo Institute of Technology | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  6. Demand Management Institute (DMI) | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Demand Management Institute (DMI) Jump to: navigation, search Name: Demand Management Institute (DMI) Address: 35 Walnut Street Place: Wellesley, Massachusetts Zip: 02481 Region:...

  7. Victoria Transport Policy Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Transport Policy Institute Jump to: navigation, search Name: Victoria Transport Policy Institute Address: 1250 Rudlin Street, Place: Victoria, British Columbia Website:...

  8. Hahn Meitner Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Meitner Institute Jump to: navigation, search Name: Hahn-Meitner-Institute Place: Berlin, Germany Zip: 14109 Product: Berlin-based, scientific research centre. Coordinates:...

  9. Global Climate Change Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Change Institute Jump to: navigation, search Name: Global Climate Change Institute Place: Tsinghua University, Beijing Municipality, China Zip: 100084 Product: Global Climate...

  10. Renewable Energy Institute International | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    International Jump to: navigation, search Logo: Renewable Energy Institute International Name: Renewable Energy Institute International Address: 5022 Bailey Loop Place: McClellan,...

  11. Solar Living Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Living Institute Jump to: navigation, search Name: Solar Living Institute Address: 13771 S. Hwy. 101 Place: Hopland, California Zip: 95449 Region: Bay Area Website:...

  12. Alternative Energy Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  13. Category:Public Institutions | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    :,"polygons":,"circles":,"rectangles":,"locations":"text":"Institute" title"Alternative Energy Institute">Alternative Energy...

  14. International Institute for Sustainable Development (IISD) |...

    OpenEI (Open Energy Information) [EERE & EIA]

    by working collaboratively with other institutions -building long term strategic alliances, while retaining the institutional agility necessary to confront the challenges of...

  15. Institute of Geophysics, Planetary Physics, and Signatures

    U.S. Department of Energy (DOE) - all 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...

  16. Officials Establish Training Institute, Creating Enterprise Solution...

    Office of Environmental Management (EM)

    Officials Establish Training Institute, Creating Enterprise Solution for Worker Safety Officials Establish Training Institute, Creating Enterprise Solution for Worker Safety March ...

  17. Edison Welding Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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...

  18. Energy Biosciences Institute EBI | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    EBI Jump to: navigation, search Name: Energy Biosciences Institute (EBI) Place: Berkeley, California Zip: 94720 Sector: Biofuels Product: US-based research institution...

  19. Manufacturing Institutes Exhibit American Innovation at Hannover...

    Office of Environmental Management (EM)

    Manufacturing Institutes Exhibit American Innovation at Hannover Messe Manufacturing Institutes Exhibit American Innovation at Hannover Messe April 25, 2016 - 4:30pm Addthis The ...

  20. Australian Solar Institute | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    search Name: Australian Solar Institute Place: Newcastle, New South Wales, Australia Zip: 2300 Sector: Solar Product: New South Wales-based institute providing support...

  1. Comprehensive Legacy Management and Institutional Controls Plan

    Office of Legacy Management (LM)

    Preserve, Fernald, Ohio Comprehensive Legacy Management and Institutional Controls Plan ... blank LMSFERS03496-9.0 Comprehensive Legacy Management and Institutional Controls ...

  2. 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 ...

  3. Paul Scherrer Institut | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    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:...

  4. Institute for Environmental Solutions | Open Energy Information

    OpenEI (Open Energy Information) [EERE & EIA]

    Environmental Solutions Jump to: navigation, search Logo: Institute for Environmental Solutions Name: Institute for Environmental Solutions Address: 761 Newport St. Place: Denver,...

  5. ORISE: Oak Ridge Sitewide Institutional Review Board

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    the Protection of Human Subjects, also known as the Common Rule, requires that each institution that engages in human subjects research establish an institutional review board (IRB). ...

  6. Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

    ScienceCinema

    Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

    2016-07-12

    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 field 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 Officer 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 field 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.

  7. The Petascale Data Storage Institute

    SciTech Connect

    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. Institutional

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Expand Utility Resources News & Events Expand News & Events Skip navigation links Marketing Resources Reports, Publications, and Research Agricultural Commercial Consumer...

  9. Cyclotron Institute » Related Websites

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Related Websites Texas A&M University College of Science Department of Chemistry Department of Physics and Astronomy Department of Nuclear Engineering Cyclotron Facility Upgrade Nuclear Solutions Institute Faculty Websites Radiation Effects Facility Saturday Morning Physics Science with Beams of Radioactive Isotopes (at Pacifichem 2015) International Symposium on Super Heavy Nuclei (SHE 2015) Carpathian Summer School of Physics (2014) World Consensus Initiative

  10. Joint BioEnergy Institute

    SciTech Connect

    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 biofuels—liquid fuels derived from the solar energy stored in plant biomass that can replace gasoline, diesel and jet fuels.

  11. PROJECT PROFILE: Southwest Research Institute

    Office of Energy Efficiency and Renewable Energy (EERE)

    The Southwest Research Institute (SwRI) will design, manufacture, and test an ultra-high efficiency supercritical carbon dioxide (sCO2) compressor-expander, or “compander,” for power generation at CSP plants. SwRI will collaborate with Samsung Techwin America to develop the technology.

  12. Edison Electric Institute Comments | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Comments Edison Electric Institute Comments The Edison Electric Institute (EEi) is submitting this letter and the enclosed comments in response to the above-referenced request for infonnation (RFI). DOE - Reg review - EEI cmts 7-11-16 (497.95 KB) More Documents & Publications Edison Electric Institute (EEI) Regulatory Burden RFI, 77 Fed. Reg. 47328 Edison Electric Institute (EEI) Reducing Regulatory Burden RFI, 77 Fed. Reg. 28518 (May 15, 2012) Edison Electric Institute (EEI) Reducing

  13. Institutional Change for Sustainability | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) (indexed site)

    Institutional Change » Institutional Change for Sustainability Institutional Change for Sustainability Inspire Change with an Awards Program Inspire Change with an Awards Program Report shares 22 stories of FEMP Federal Energy and Water Management Award winners whose projects fostered institutional change in agencies. Read more Continuous Improvement Process Continuous Improvement Process Institutional change is anchored in five steps that are repeated for continuous improvement. Read more The

  14. Human Genome Research: Decoding DNA

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Human Genome Research: 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

  15. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    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.

  16. Fungal Genome Sequencing and Bioenergy

    SciTech Connect

    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.

  17. Structural Genomics: Expectations and Reality

    Office of Scientific and Technical Information (OSTI)

    ... TB Structural Genomics Consortium, http:www.doe-mbi.ucla.eduTB (TB) Structures of M. tuberculosis proteome, with emphasis on functionally important proteins. Non-PSI ...

  18. Human Genome Program Image Gallery (from genomics.energy.gov)

    DOE Data Explorer

    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.

  19. Institutional Support | Grid Modernization | NREL

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Institutional Support NREL delivers high-quality technical assistance and objective information to policy makers, regulatory agencies, and regional planning organizations to address the challenges posed by grid modernization. Photo of two people standing in front of a display showing results from a grid study. The demand for objective technical assistance and information on grid modernization is high. State policy makers, regulators, and regional planners must address the complex issues related

  20. Cyclotron Institute » Facility Upgrade

    U.S. Department of Energy (DOE) - all webpages (Extended Search)

    Facility Upgrade Facility Upgrade Layout On January 3, 2005 the Cyclotron Institute Upgrade Project (CIUP) began with the approval of the CIUP management plan by the Department of Energy Office of Nuclear Physics. When completed, the upgraded facility will provide high-quality re-accelerated secondary beams in a unique energy range in the world. Funding for the upgrade comes from several sources: the Department of Energy, matching support from TAMU, the Robert A. Welch Foundation and beam time