WorldWideScience

Sample records for genome institute user

  1. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... Landscape Social Media Videos Image Gallery Fact Sheets Human Genome Project Clinical Studies Genomic Careers DNA Day Calendar ...

  2. Joint Genome Institute's Automation Approach and History

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. DOE Joint Genome Institute 2008 Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    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

  4. 2013 Progress Report -- DOE Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    None

    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.

  5. DOE Joint Genome Institute 2008 Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2013-11-12

    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. In this paper, 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.

  7. The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, Steve

    2010-03-24

    Francis Martin from the French agricultural research institute INRA talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. Public procurement of innovation; endogenous institutions in user producer interaction

    DEFF Research Database (Denmark)

    Hjaltadóttir, Rannveig Edda

    2013-01-01

    and the participants in this interaction need a common code of communication to efficiently work together. The institutions that govern user-producer interaction have therefore been seen as a possible explanation for success or failure in public procurement of innovation. Endogenous institutions were found......This article sets out to explore endogenous institutions as the rules that govern the interaction between users and producers in public procurement of innovation in a regional context. It further aims to study how this interaction influences the results of the procurement process by investigating...... possible institutional barriers and what can be done to fence against them. The article addresses the question: How do endogenous institutions in the context of user-producer interaction affect performance in public procurement of innovation? Innovation is an interactive learning process...

  10. 76 FR 58023 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-09-19

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Review, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892,...

  11. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-05-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group, Genome Research Review... Scientific Review, National Human Genome Research Institute, National Institutes of Health, Bethesda,...

  12. 77 FR 61770 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Genomic Medicine RFAs..., Human Genome Research, National Institutes of Health, HHS) ] Dated: October 4, 2012. David...

  13. 77 FR 28888 - National Human Genome Research Institute Notice of Closed Meeting

    Science.gov (United States)

    2012-05-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... applications. Place: National Human Genome Research Institute, 3635 Fishers Lane, Suite 4076, ] Rockville,...

  14. Indian Institutional Repositories: A Study of User's Perspective

    Science.gov (United States)

    Sawant, Sarika

    2012-01-01

    Purpose: The present study aims to investigate the experience, contribution and opinions of users of respective institutional repositories (IRs) developed in India. Design/methodology/approach: The survey method was used. The data collection tool was a web questionnaire, which was created with the help of software provided by surveymonkey.com…

  15. MUTAGEN: Multi-user tool for annotating GENomes

    DEFF Research Database (Denmark)

    Brugger, K.; Redder, P.; Skovgaard, Marie

    2003-01-01

    MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus...

  16. 77 FR 60706 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-04

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Name of Committee: National Human Genome Research Institute Special Emphasis Panel; Special Emphasis... Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes of...

  17. 75 FR 8374 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Revolutionary..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076,...

  18. 78 FR 68856 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-11-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Review Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  19. Conceptualizing a Genomics Software Institute (GSI).

    Science.gov (United States)

    Gilbert, Jack A; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

    2012-03-19

    Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

  20. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.

  1. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, David [DOE JGI Public Affairs Manager

    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.

  2. 75 FR 10488 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2010-03-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; NHGRI MAP Review... Human Genome Research Institute Special Emphasis Panel; LRP 2010 Teleconference. Date: April 7,...

  3. 78 FR 20933 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel Loan Repayment Program... applications. Place: National Human Genome Research Institute, Room 3055, 5635 Fishers Lane, Rockville,...

  4. 75 FR 52538 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel. Date: November 19-20..., Scientific Review Officer, Scientific Review Branch, National Human Genome Research Institute,...

  5. 78 FR 14806 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-03-07

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel: Clinically Relevant... grant applications. Place: National Human Genome Research Institute, 4th Floor Conference Room,...

  6. 76 FR 35223 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Sequencing Centers...D, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...

  7. 76 FR 65204 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-10-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Genomic Resource...: Rudy O. Pozzatti, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human...

  8. Plant database resources at The Institute for Genomic Research.

    Science.gov (United States)

    Chan, Agnes P; Rabinowicz, Pablo D; Quackenbush, John; Buell, C Robin; Town, Chris D

    2007-01-01

    With the completion of the genome sequences of the model plants Arabidopsis and rice, and the continuing sequencing efforts of other economically important crop plants, an unprecedented amount of genome sequence data is now available for large-scale genomics studies and analyses, such as the identification and discovery of novel genes, comparative genomics, and functional genomics. Efficient utilization of these large data sets is critically dependent on the ease of access and organization of the data. The plant databases at The Institute for Genomic Research (TIGR) have been set up to maintain various data types including genomic sequence, annotation and analyses, expressed transcript assemblies and analyses, and gene expression profiles from microarray studies. We present here an overview of the TIGR database resources for plant genomics and describe methods to access the data.

  9. 75 FR 52537 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  10. 75 FR 2148 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-01-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group, Genome Research Review... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  11. 78 FR 24223 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... applications. Place: National Human Genome Research Institute, 3rd floor Conf. Room 3146, 5635 Fishers...

  12. 76 FR 3643 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Initial Review Group; Genome Research Review... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: January...

  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)

    Energy Technology Data Exchange (ETDEWEB)

    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. 75 FR 62548 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-10-12

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes... . Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  15. 76 FR 19780 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-08

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Officer, CIDR, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane... Assistance Program No. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: April...

  16. 75 FR 80509 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-12-22

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes..., Human Genome Research, National Institutes of Health, HHS) Dated: December 16, 2010. Jennifer S....

  17. 76 FR 9031 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-02-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  18. 75 FR 19984 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2010-04-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers...

  19. 78 FR 47715 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-08-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health,...

  20. 77 FR 71604 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-12-03

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel. Date: January 11, 2013..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076,...

  1. 78 FR 107 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-01-02

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: National Human Genome Research Institute, 3rd Floor Conference Room, 5635 Fishers Lane, Rockville, MD 20851... Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers...

  2. 76 FR 79199 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-12-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health,...

  3. 75 FR 35821 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-06-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed..., Scientific Review Officer, CIDR, National Human Genome Research Institute, National Institutes of Health... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health,...

  4. 78 FR 55752 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-09-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Clinical Sites for..., Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC...

  5. 76 FR 35224 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  6. 76 FR 5390 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-31

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Place: National Human Genome Research Institute Special Emphasis Panel; NHGRI Sample Repository..., National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD...

  7. 77 FR 58402 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-09-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; R25 DAP Sept. 2012...: National Human Genome Research Institute, 5635 Fishers Lane, 3rd Floor Conference Room, Rockville, MD...

  8. 76 FR 22112 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Special Emphasis Panel... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: April...

  9. 77 FR 20646 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-04-05

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Loan Repayment Program...: National Human Genome Research Institute, 5635 Fishers Lane, 3rd Floor Conference Room, Rockville, MD...

  10. 77 FR 59933 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-10-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; ELSI CEERS RFA (SEP... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville,...

  11. 76 FR 66076 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-25

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National..., Human Genome Research, National Institutes of Health, HHS) Dated: October 19, 2011. Jennifer S....

  12. 77 FR 64816 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  13. 78 FR 56905 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-09-16

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; H3AFRICA ELSI Research.... Place: National Human Genome Research Institute, Suite 3055, 5635 Fishers Lane, Rockville, MD...

  14. 78 FR 77477 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-12-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  15. 77 FR 35991 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-06-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  16. 78 FR 31953 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-05-28

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; SEP-UDN Coordinating... applications. Place: National Human Genome Research Institute, 3rd Floor Conference Room, 3146, 5635...

  17. 78 FR 11898 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-02-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, Ph.D., Scientific Review Officer CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  18. 75 FR 8373 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-24

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, GWAS Comparing Design... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  19. 75 FR 60467 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2010-09-30

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute,...

  20. 76 FR 50486 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-08-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  1. 77 FR 50140 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-08-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  2. 76 FR 17930 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-03-31

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Name of Committee: National Human Genome Research Institute Special Emphasis Panel; Genetic... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville,...

  3. 78 FR 9707 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-02-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; H3Africa (RM-006, RM... Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD 20852, (301)...

  4. 77 FR 22332 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-04-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, H3Africa Biorepository... applications. Place: National Human Genome Research Institute, 5635 Fishers Lane, 4076, Rockville, MD...

  5. 77 FR 12604 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-03-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... >Name of Committee: National Human Genome Research Institute Special Emphasis Panel, CIDR Contract. Date...: National Human Genome Reseach Institute, 5635 Fishers Lane, Room 4076, Rockville, MD 20852,...

  6. 75 FR 56115 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-09-15

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; CEGS DAP. Date... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: September...

  7. 75 FR 48977 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-12

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  8. 76 FR 65204 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2011-10-20

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute,...

  9. 77 FR 31863 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-05-30

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel DAP R25 Eppig.... (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  10. 75 FR 32957 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-06-10

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, Protein Resource RFA... of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes...

  11. 77 FR 64816 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2012-10-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research Institute... intramural programs and projects conducted by the National Human Genome Research Institute,...

  12. 76 FR 22407 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; Loan Repayment Program....172, Human Genome Research, National Institutes of Health, HHS) Dated: April 12, 2011. Jennifer...

  13. 77 FR 6810 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-09

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; CIDR Contract Renewal... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville,...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. 76 FR 66731 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-27

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, DAP for CEGS-SEP. Date...@mail.nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  16. 75 FR 67380 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-11-02

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...: Ken D. Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome... Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: October 26,...

  17. 76 FR 36930 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, DAP R-25. Date: July...@mail.nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  18. 77 FR 2304 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2012-01-17

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... given that the National Human Genome Research Institute (NHGRI) will host a series of meetings to enable... for Human Genome Research. Background materials on the proposed reorganization and...

  19. 77 FR 74676 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-12-17

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute...@nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  20. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-05-13

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research... individual intramural programs and projects conducted by the National Human Genome Research...

  1. 78 FR 61851 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-10-04

    ... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... Human Genome Research Institute, 4076 Conference Room, 5635 Fishers Lane, Rockville, MD 20852... Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS)...

  2. 77 FR 8268 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...:30 a.m. to 1 p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome...). Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome...

  3. 75 FR 13558 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-03-22

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research... individual intramural programs and projects conducted by the National Human Genome Research...

  4. 75 FR 8977 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-26

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...-402-0838. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  5. 75 FR 2147 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2010-01-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of....), notice is hereby given of meetings of the National Advisory Council for Human Genome Research. The... of Committee: National Advisory Council for Human Genome Research. Date: February 8-9, 2010....

  6. 78 FR 70063 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-11-22

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the Board of Scientific Counselors, National Human Genome Research... individual intramural programs and projects conducted by the NATIONAL HUMAN GENOME RESEARCH...

  7. 76 FR 10909 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-02-28

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed.... Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...-402-0838. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome...

  8. 77 FR 2735 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2012-01-19

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of....), notice is hereby given of meetings of the National Advisory Council for Human Genome Research. The... of Committee: National Advisory Council for Human Genome Research. Date: February 13-14, 2012....

  9. 78 FR 21382 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-10

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed...:00 p.m. to 4:00 p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome... Person: Camilla E. Day, PhD., Scientific Review Officer, CIDR, National Human Genome Research...

  10. 75 FR 46951 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2010-08-04

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the National Advisory Council for Human Genome Research. The meeting will be...: National Advisory Council for Human Genome Research. Date: September 13-14, 2010. Open: September 13,...

  11. 75 FR 44800 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-07-29

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed....), notice is hereby given of a meeting of the National Advisory Council for Human Genome Research. The... Call). Contact Person: Mark S. Guyer, Director for Extramural Research, National Human Genome...

  12. 78 FR 66752 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2013-11-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, October 15, 2013, 01:00 p.m. to October 15, 2013, 02:30 p.m., National...

  13. 76 FR 3917 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-21

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... privacy. Name of Committee: National Human Genome Research Institute Special Emphasis Panel, TRND--RFP... Person: Rudy O. Pozzatti, PhD, Scientific Review Officer, Scientific Review Branch, National Human...

  14. 77 FR 55853 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2012-09-11

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for Human Genome Research, September 10, 2012, 8:30 a.m. to September 11, 2012, 5 p.m., National Institutes...

  15. 77 FR 5035 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-01

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel Sequencing Technology..., Rockville, MD 20852, (301) 402-0838, nakamurk@mail.nih.gov . Name of Committee: National Human...

  16. 76 FR 63932 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-14

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel, ENCODE Technology RFA...- 4280, mckenneyk@mail.nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172,...

  17. 75 FR 53703 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-09-01

    ... National Human Genome Research Institute; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Review Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes... review and funding cycle. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human...

  18. 76 FR 29772 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-05-23

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Closed... of Committee: National Human Genome Research Institute Special Emphasis Panel; ELSI-SEP. Date: June...: Rudy O. Pozzatti, PhD, Scientific Review Officer, Office of Scientific Review, National Human...

  19. 77 FR 27471 - National Human Genome Research Institute Amended Notice of Meeting

    Science.gov (United States)

    2012-05-10

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for Human Genome Research, May 21, 2012, 8:30 a.m. to May 22, 2012, 5:00 p.m., National Institutes of Health,...

  20. Genome3D: exploiting structure to help users understand their sequences

    OpenAIRE

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W. A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina

    2014-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and exte...

  1. 77 FR 67385 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2012-11-09

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  2. 76 FR 65738 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2011-10-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  3. 78 FR 47715 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2013-08-06

    ... HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Notice of Meeting... hereby given of a meeting of the National Advisory Council for Human Genome Research. The meeting will be... unwarranted invasion of personal privacy. Name of Committee: National Advisory Council for Human...

  4. 76 FR 71581 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2011-11-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  5. 78 FR 65342 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2013-10-31

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research...

  6. 78 FR 64222 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-10-28

    ... Committee, CEGS-- Initiative to Maximize Research Education in Genomics. Date: November 7-8, 2013. Time: 8..., Ph.D., Scientific Review Officer, Office of Scientific Review, National Human Genome Research...: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research Institute, National...

  7. 75 FR 51828 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2010-08-23

    ... for Human Genome Research. The meetings will be open to the public as indicated below, with attendance..., PhD, Director for Extramural Research, National Human Genome Research Institute, 5635 Fishers Lane...: National Advisory Council for Human Genome Research. Date: May 16-17, 2011. Open: May 16, 2011, 8:30...

  8. Public Procurement of Innovation; Endogenous Institutions in User-Producer Interaction

    DEFF Research Database (Denmark)

    Hjaltadóttir, Rannveig Edda

    2013-01-01

    Introduction 2010 government expenditure on works, goods and services in EU 19.7% of GDP - 2.406,98€ billion. Can be used to stimulate innovation Focus on public procurement of innovation in EU maintain competitive advantage and welfare Governments are important first users for high technology...... (Urban & von Hippel, 1988). Need interaction in public procurement of innovation (PPI). The aim of this research is to investigate the institutions that govern this interaction and how they influence performance in PPI. Institutions are “the rules of the game” (North, 1990)...

  9. Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

    Directory of Open Access Journals (Sweden)

    Sale Kevin

    2011-09-01

    Full Text Available Abstract Background Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI. The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data. Results We have chosen a data grid system, iRODS (Rule-Oriented Data management systems, to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data. The aim of this paper is to describe how we designed and used (from both system and user viewpoints iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced. Conclusions iRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.

  10. Dana-Farber Cancer Institute | Office of Cancer Genomics

    Science.gov (United States)

    Functional Annotation of Cancer Genomes Principal Investigator: William C. Hahn, M.D., Ph.D. The comprehensive characterization of cancer genomes has and will continue to provide an increasingly complete catalog of genetic alterations in specific cancers. However, most epithelial cancers harbor hundreds of genetic alterations as a consequence of genomic instability. Therefore, the functional consequences of the majority of mutations remain unclear.

  11. Development of disposal technologies for radioactive waste generated from radioisotope users and research institutes

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Akihiro; Yoshimori, Michiro [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    2001-12-01

    In order to safely dispose of a radioactive waste, which is generated from radioisotope users and research institutes, investigation of characteristics of the waste and conceptual design of disposal facility were carried out. As a result of investigating JAERI that the waste has mainly been stored, it became clear that radioactivities of 19 nuclides are important from the viewpoint of the safety of the disposal. And the result of the conceptual design of disposal facilities on the assumption of 3 kinds of sites, the differences on the safety could not be recognized in either case, though the installation depth to construct the facilities influenced the economical efficiency. (author)

  12. Being the Pioneer of Life Sciences in China--Introduction to Beijing Genomics Institute

    Institute of Scientific and Technical Information of China (English)

    Beijing Genomics Institute; Xin Zhang

    2004-01-01

    @@ The Beijing Genomics Institute (BGI) of Chinese Academy of Sciences (CAS) was officially founded in December 2003. Its predecessor, Beijing Huada Genomics Research Center, has presented significant contributions to the development of life sciences in China by its excellent scientific innovations and achievements in the last five years.

  13. Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard

    Science.gov (United States)

    Kanda, Kohzo; Nakashima, Kaede

    2015-01-01

    The genome sequence of Bacillus thuringiensis serovar tolworthi strain Pasteur Institute Standard was determined. The genome consists of a 5.9-Mb chromosome and eight plasmids, one of which is linear. The second largest plasmid (293 kb) carries the genes encoding insecticidal proteins. PMID:26139717

  14. 75 FR 26762 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-05-12

    ... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research....nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research... No: 2010-11051] DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National...

  15. AutoAssemblyD: a graphical user interface system for several genome assemblers.

    Science.gov (United States)

    Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

    2013-01-01

    Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

  16. Virginia Bioinformatics Institute scientists sequence genome of the nitrogen-fixing, soil-living bacterium

    OpenAIRE

    Bland, Susan

    2009-01-01

    A collaboration of researchers, which includes scientists at the Virginia Bioinformatics Institute and Virginia Tech, recently completed the genome sequence of Azotobacter vinelandii, uncovering important genetic information that will contribute to a more complete understanding of the biology of this versatile, soil-living bacterium.

  17. Institutions, technology and water control; water users associations and irrigation management reform in two large-scale systems in India

    NARCIS (Netherlands)

    Narain, V.

    2003-01-01

    Few studies of resource management have paid as much attention or intelligently surveyed the operational aspects of Water User Associations (WUAs) as Institutions, Technology and Water Control. The implementation of WUAs policies, argues this pioneering study, is shaped by the aspirations of its use

  18. Installed Base as a Facilitator for User-Driven Innovation: How Can User Innovation Challenge Existing Institutional Barriers?

    Directory of Open Access Journals (Sweden)

    Synnøve Thomassen Andersen

    2012-01-01

    Full Text Available The paper addresses an ICT-based, user-driven innovation process in the health sector in rural areas in Norway. The empirical base is the introduction of a new model for psychiatric health provision. This model is supported by a technical solution based on mobile phones that is aimed to help the communication between professional health personnel and patients. This innovation was made possible through the use of standard mobile technology rather than more sophisticated systems. The users were heavily involved in the development work. Our analysis shows that by thinking simple and small-scale solutions, including to take the user’s needs and premises as a point of departure rather than focusing on advanced technology, the implementation process was made possible. We show that by combining theory on information infrastructures, user-oriented system development, and innovation in a three-layered analytical framework, we can explain the interrelationship between technical, organizational, and health professional factors that made this innovation a success.

  19. Mapping mutations in plant genomes with the user-friendly web application CandiSNP.

    Science.gov (United States)

    Etherington, Graham J; Monaghan, Jacqueline; Zipfel, Cyril; MacLean, Dan

    2014-01-01

    Analysis of mutants isolated from forward-genetic screens has revealed key components of several plant signalling pathways. Mapping mutations by position, either using classical methods or whole genome high-throughput sequencing (HTS), largely relies on the analysis of genome-wide polymorphisms in F2 recombinant populations. Combining bulk segregant analysis with HTS has accelerated the identification of causative mutations and has been widely adopted in many research programmes. A major advantage of HTS is the ability to perform bulk segregant analysis after back-crossing to the parental line rather than out-crossing to a polymorphic ecotype, which reduces genetic complexity and avoids issues with phenotype penetrance in different ecotypes. Plotting the positions of homozygous polymorphisms in a mutant genome identifies areas of low recombination and is an effective way to detect molecular linkage to a phenotype of interest. We describe the use of single nucleotide polymorphism (SNP) density plots as a mapping strategy to identify and refine chromosomal positions of causative mutations from screened plant populations. We developed a web application called CandiSNP that generates density plots from user-provided SNP data obtained from HTS. Candidate causative mutations, defined as SNPs causing non-synonymous changes in annotated coding regions are highlighted on the plots and listed in a table. We use data generated from a recent mutant screen in the model plant Arabidopsis thaliana as proof-of-concept for the validity of our tool. CandiSNP is a user-friendly application that will aid in novel discoveries from forward-genetic mutant screens. It is particularly useful for analysing HTS data from bulked back-crossed mutants, which contain fewer polymorphisms than data generated from out-crosses. The web-application is freely available online at http://candisnp.tsl.ac.uk.

  20. Dana-Farber Cancer Institute: Identification of Therapeutic Targets Across Cancer Types | Office of Cancer Genomics

    Science.gov (United States)

    The Dana Farber Cancer Institute CTD2 Center focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Effect of an institutional development plan for user participation on professionals' knowledge, practice, and attitudes. A controlled study

    Directory of Open Access Journals (Sweden)

    Rise Marit By

    2011-11-01

    Full Text Available Abstract Background Governments in several countries attempt to strengthen user participation through instructing health care organisations to plan and implement activities such as user representation in administrational boards, improved information to users, and more individual user participation in clinical work. The professionals are central in implementing initiatives to enhance user participation in organisations, but no controlled studies have been conducted on the effect on professionals from implementing institutional development plans. The objective was to investigate whether implementing a development plan intending to enhance user participation in a mental health hospital had any effect on the professionals' knowledge, practice, or attitudes towards user participation. Methods This was a non-randomized controlled study including professionals from three mental health hospitals in Central Norway. A development plan intended to enhance user participation was implemented in one of the hospitals as a part of a larger re-organizational process. The plan included i.e. establishing a patient education centre and a user office, purchasing of user expertise, appointing contact professionals for next of kin, and improving of the centre's information and the professional culture. The professionals at the intervention hospital thus constituted the intervention group, while the professionals at two other hospitals participated as control group. All professionals were invited to answer the Consumer Participation Questionnaire (CPQ and additional questions, focusing on knowledge, practice, and attitudes towards user participation, two times with a 16 months interval. Results A total of 438 professionals participated (55% response rate. Comparing the changes in the intervention group with the changes in the control group revealed no statistically significant differences at a 0.05 level. The implementation of the development plan thus had no

  3. The library of the Institute of Alajuela address the information and communication technologies: User training and information literacy

    OpenAIRE

    Garmendia Bonilla, Lovania

    2011-01-01

    The Library of the Institute of Alajuela made an induction experience and training of users and ventured into the information literacy and engaged in the work of the teaching-learning as an integral part of the curriculum. The actions of the library in developing search strategies, location, selection and use of information brought inthe health service, changes to the role of the library, the librarian, the book and the information in the educational environment.By sharing this experience is ...

  4. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Directory of Open Access Journals (Sweden)

    Konrad J Karczewski

    Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  5. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

    Science.gov (United States)

    Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

    2014-01-01

    The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

  6. Use and User Perception of Electronic Information Resources: A Case Study of Siva Institute of Frontier Technology, India

    Directory of Open Access Journals (Sweden)

    Velmurugan Chandran

    2013-12-01

    Full Text Available The present study aims to explore the use and user perception of electronic resources in Siva Institute of Frontier Technology, India. A total number of 123 users were taken into account for the study through a questionnaire-based survey method. A well-structured questionnaire was designed and distributed to the selected 200 students and staff members. 123 copies of the questionnaires were returned dully filled in and the overall response rate was 61.50 percent. The questionnaire contained both open- and close-ended questions. The collected data were classified, analyzed, and tabulated by using simple statistical methods. This study covers the impact of electronic resources on students and faculty in their academic pursuit.

  7. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    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. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

    Directory of Open Access Journals (Sweden)

    Yevgeny Nikolaichik

    2016-05-01

    Full Text Available The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp. and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci.

  9. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

    Science.gov (United States)

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a 'gene by gene' approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn't fit with regulatory information allowed us to correct product and gene names for over 300 loci.

  10. MaPSeq, A Service-Oriented Architecture for Genomics Research within an Academic Biomedical Research Institution

    Directory of Open Access Journals (Sweden)

    Jason Reilly

    2015-07-01

    Full Text Available Genomics research presents technical, computational, and analytical challenges that are well recognized. Less recognized are the complex sociological, psychological, cultural, and political challenges that arise when genomics research takes place within a large, decentralized academic institution. In this paper, we describe a Service-Oriented Architecture (SOA—MaPSeq—that was conceptualized and designed to meet the diverse and evolving computational workflow needs of genomics researchers at our large, hospital-affiliated, academic research institution. We present the institutional challenges that motivated the design of MaPSeq before describing the architecture and functionality of MaPSeq. We then discuss SOA solutions and conclude that approaches such as MaPSeq enable efficient and effective computational workflow execution for genomics research and for any type of academic biomedical research that requires complex, computationally-intense workflows.

  11. "Less Clicking, More Watching": Results from the User-Centered Design of a Multi-Institutional Web Site for Art and Culture.

    Science.gov (United States)

    Vergo, John; Karat, Clare-Marie; Karat, John; Pinhanez, Claudio; Arora, Renee; Cofino, Thomas; Riecken, Doug; Podlaseck, Mark

    This paper summarizes a 10-month long research project conducted at the IBM T.J. Watson Research Center aimed at developing the design concept of a multi-institutional art and culture web site. The work followed a user-centered design (UCD) approach, where interaction with prototypes and feedback from potential users of the web site were sought…

  12. Institutional Repositories in the UK: What Can the Google User Find There?

    Science.gov (United States)

    Markland, Margaret

    2006-01-01

    This study investigates the efficiency of the Google search engine at retrieving items from 26 UK Institutional Repositories, covering a wide range of subject areas. One item is chosen from each repository and four searches are carried out: two keyword searches and two full title searches, each using both Google and then Google Scholar. A further…

  13. Heuristics of the algorithm: Big Data, user interpretation and institutional translation

    Directory of Open Access Journals (Sweden)

    Göran Bolin

    2015-10-01

    Full Text Available Intelligence on mass media audiences was founded on representative statistical samples, analysed by statisticians at the market departments of media corporations. The techniques for aggregating user data in the age of pervasive and ubiquitous personal media (e.g. laptops, smartphones, credit cards/swipe cards and radio-frequency identification build on large aggregates of information (Big Data analysed by algorithms that transform data into commodities. While the former technologies were built on socio-economic variables such as age, gender, ethnicity, education, media preferences (i.e. categories recognisable to media users and industry representatives alike, Big Data technologies register consumer choice, geographical position, web movement, and behavioural information in technologically complex ways that for most lay people are too abstract to appreciate the full consequences of. The data mined for pattern recognition privileges relational rather than demographic qualities. We argue that the agency of interpretation at the bottom of market decisions within media companies nevertheless introduces a ‘heuristics of the algorithm’, where the data inevitably becomes translated into social categories. In the paper we argue that although the promise of algorithmically generated data is often implemented in automated systems where human agency gets increasingly distanced from the data collected (it is our technological gadgets that are being surveyed, rather than us as social beings, one can observe a felt need among media users and among industry actors to ‘translate back’ the algorithmically produced relational statistics into ‘traditional’ social parameters. The tenacious social structures within the advertising industries work against the techno-economically driven tendencies within the Big Data economy.

  14. Heuristics of the algorithm: Big Data, user interpretation and institutional translation

    Directory of Open Access Journals (Sweden)

    Göran Bolin

    2015-10-01

    Full Text Available Intelligence on mass media audiences was founded on representative statistical samples, analysed by statisticians at the market departments of media corporations. The techniques for aggregating user data in the age of pervasive and ubiquitous personal media (e.g. laptops, smartphones, credit cards/swipe cards and radio-frequency identification build on large aggregates of information (Big Data analysed by algorithms that transform data into commodities. While the former technologies were built on socio-economic variables such as age, gender, ethnicity, education, media preferences (i.e. categories recognisable to media users and industry representatives alike, Big Data technologies register consumer choice, geographical position, web movement, and behavioural information in technologically complex ways that for most lay people are too abstract to appreciate the full consequences of. The data mined for pattern recognition privileges relational rather than demographic qualities. We argue that the agency of interpretation at the bottom of market decisions within media companies nevertheless introduces a ‘heuristics of the algorithm’, where the data inevitably becomes translated into social categories. In the paper we argue that although the promise of algorithmically generated data is often implemented in automated systems where human agency gets increasingly distanced from the data collected (it is our technological gadgets that are being surveyed, rather than us as social beings, one can observe a felt need among media users and among industry actors to ‘translate back’ the algorithmically produced relational statistics into ‘traditional’ social parameters. The tenacious social structures within the advertising industries work against the techno-economically driven tendencies within the Big Data economy.

  15. Unclassified Computing Capability: User Responses to a Multiprogrammatic and Institutional Computing Questionnaire

    Energy Technology Data Exchange (ETDEWEB)

    McCoy, M; Kissel, L

    2002-01-29

    We are experimenting with a new computing model to be applied to a new computer dedicated to that model. Several LLNL science teams now have computational requirements, evidenced by the mature scientific applications that have been developed over the past five plus years, that far exceed the capability of the institution's computing resources. Thus, there is increased demand for dedicated, powerful parallel computational systems. Computation can, in the coming year, potentially field a capability system that is low cost because it will be based on a model that employs open source software and because it will use PC (IA32-P4) hardware. This incurs significant computer science risk regarding stability and system features but also presents great opportunity. We believe the risks can be managed, but the existence of risk cannot be ignored. In order to justify the budget for this system, we need to make the case that it serves science and, through serving science, serves the institution. That is the point of the meeting and the White Paper that we are proposing to prepare. The questions are listed and the responses received are in this report.

  16. Guidelines for collecting vouchers and tissues intended for genomic work (Smithsonian Institution: Botany Best Practices

    Directory of Open Access Journals (Sweden)

    Vicki Funk

    2017-01-01

    Full Text Available The introduction of Next Generation Sequencing into the disciplines of plant systematics, ecology, and metagenomics, among others, has resulted in a phenomenal increase in the collecting and storing of tissue samples and their respective vouchers. This manual suggests standard practices that will insure the quality and preservation of the tissue and vouchers and their respective data. Although written for use by the Smithsonian Institution botanists it suggests a framework for collecting tissues and vouchers that other research programs can adapt to their own needs. It includes information on collecting voucher specimens, collecting plant tissue intended for genomic analysis, how to manage these collections, and how to incorporate the data into a database management system. It also includes many useful references for collecting and processing collections. We hope it will be useful for a variety of botanists but especially those who know how to collect plants and want to collect tissue samples that will be useful for genomic research, and those who are skilled in lab work and want to know how to properly voucher and record their tissue collections.

  17. The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: reflections on an ongoing experiment.

    Science.gov (United States)

    McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y; Rothenberg, Karen H; Lockhart, Nicole C; Guyer, Mark S

    2014-01-01

    For more than 20 years, the Ethical, Legal, and Social Implications (ELSI) Program of the National Human Genome Research Institute has supported empirical and conceptual research to anticipate and address the ethical, legal, and social implications of genomics. As a component of the agency that funds much of the underlying science, the program has always been an experiment. The ever-expanding number of issues the program addresses and the relatively low level of commitment on the part of other funding agencies to support such research make setting priorities especially challenging. Program-supported studies have had a significant impact on the conduct of genomics research, the implementation of genomic medicine, and broader public policies. The program's influence is likely to grow as ELSI research, genomics research, and policy development activities become increasingly integrated. Achieving the benefits of increased integration while preserving the autonomy, objectivity, and intellectual independence of ELSI investigators presents ongoing challenges and new opportunities.

  18. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    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

  20. DivStat: a user-friendly tool for single nucleotide polymorphism analysis of genomic diversity.

    Directory of Open Access Journals (Sweden)

    Inês Soares

    Full Text Available Recent developments have led to an enormous increase of publicly available large genomic data, including complete genomes. The 1000 Genomes Project was a major contributor, releasing the results of sequencing a large number of individual genomes, and allowing for a myriad of large scale studies on human genetic variation. However, the tools currently available are insufficient when the goal concerns some analyses of data sets encompassing more than hundreds of base pairs and when considering haplotype sequences of single nucleotide polymorphisms (SNPs. Here, we present a new and potent tool to deal with large data sets allowing the computation of a variety of summary statistics of population genetic data, increasing the speed of data analysis.

  1. User Satisfaction and Acceptance of Web Based Marketing Information System among Microfinance Institutions in Nairobi Region, Kenya

    Directory of Open Access Journals (Sweden)

    Silvance O. Abeka

    2012-09-01

    Full Text Available Acceptance of web based marketing information system has remained a topic of interest for a last few decades. Several theories, specifically over the conceptualisation of the technology acceptance model (TAM have emerged and they have been applied in different contexts to investigate new insights into the acceptance behaviour at individual and organisational levels. The purpose of this paper is to determine whether a relationship exist between user satisfaction and acceptance of web based marketing information system (MKIs among micro- finance institutions in Nairobi Region, Kenya. Anonymous and self-administered questionnaires were distributed to 383 respondents. A total of 370 usable responses were received, resulting in a response rate of 96.6% which was considered satisfactory for subsequent analysis. Due to the quantitative nature of the study, the results are analysed with statistical measures. The results indicated that Satisfaction was influential determinant of acceptance with t= 5.1568, p- value= 0.005 at 1% significant level. Theoretical contributions and practical implications of the findings are discussed and suggestions for future research are presented.

  2. Dana-Farber Cancer Institute: Identification of Therapeutic Targets in KRAS Driven Lung Cancer | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Dana Farber Cancer Institute focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Differential profiles of crack users in respondent-driven and institutional samples: a three-site comparison

    NARCIS (Netherlands)

    Oteo Pérez, A.; Benschop, A.; Korf, D.J.

    2012-01-01

    Background/Aim: Respondent-driven sampling (RDS) is increasingly applied in social epidemiological surveys among ‘hidden populations’ of hard drug users. The objective of the present study was to assess whether the profile of frequent crack users recruited through RDS differed from those surveyed in

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

    Energy Technology Data Exchange (ETDEWEB)

    Mosier, Annika [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

  6. Automatic genomics: a user-friendly program for the automatic designing and plate loading of medium-throughput qPCR experiments.

    Science.gov (United States)

    Callejas, Sergio; Alvarez, Rebeca; Dopazo, Ana

    2011-01-01

    Quantitative PCR (qPCR) remains the method of choice for gene and microRNA (miRNA) expression studies. Many laboratories wish to automate some or all of the steps of medium-throughput qPCR experiments through the use of various types of liquid handling robots. However, it is not uncommon to find cases in which scripts provided by the robot supplier are too rigid for user-specific applications, do not include all the desired options, or are too complicated to be modified by a nonprofessional programmer. Here, we present Automatic Genomics, a program that allows users with a limited programming background to automate medium-throughput qPCR experiments by using commercially available liquid-handling robots. The user is able to optimize the plate design in terms of number of genes, number of samples, and controls.

  7. Dana-Farber Cancer Institute: Discovery of Novel Oncogenes | Office of Cancer Genomics

    Science.gov (United States)

    Widespread recurrent copy number alterations are observed across the majority of human cancers, yet the specific targets of such amplified or deleted regions remain undefined. Here, the CTD2 Center at the Dana Farber Cancer Institute took a systematic approach using cDNA overexpression screening to identify and validate oncogenes residing in such amplified regions. In representative examples, these experiments have identified the adaptor proteins CRKL, GAB2, FRS2 and the TLOC and SKIL proteins as novel amplified oncogenes.

  8. Dana-Farber Cancer Institute: Discovery of Resistance Mechanisms | Office of Cancer Genomics

    Science.gov (United States)

    Resistance to targeted therapy is emerging as a bottleneck to achieving durable drug responses in cancer. The goal of the CTD2 Center at Dana Farber Cancer Institute is to identify mechanisms of resistance for both existing therapeutics as well as for emerging targets even prior to the identification of lead compounds. They aim to use this information to inform combinatorial treatments. In representative examples they have found that YAP1 leads to resistance after KRAS targeting and that PRKACA mediates resistance to HER2 therapy.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

    Science.gov (United States)

    Stoesser, Nicole; Sheppard, Anna E.; Pankhurst, Louise; Giess, Adam; Yeh, Anthony J.; Didelot, Xavier; Turner, Stephen D.; Sebra, Robert; Kasarskis, Andrew; Peto, Tim; Crook, Derrick; Sifri, Costi D.

    2015-01-01

    The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an outbreak mediated by an endemic plasmid. We describe the interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from a single institution over 5 years following the introduction of blaKPC in August 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16 distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp was imported into the institution on numerous occasions, with other blaKPC plasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and spread locally, making it a future candidate for clinical persistence and dissemination. PMID:25561339

  11. A Survey of the Perception of the Services of Micro Finance Institutions by the Female Service Users in Benin City, South-South, Nigeria

    Directory of Open Access Journals (Sweden)

    Ernest Osas Ugiagbe

    2014-04-01

    Full Text Available The study examines the perceptions of the services of the micro finance Institutions by the women service users, and how the services of micro Institutions affect businesses of the beneficiaries of the micro credit loans. The research design for the study was the survey method. The instruments of data collection were structured questionnaires and in-depth interview. A total of 450 questionnaires were administered to the female participants, and senior management personnel of the micro credit institutions were interviewed. The cluster and simple random sampling were used to select the participants for the study. The leaders of registered unions were the informants.  The result reveals that the poor services and attitude of officials of micro finance institutions and other problems like the regressive tax regimes, harsh economic climate and patriarchy are negatively affecting the business ventures of the loan beneficiaries and by implication the goals of poverty reduction via micro credit scheme . The women beneficiaries are groaning under the burden of loan repayment and meeting other obligations as mothers and wives. This study is applicable in the context of social policy development at this time when social services delivery is not only poor but at dismal level. The need for gender sensitive and social development becomes imperative. It is critical to social work practice in the context of advocacy, empowerment programs, facilitating and initiating service delivery and Community organizing by social workers that will enhance the war against Poverty and other social impediments against women empowerment in Nigeria.  Normal 0 false false false EN-GB X-NONE X-NONE

  12. Enlisting User Community Perspectives to Inform Development of a Semantic Web Application for Discovery of Cross-Institutional Research Information and Data

    Science.gov (United States)

    Johns, E. M.; Mayernik, M. S.; Boler, F. M.; Corson-Rikert, J.; Daniels, M. D.; Gross, M. B.; Khan, H.; Maull, K. E.; Rowan, L. R.; Stott, D.; Williams, S.; Krafft, D. B.

    2015-12-01

    Researchers seek information and data through a variety of avenues: published literature, search engines, repositories, colleagues, etc. In order to build a web application that leverages linked open data to enable multiple paths for information discovery, the EarthCollab project has surveyed two geoscience user communities to consider how researchers find and share scholarly output. EarthCollab, a cross-institutional, EarthCube funded project partnering UCAR, Cornell University, and UNAVCO, is employing the open-source semantic web software, VIVO, as the underlying technology to connect the people and resources of virtual research communities. This study will present an analysis of survey responses from members of the two case study communities: (1) the Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory (EOL), and (2) UNAVCO, a geodetic facility and consortium that supports diverse research projects informed by geodesy. The survey results illustrate the types of research products that respondents indicate should be discoverable within a digital platform and the current methods used to find publications, data, personnel, tools, and instrumentation. The responses showed that scientists rely heavily on general purpose search engines, such as Google, to find information, but that data center websites and the published literature were also critical sources for finding collaborators, data, and research tools.The survey participants also identify additional features of interest for an information platform such as search engine indexing, connection to institutional web pages, generation of bibliographies and CVs, and outward linking to social media. Through the survey, the user communities prioritized the type of information that is most important to display and describe their work within a research profile. The analysis of this survey will inform our further development of a platform that will

  13. Laying the Foundation for a Genomic Rosetta Stone: Creating Information Hubs through the User of Consensus Idenifiers

    Energy Technology Data Exchange (ETDEWEB)

    Van Brabant, Bart; Kyrpides, Nikos; Glockner, Frank Oliver; Gray, Tanya; Field, Dawn; De Vos, Paul; De Baets, Bernard; Dawyndt, Peter

    2007-05-01

    This paper presents a holistic approach that illustrates how the semantic hurdle for integration of biological databases might be overcome when mapping sources that provide information on individual genes and complete genomes to sources that provide information on the biological resources from which these sequences where derived, and vice versa. In particular we will explain how each of the completed and ongoing whole-genome sequencing projects in the Genomes OnLine Database and each of the ribosomal RNA sequences in the SILVA ribosomal RNA database have been persistently cross-referenced with the StrainInfo.net bioportal, serving both a genome centric and an organism centric view to the life on our blue planet as one more stepping stone towards the establishment of fully integrated and flexible biological information networks.

  14. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    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). One of its projects, 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) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing 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 200 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.

  15. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    Science.gov (United States)

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L. M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David; Elgin, Sarah C. R.

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington…

  16. The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop.

    Science.gov (United States)

    Khoury, Muin J; McBride, Colleen M; Schully, Sheri D; Ioannidis, John P A; Feero, W Gregory; Janssens, A Cecile J W; Gwinn, Marta; Simons-Morton, Denise G; Bernhardt, Jay M; Cargill, Michele; Chanock, Stephen J; Church, George M; Coates, Ralph J; Collins, Francis S; Croyle, Robert T; Davis, Barry R; Downing, Gregory J; Duross, Amy; Friedman, Susan; Gail, Mitchell H; Ginsburg, Geoffrey S; Green, Robert C; Greene, Mark H; Greenland, Philip; Gulcher, Jeffrey R; Hsu, Andro; Hudson, Kathy L; Kardia, Sharon L R; Kimmel, Paul L; Lauer, Michael S; Miller, Amy M; Offit, Kenneth; Ransohoff, David F; Roberts, J Scott; Rasooly, Rebekah S; Stefansson, Kari; Terry, Sharon F; Teutsch, Steven M; Trepanier, Angela; Wanke, Kay L; Witte, John S; Xu, Jianfeng

    2009-08-01

    The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed.

  17. The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop

    Science.gov (United States)

    Khoury, Muin J.; McBride, Colleen M.; Schully, Sheri D.; Ioannidis, John P. A.; Feero, W. Gregory; Janssens, A. Cecile J. W.; Gwinn, Marta; Simons-Morton, Denise G.; Bernhardt, Jay M.; Cargill, Michele; Chanock, Stephen J.; Church, George M.; Coates, Ralph J.; Collins, Francis S.; Croyle, Robert T.; Davis, Barry R.; Downing, Gregory J.; DuRoss, Amy; Friedman, Susan; Gail, Mitchell H.; Ginsburg, Geoffrey S.; Green, Robert C.; Greene, Mark H.; Greenland, Philip; Gulcher, Jeffrey R.; Hsu, Andro; Hudson, Kathy L.; Kardia, Sharon L. R.; Kimmel, Paul L.; Lauer, Michael S.; Miller, Amy M.; Offit, Kenneth; Ransohoff, David F.; Roberts, J. Scott; Rasooly, Rebekah S.; Stefansson, Kari; Terry, Sharon F.; Teutsch, Steven M.; Trepanier, Angela; Wanke, Kay L.; Witte, John S.; Xu, Jianfeng

    2010-01-01

    The increasing availability of personal genomic tests has led to discussions about the validity and utility of such tests and the balance of benefits and harms. A multidisciplinary workshop was convened by the National Institutes of Health and the Centers for Disease Control and Prevention to review the scientific foundation for using personal genomics in risk assessment and disease prevention and to develop recommendations for targeted research. The clinical validity and utility of personal genomics is a moving target with rapidly developing discoveries but little translation research to close the gap between discoveries and health impact. Workshop participants made recommendations in five domains: (1) developing and applying scientific standards for assessing personal genomic tests; (2) developing and applying a multidisciplinary research agenda, including observational studies and clinical trials to fill knowledge gaps in clinical validity and utility; (3) enhancing credible knowledge synthesis and information dissemination to clinicians and consumers; (4) linking scientific findings to evidence-based recommendations for use of personal genomics; and (5) assessing how the concept of personal utility can affect health benefits, costs, and risks by developing appropriate metrics for evaluation. To fulfill the promise of personal genomics, a rigorous multidisciplinary research agenda is needed. PMID:19617843

  18. Perception and Information Behaviour of Institutional Repository End-Users Provides Valuable Insight for Future Development. A Review of: St. Jean, B., Rieh, S. Y., Yakel, E., & Markey, K. (2011. Unheard voices: Institutional repository end-users. College & Research Libraries, 72(1, 21-42.

    Directory of Open Access Journals (Sweden)

    Lisa Shen

    2012-06-01

    Full Text Available Objective – To determine the perceptions andinformation behavior of institutionalrepository (IR end-users.Design – Semi-structured interviews.Setting – The interviews were conducted overthe telephone.Subjects – Twenty end-users of five differentIRs were interviewed for the study. Seventeenof the interviewees were recruited viarecruitment forms the researchers placed on IRhomepages and the other three intervieweeswere referred to researchers by IR managers.The interviewees’ academic backgroundsvaried, including six undergraduates, fourmasters’ students, three doctorial students, fivefaculty, and two library or museum staffmembers. They represented disciplines in Artsand Humanities (5, Science and HealthSciences (10, and Social Sciences (5. Fifteen ofthe 20 interviewees were recruited throughtheir own institution’s IR. All except two of theinterviewees had used the IR for which theywere recruited less than six times.Methods – Forty-three potential intervieweeswere recruited using web recruitment formsand IR manager recommendations.Researchers subsequently excluded 23 (53.5%of the interviewees because they wereprimarily IR contributors rather than endusers,or could not be reached by phone.Twenty interviews ranging from 17 to 60 minutes were conducted between January and June 2008. The average interview time was 34 minutes. The recordings were transcribed then analyzed using qualitative data analysis software NVivo7. Coding categories were developed using both the original research questions and emerging themes from the actual transcripts. The final coding scheme had a Holsi Coefficient of Reliability of 0.732 for inter-coder reliability.Main Results – Researchers identified six common themes from the results:How do end-users characterize IRs?While most interviewees recognized that there is a relationship between the IR and its host institution, their understandings of the function and content of IRs varied widely. Interviewees

  19. The genomic CDS sandbox: An assessment among domain experts.

    Science.gov (United States)

    Aziz, Ayesha; Kawamoto, Kensaku; Eilbeck, Karen; Williams, Marc S; Freimuth, Robert R; Hoffman, Mark A; Rasmussen, Luke V; Overby, Casey L; Shirts, Brian H; Hoffman, James M; Welch, Brandon M

    2016-04-01

    Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate a proposed approach for such a genomic CDS sandbox among domain experts and potential users. Survey results indicate a significant interest and desire for a genomic CDS sandbox environment among domain experts. These results will be used to guide the development of a genomic CDS sandbox.

  20. Frontiers in cancer epidemiology: a challenge to the research community from the Epidemiology and Genomics Research Program at the National Cancer Institute.

    Science.gov (United States)

    Khoury, Muin J; Freedman, Andrew N; Gillanders, Elizabeth M; Harvey, Chinonye E; Kaefer, Christie; Reid, Britt C; Rogers, Scott; Schully, Sheri D; Seminara, Daniela; Verma, Mukesh

    2012-07-01

    The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is developing scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop in December 2012 to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies.

  1. Transparent Institutions

    Directory of Open Access Journals (Sweden)

    Javier Fombona

    2011-04-01

    Full Text Available The objective of this project is to create sets of media-based imagery that illustrate the internal workings of public institutions to the common citizen. This is an important need in countries that are seeking to open up their public and private institutions and bring them closer to their users. Method: There is a clear need to carry out proposals that tackle organizational lack of transparency; to this end, through an interdisciplinary approach, we propose the creation of a freeaccess Web-based portal that shows the interior of the institutions at hand, learning institutions to start with, this scope will be broadened later to institutions of health and public safety. The project chooses and shows a core selection of features capable of becoming international models for each kind of institutions, elementary schools in this phase. These features are shown in short videos, depicting every core element found: installations, governing bodies, documentation, samples of learning and teaching methodologies in use, etc. Results: the propossed project succeeds in getting institutions closer to their users. It has been developed in Spain, and translated to other Latin-American countries and the United States.

  2. Transparent Institutions

    Directory of Open Access Journals (Sweden)

    Javier Fombona

    2011-04-01

    Full Text Available The objective of this project is to create sets of media-based imagery that illustrate the internal workings of public institutions to the common citizen. This is an important need in countries that are seeking to open up their public and private institutions and bring them closer to their users. Method: There is a clear need to carry out proposals that tackle organizational lack of transparency; to this end, through an interdisciplinary approach, we propose the creation of a freeaccess Web-based portal that shows the interior of the institutions at hand, learning institutions to start with, this scope will be broadened later to institutions of health and public safety. The project chooses and shows a core selection of features capable of becoming international models for each kind of institutions, elementary schools in this phase. These features are shown in short videos, depicting every core element found: installations, governing bodies, documentation, samples of learning and teaching methodologies in use, etc. Results: the propossed project succeeds in getting institutions closer to their users. It has been developed in Spain, and translated to other Latin-American countries and the United States.

  3. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  4. The Broad Institute: Screening for Dependencies in Cancer Cell Lines Using Small Molecules | Office of Cancer Genomics

    Science.gov (United States)

    Using cancer cell-line profiling, we established an ongoing resource to identify, as comprehensively as possible, the drug-targetable dependencies that specific genomic alterations impart on human cancers. We measured the sensitivity of hundreds of genetically characterized cancer cell lines to hundreds of small-molecule probes and drugs that have highly selective interactions with their targets, and that collectively modulate many distinct nodes in cancer cell circuitry.

  5. [Levels of dissatisfaction of external users of the Instituto Nacional de Salud del Niño (National Institute of Child Health) in Lima, Peru].

    Science.gov (United States)

    Shimabuku, Roberto; Huicho, Luis; Fernández, Danitza; Nakachi, Graciela; Maldonado, Ruth; Barrientos, Armando

    2012-01-01

    To determine the changes in the levels of dissatisfaction of the external users of the Instituto Nacional de Salud del Niño, in Lima, Peru. Observational study based on a software to evaluate surveys completed by health care users (Software de Evaluación de Encuestas de Usuarios en Salud - SEEUS). The population consisted of every person accompanying external users to outpatient visits, inpatient visits or emergency treatment in the years 2008, 2009 and 2010. To calculate the sample size, last year's proportion of users dissatisfied with each service was used, with an estimated error of 5% at a 95% confidence level. A sample of 2051 people was obtained, which revealed a decreasing trend in the levels of dissatisfaction with outpatient visits, and an increased dissatisfaction in the medical capabilities dimension for hospitalization and emergency services. In addition, a dissatisfaction index lower than 0.20 was registered in the medical capabilities dimension for outpatient visits. In contrast, the highest dissatisfaction indexes were registered in the hygiene dimension for 2009 (0.25) and 2010 (0.25), and in the others dimension for emergency services in 2009 (0.25). The dimensions showing an increase in the dissatisfaction index were tangible aspects, hygiene and others for hospitalization and emergency services. On the other hand, the medical capabilities dimension for outpatient visits showed a decrease in the level of dissatisfaction over the evaluated period.

  6. 产学研用合作培养人才的动力模型及其应用%Dynamic Model of Cooperation in Training Talent for Industry, University, Institute and User and Its Application

    Institute of Scientific and Technical Information of China (English)

    姜鸿; 王卫星; 王永利

    2013-01-01

    产学研用合作培养人才动力不足的根本原因是人才培养具有正外部性,参与人才培养的单位得不到全部的利益,而其他单位却可以分享人才培养带来的部分利益。产学研用合作培养人才的动力来自于政府的推力和合作各方共同利益的引力。因此,政府应大力推动产学研用合作培养人才,产学研用各方要寻找合作培养人才共同的利益点。%The main reason for lack of cooperation motivity in training talent for industry,university,institute and user is the positive externality of training talent,units participating in training talent don’t get all of the interests,while other units can share part of benefits of training talent. Cooperation motivity in training talent comes from pushing of government and gravity of the common interests of the parties.Therefore ,government should promote vigorously cooperation in training talent for industry,university,institute and user,the parties should find common interests of cooperation in training talent.

  7. Perception and Information Behaviour of Institutional Repository End-Users Provides Valuable Insight for Future Development. A Review of: St. Jean, B., Rieh, S. Y., Yakel, E., & Markey, K. (2011). Unheard voices: Institutional repository end-users. College & Research Libraries, 72(1), 21-42.

    OpenAIRE

    Lisa Shen

    2012-01-01

    Objective – To determine the perceptions andinformation behavior of institutionalrepository (IR) end-users.Design – Semi-structured interviews.Setting – The interviews were conducted overthe telephone.Subjects – Twenty end-users of five differentIRs were interviewed for the study. Seventeenof the interviewees were recruited viarecruitment forms the researchers placed on IRhomepages and the other three intervieweeswere referred to researchers by IR managers.The interviewees’ academic backgroun...

  8. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    Energy Technology Data Exchange (ETDEWEB)

    Allen, Eric [Scripps and UCSD

    2013-03-01

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

  11. User 2020

    DEFF Research Database (Denmark)

    Porras, Jari; Heikkinen, Kari; Kinnula, Marianne

    2014-01-01

    and environment, and each has had its effect on the development of technology. The closer we come to the current generation, the bigger is the effect of technology on the characteristics of that generation. User needs guide the technology and the technology shapes the users. This WWRF Outlook analyses......The User 2020 vision is of the changing needs and habits of a user in the future digital world. In order to understand the needs of the future users, we need to look at how users and technology have changed during recent years. The different generations of users are products of their own time...... determined by the era in which they were born. This is due to the fact that digital natives, born in an already “fully” digitalized world with a plethora of ICT services, have a much closer relationship to these solutions than generations before them. This has also shaped the users perspectives and had...

  12. Understanding users

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav Viggo

    2014-01-01

    Segmentation of users can help libraries in the process of understanding user similarities and differences. Segmentation can also form the basis for selecting segments of target users and for developing tailored services for specific target segments. Several approaches and techniques have been...... segmentation project using computer-generated clusters. Compared to traditional marketing texts, this article also tries to identify user segments or images or metaphors by the library profession itself....

  13. Understanding users

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav Viggo

    2014-01-01

    Segmentation of users can help libraries in the process of understanding user similarities and differences. Segmentation can also form the basis for selecting segments of target users and for developing tailored services for specific target segments. Several approaches and techniques have been te...... segmentation project using computer-generated clusters. Compared to traditional marketing texts, this article also tries to identify user segments or images or metaphors by the library profession itself....

  14. Linked data and user interaction

    CERN Document Server

    Cervone, H Frank

    2015-01-01

    This collection of research papers provides extensive information on deploying services, concepts, and approaches for using open linked data from libraries and other cultural heritage institutions. With a special emphasis on how libraries and other cultural heritage institutions can create effective end user interfaces using open, linked data or other datasets. These papers are essential reading for any one interesting in user interface design or the semantic web.

  15. User design

    CERN Document Server

    Carr-Chellman, Alison A

    2012-01-01

    User Design offers a fresh perspective on how front-line learners (users) can participate in the design of learning environments. The author challenges the universal assumption that front-line users must be relegated to the role of offering input, and that the actual design activity of learning systems must still be conducted only by experts. The book presents a new set of methods and strategies that show how the tools of professional designers can be effectively shared with broad groups of users and other participants in the process of creating their own learning. Drawing

  16. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  17. Center for Cancer Genomics | Office of Cancer Genomics

    Science.gov (United States)

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  18. Ensembl Genomes 2013

    DEFF Research Database (Denmark)

    Kersey, Paul Julian; Allen, James E; Christensen, Mikkel

    2014-01-01

    genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely...

  19. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  20. Danish User-Centered Innovation

    DEFF Research Database (Denmark)

    Jeppesen, Lars Bo

    2007-01-01

    Danish User-centered Innovation Lab (DUCI lab) is a collaboration between faculty at Copenhagen Business School, Aarhus School of Business and Massachusetts Institute of Technology, based at Copenhagen Business School. DUCI lab is a unique effort to understand the issues involved in user innovati...... companies and on how such practices can be diffused broadly for the benefit of start-ups, SME's and other types of organizations....

  1. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  2. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  3. Ten years of maintaining and expanding a microbial genome and metagenome analysis system.

    Science.gov (United States)

    Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

    2015-11-01

    Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure.

  4. Google Scholar Users and User Behaviors: An Exploratory Study

    Science.gov (United States)

    Herrera, Gail

    2011-01-01

    The University of Mississippi Library created a profile to provide linking from Google Scholar (GS) to library resources in 2005. Although Google Scholar does not provide usage statistics for institutions, use of Google Scholar is clearly evident in looking at library link resolver logs. The purpose of this project is to examine users of Google…

  5. Google Scholar Users and User Behaviors: An Exploratory Study

    Science.gov (United States)

    Herrera, Gail

    2011-01-01

    The University of Mississippi Library created a profile to provide linking from Google Scholar (GS) to library resources in 2005. Although Google Scholar does not provide usage statistics for institutions, use of Google Scholar is clearly evident in looking at library link resolver logs. The purpose of this project is to examine users of Google…

  6. The Virtual Institute for Integrative Biology (VIIB)

    Energy Technology Data Exchange (ETDEWEB)

    Rivera, G.; Gonzalez-Nieto, F.; Perez-Acle, T.; Isea, R.; Holmes, D. S.

    2007-07-01

    The Virtual Institute for Integrative Biology (VII B) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, Metagenomic, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomic, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: inter operability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible work flows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions. (Author)

  7. UCSC genome browser tutorial.

    Science.gov (United States)

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/.

  8. Justine user`s manual

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S.R.

    1995-10-01

    Justine is the graphical user interface to the Los Alamos Radiation Modeling Interactive Environment (LARAMIE). It provides LARAMIE customers with a powerful, robust, easy-to-use, WYSIWYG interface that facilitates geometry construction and problem specification. It is assumed that the reader is familiar with LARAMIE, and the transport codes available, i.e., MCNPTM and DANTSYSTM. No attempt is made in this manual to describe these codes in detail. Information about LARAMIE, DANTSYS, and MCNP are available elsewhere. It i also assumed that the reader is familiar with the Unix operating system and with Motif widgets and their look and feel. However, a brief description of Motif and how one interacts with it can be found in Appendix A.

  9. TCGA Workshop: Genomics and Biology of Glioblastoma Multiforme (GBM) - TCGA

    Science.gov (United States)

    The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) held a workshop entitled, “Genomics and Biology of Glioblastoma Multiforme (GBM),” to review the initial GBM data from the TCGA pilot project.

  10. The integrated microbial genome resource of analysis.

    Science.gov (United States)

    Checcucci, Alice; Mengoni, Alessio

    2015-01-01

    Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

  11. NIG_MoG: a mouse genome navigator for exploring intersubspecific genetic polymorphisms.

    Science.gov (United States)

    Takada, Toyoyuki; Yoshiki, Atsushi; Obata, Yuichi; Yamazaki, Yukiko; Shiroishi, Toshihiko

    2015-08-01

    The National Institute of Genetics Mouse Genome database (NIG_MoG; http://molossinus.lab.nig.ac.jp/msmdb/) primarily comprises the whole-genome sequence data of two inbred mouse strains, MSM/Ms and JF1/Ms. These strains were established at NIG and originated from the Japanese subspecies Mus musculus molossinus. NIG_MoG provides visualized genome polymorphism information, browsing single-nucleotide polymorphisms and short insertions and deletions in the genomes of MSM/Ms and JF1/Ms with respect to C57BL/6J (whose genome is predominantly derived from the West European subspecies M. m. domesticus). This allows users, especially wet-lab biologists, to intuitively recognize intersubspecific genome divergence in these mouse strains using visual data. The database also supports the in silico screening of bacterial artificial chromosome (BAC) clones that contain genomic DNA from MSM/Ms and the standard classical laboratory strain C57BL/6N. NIG_MoG is thus a valuable navigator for exploring mouse genome polymorphisms and BAC clones that are useful for studies of gene function and regulation based on intersubspecific genome divergence.

  12. Institutional advantage

    NARCIS (Netherlands)

    Martin, Xavier

    Is there such a thing as institutional advantage—and what does it mean for the study of corporate competitive advantage? In this article, I develop the concept of institutional competitive advantage, as distinct from plain competitive advantage and from comparative institutional advantage. I first

  13. Institutional advantage

    NARCIS (Netherlands)

    Martin, Xavier

    2014-01-01

    Is there such a thing as institutional advantage—and what does it mean for the study of corporate competitive advantage? In this article, I develop the concept of institutional competitive advantage, as distinct from plain competitive advantage and from comparative institutional advantage. I first i

  14. Confucius Institute

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    @@ Confucius Institute(simplified Chinese:孔子学院;traditional Chinese:孔子學院;pinyin:kǒngzǐ xuéyuàn)is a non-profit public institute which aims at promoting Chinese language and culture and supporting local Chinese teaching internationally through affiliated Confucius Institutes.

  15. Institutional advantage

    NARCIS (Netherlands)

    Martin, Xavier

    2014-01-01

    Is there such a thing as institutional advantage—and what does it mean for the study of corporate competitive advantage? In this article, I develop the concept of institutional competitive advantage, as distinct from plain competitive advantage and from comparative institutional advantage. I first i

  16. A user's manual to the PMBOK guide

    CERN Document Server

    Stackpole Snyder, Cynthia

    2013-01-01

    The must-have manual to understand and use the latest edition of the Fifth Edition The professional standard in the field of project management, A Guide to the Project Management Body of Knowledge (PMBOK® Guide-Fifth Edition) published by the Project Management Institute (PMI) serves as the ultimate resource for professionals and as a valuable studying and training device for students taking the PMP® Exam. A User''s Manual to the PMBOK® Guide takes the next logical step to act as a true user''s manual. With an accessible format and easy-to-understand language, it helps to not only distill es

  17. Trustworthy SNS for Institutional Repositories

    OpenAIRE

    Inoue, Sozo; Hori, Yuko; Ikeda, Daisuke

    2008-01-01

    In recent years, SNS (Social Networking Service) are attracting attention in the field of web services. SNS is the communication system which focuses on social relations between users, such as a friend and a group, named a community. Thus, SNS is useful for the institutional repositories in the sense that they can 1) increase the time and frequency of use by users, and 2) categorize or utilize the contents using the community information. However in SNS nowadays, the increase of spam messages...

  18. Digital Archival Image Collections: Who Are the Users?

    Science.gov (United States)

    Herold, Irene M. H.

    2010-01-01

    Archival digital image collections are a relatively new phenomenon in college library archives. Digitizing archival image collections may make them accessible to users worldwide. There has been no study to explore whether collections on the Internet lead to users who are beyond the institution or a comparison of users to a national or…

  19. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  20. HANARO user support and training

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Shin Ae; Kim, K. Y.; Kim, B. K. (and others)

    2008-06-15

    This project is aimed to support external users for the effective use of HANARO. The total number of projects selected as the beneficiary of the supporting program by MEST was 21 including this project in this year. We supported 2,339 hr measurements for the 31 requests of the 14 projects selected on the field of neutron beam utilization. In the field of materials and nuclear fuel irradiation test the 3 projects were selected and supported for 80 samples. In the fields of neutron activation analysis and radioisotope production the number of selected and supported projects were 1 and 2 respectively. In order to broaden potential user base, maximize instrument utilization, and enhance cooperation with industries, universities and institutes, practice-oriented HANARO user training courses were held for neutron beam utilization and materials and nuclear fuel irradiation fields. In the fields of neutron activation analysis 3 times training courses were held for the university students. The online neutron beam time allocation system was developed and applied successfully for the HRPD in this year. We are planing to apply this system to other neutron beam instruments in the near future. This project is a kind of the user-based supporting program for the maximize of HANARO utilization. The development products and the ideas and suggestions of users obtained through this projects will be collected and applied to the development of next new facilities. Also, by using the 'HANARO utilization and research information management system(HANARO4U)' we construct the research network among users at industries, universities and institutes. This network is expected to increase HANARO utilization and enhance productivity of the facilities.

  1. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

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

  2. A Review on Genomics APIs

    Directory of Open Access Journals (Sweden)

    Rajeswari Swaminathan

    2016-01-01

    Full Text Available The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a Google Genomics, b SMART Genomics, and c 23andMe. The functionalities, reference implementations (if available and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

  3. Institutional ethnography

    DEFF Research Database (Denmark)

    Lund, Rebecca; Tienari, Janne

    2016-01-01

    . In institutional ethnography the notion of objectification is applied to describe research processes like those that have been found to dominate in scholarly work on M&As. In this chapter, we offer an outline of Smiths critique of objectification, elucidate how institutional ethnography seeks to address it...

  4. Colonial Institutions

    DEFF Research Database (Denmark)

    McAtackney, Laura; Palmer, Russell

    2016-01-01

    and the USA which reveal that the study of colonial institutions should not be limited to the functional life of these institutions—or solely those that take the form of monumental architecture—but should include the long shadow of “imperial debris” (Stoler 2008) and immaterial institutions....

  5. Institutional actorhood

    DEFF Research Database (Denmark)

    Madsen, Christian Uhrenholdt

    In this paper I describe the changing role of intra-organizational experts in the face of institutional complexity of their field. I do this through a qualitative investigation of the institutional and organizational roles of actors in Danish organizations who are responsible for the efforts to c...... to comply with the Danish work environment regulation. And by doing so I also describe how institutional complexity and organizational responses to this complexity are particular important for the changing modes of governance that characterizes contemporary welfare states.......In this paper I describe the changing role of intra-organizational experts in the face of institutional complexity of their field. I do this through a qualitative investigation of the institutional and organizational roles of actors in Danish organizations who are responsible for the efforts...

  6. Institutional upbringing

    DEFF Research Database (Denmark)

    Gulløv, Eva

    2008-01-01

    In the chapter, I discuss the role day care institutions play in the construction of the idea of proper childhood in Denmark. Drawing on findings from research on ethnic minority children in two Danish day care institutions, I begin with a discussion of how childcare institutions act as civilising...... agents, empowered with the legitimate right to define and control normality and proper ways of behaving oneself. I aim to show how institutions come to define the normal child and proper childhood in accordance with current efforts toward reinventing national culture, exemplified by legislation requiring...... current testing of Danish language fluency levels among pre-school minority children. Testing language skills marks and defines distinctions that reinforce images of deviance that, in turn, legitimize initiatives to enrol children, specifically minority children, in child care institutions....

  7. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    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.

  8. Genomic Datasets for Cancer Research

    Science.gov (United States)

    A variety of datasets from genome-wide association studies of cancer and other genotype-phenotype studies, including sequencing and molecular diagnostic assays, are available to approved investigators through the Extramural National Cancer Institute Data Access Committee.

  9. Collaborators | Office of Cancer Genomics

    Science.gov (United States)

    The TARGET initiative is jointly managed within the National Cancer Institute (NCI) by the Office of Cancer Genomics (OCG)Opens in a New Tab and the Cancer Therapy Evaluation Program (CTEP)Opens in a New Tab.

  10. MTGD: The Medicago truncatula genome database.

    Science.gov (United States)

    Krishnakumar, Vivek; Kim, Maria; Rosen, Benjamin D; Karamycheva, Svetlana; Bidwell, Shelby L; Tang, Haibao; Town, Christopher D

    2015-01-01

    Medicago truncatula, a close relative of alfalfa (Medicago sativa), is a model legume used for studying symbiotic nitrogen fixation, mycorrhizal interactions and legume genomics. J. Craig Venter Institute (JCVI; formerly TIGR) has been involved in M. truncatula genome sequencing and annotation since 2002 and has maintained a web-based resource providing data to the community for this entire period. The website (http://www.MedicagoGenome.org) has seen major updates in the past year, where it currently hosts the latest version of the genome (Mt4.0), associated data and legacy project information, presented to users via a rich set of open-source tools. A JBrowse-based genome browser interface exposes tracks for visualization. Mutant gene symbols originally assembled and curated by the Frugoli lab are now hosted at JCVI and tie into our community annotation interface, Medicago EuCAP (to be integrated soon with our implementation of WebApollo). Literature pertinent to M. truncatula is indexed and made searchable via the Textpresso search engine. The site also implements MedicMine, an instance of InterMine that offers interconnectivity with other plant 'mines' such as ThaleMine and PhytoMine, and other model organism databases (MODs). In addition to these new features, we continue to provide keyword- and locus identifier-based searches served via a Chado-backed Tripal Instance, a BLAST search interface and bulk downloads of data sets from the iPlant Data Store (iDS). Finally, we maintain an E-mail helpdesk, facilitated by a JIRA issue tracking system, where we receive and respond to questions about the website and requests for specific data sets from the community.

  11. Universal Service for Socially Excluded Users

    Directory of Open Access Journals (Sweden)

    B. Bakmaz

    2009-06-01

    Full Text Available This paper is about defining special measures within a universal service for potential socially excluded users, as a part of Project on US in Serbia. In the centre of research are people with disabilities, low income households, and welfare institutions in the Republic of Serbia. After analyzing regulations and statistical data, proposals for telecommunications services for these users are analyzed together with the costs of their realizations. At the end preliminary results of research are discussed.

  12. Burn Institute

    Science.gov (United States)

    ... Now Help keep local seniors safe from fire! Burn Survivor Support If you are reading this, chances ... year – a burn injury. Learn more Fire and Burn Prevention Each year, the Burn Institute provides fire ...

  13. CSCAPES Institute

    Energy Technology Data Exchange (ETDEWEB)

    Alex Pothen

    2008-10-26

    We report on the progress made by researchers of the CSCAPES Institute at Old Dominion University for the years 2007 and 2008 in the areas of research, software creation, education and training, and outreach activities.

  14. Institutional Controls

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of institutional control data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different...

  15. The User Experience

    Science.gov (United States)

    Schmidt, Aaron

    2010-01-01

    User experience (UX) is about arranging the elements of a product or service to optimize how people will interact with it. In this article, the author talks about the importance of user experience and discusses the design of user experiences in libraries. He first looks at what UX is. Then he describes three kinds of user experience design: (1)…

  16. User Innovation Management

    DEFF Research Database (Denmark)

    Kanstrup, Anne Marie; Bertelsen, Pernille

    User Innovation Management (UIM) is a method for fo-opereation with users in innovation projects. The UIM method emphasizes the practice of a participatorty attitude.......User Innovation Management (UIM) is a method for fo-opereation with users in innovation projects. The UIM method emphasizes the practice of a participatorty attitude....

  17. User Behavior Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Turcotte, Melissa [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Moore, Juston Shane [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-28

    User Behaviour Analytics is the tracking, collecting and assessing of user data and activities. The goal is to detect misuse of user credentials by developing models for the normal behaviour of user credentials within a computer network and detect outliers with respect to their baseline.

  18. Franklin: User Experiences

    Energy Technology Data Exchange (ETDEWEB)

    National Energy Research Supercomputing Center; He, Yun (Helen); Kramer, William T.C.; Carter, Jonathan; Cardo, Nicholas

    2008-05-07

    The newest workhorse of the National Energy Research Scientific Computing Center is a Cray XT4 with 9,736 dual core nodes. This paper summarizes Franklin user experiences from friendly early user period to production period. Selected successful user stories along with top issues affecting user experiences are presented.

  19. The User Experience

    Science.gov (United States)

    Schmidt, Aaron

    2010-01-01

    User experience (UX) is about arranging the elements of a product or service to optimize how people will interact with it. In this article, the author talks about the importance of user experience and discusses the design of user experiences in libraries. He first looks at what UX is. Then he describes three kinds of user experience design: (1)…

  20. Performance Assessment Institute-NV

    Energy Technology Data Exchange (ETDEWEB)

    Lombardo, Joesph [Univ. of Nevada, Las Vegas, NV (United States)

    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.

  1. MycoCosm, an Integrated Fungal Genomics Resource

    Energy Technology Data Exchange (ETDEWEB)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  2. INSTITUT KESENIAN MAKASSAR

    Directory of Open Access Journals (Sweden)

    Fahrul Rizal

    2014-12-01

    Full Text Available Development of the value of art and culture in Makassar fading , while the higher the education that is expected to help develop arts and cultural preservation . The number of art enthusiasts are having trouble finding a good college and adequate facilities in Makassar divert them out of the area for study. The main purpose of this paper in order to plan and merancangan Art Institute building located in Makassar, which can accommodate the needs of artists to distribute and develop creativity, the result of design art institute building is located in the subdistrict Tamalanrea location is adjusted with the direction of the located area Spatial education, it is expected that the center will be able to accommodate students in distributing and developing creativity and the provision of facilities that can accommodate the development and preservation of local culture and art according to user requirements in accordance with the planning and design standards that apply.

  3. Setting up the JBrowse genome browser.

    Science.gov (United States)

    Skinner, Mitchell E; Holmes, Ian H

    2010-12-01

    JBrowse is a Web-based tool for visualizing genomic data. Unlike most other Web-base genome browsers, JBrowse exploits the capabilities of the user's Web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all Internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a Web server, and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a Web site that other users can visit to browse the genomic data.

  4. Genomic medicine implementation: learning by example.

    Science.gov (United States)

    Williams, Marc S

    2014-03-01

    Genomic Medicine is beginning to emerge into clinical practice. The National Human Genome Research Institute's Genomic Medicine Working Group consists of organizations that have begun to implement some aspect of genomic medicine (e.g., family history, systematic implementation of Mendelian disease program, pharmacogenomics, whole exome/genome sequencing). This article concisely reviews the working group and provides a broader context for the articles in the special issue including an assessment of anticipated provider needs and ethical, legal, and social issues relevant to the implementation of genomic medicine. The challenges of implementation of innovation in clinical practice and the potential value of genomic medicine are discussed.

  5. Protecting genomic data analytics in the cloud: state of the art and opportunities.

    Science.gov (United States)

    Tang, Haixu; Jiang, Xiaoqian; Wang, Xiaofeng; Wang, Shuang; Sofia, Heidi; Fox, Dov; Lauter, Kristin; Malin, Bradley; Telenti, Amalio; Xiong, Li; Ohno-Machado, Lucila

    2016-10-13

    The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, 'anonymization' and SHaring) hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers) to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization) are needed before they are sufficiently practical for real world environments.

  6. Protecting genomic data analytics in the cloud: state of the art and opportunities

    Directory of Open Access Journals (Sweden)

    Haixu Tang

    2016-10-01

    Full Text Available Abstract The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, ‘anonymization’ and SHaring hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization are needed before they are sufficiently practical for real world environments.

  7. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) System

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos C.; Markowitz, Victor M.

    2006-03-01

    Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of interest. IMG provides graphicalviewers, summaries and occurrence profile tools for comparing genes,pathways and functions (terms) across specific genomes. Genes can befurther examined using gene neighborhoods and compared with sequencealignment tools.

  8. Genome Annotation Transfer Utility (GATU: rapid annotation of viral genomes using a closely related reference genome

    Directory of Open Access Journals (Sweden)

    Upton Chris

    2006-06-01

    Full Text Available Abstract Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU, to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. Results GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. Conclusion GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome

  9. Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome.

    Science.gov (United States)

    Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

    2006-06-13

    Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics - Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome. The program is freely

  10. Unimagined Institutions

    DEFF Research Database (Denmark)

    Zangenberg, Mikkel Bruun

    2007-01-01

    In this paper it is argued that war contains inherent and thus necessary aesthetic traits (ranging from sensory data to narrative features), but that existing research institutions throughout the West have failed to address this issue adequately, in terms of research policy, recruitment and metho......In this paper it is argued that war contains inherent and thus necessary aesthetic traits (ranging from sensory data to narrative features), but that existing research institutions throughout the West have failed to address this issue adequately, in terms of research policy, recruitment...... and methodology. Accordingly, it is suggested that scholars from the humanities in particular aggressively seek to develop new types of research institutions and methods in order to deal with the manifold forms of overlap between warfare and aesthetics. In empirical terms, focus is limited to the current...

  11. Institutional Awareness

    DEFF Research Database (Denmark)

    Ahlvik, Carina; Boxenbaum, Eva

    Drawing on dual-process theory and mindfulness research this article sets out to shed light on the conditions that need to be met to create “a reflexive shift in consciousness” argued to be a key foundational mechanism for agency in institutional theory. Although past research has identified diff...... in consciousness to emerge and argue for how the varying levels of mindfulness in the form of internal and external awareness may manifest as distinct responses to the institutional environment the actor is embedded in....

  12. Biodigester User Survey Report

    Energy Technology Data Exchange (ETDEWEB)

    Chandararot, K.; Dannet, L.

    2007-06-15

    In May 2005, SNV and the Ministry of Agriculture, Forestry and Fisheries (MAFF) agreed to a joint development of a National Biodigester Programme (NBP) in Cambodia as a way to create an indigenous, sustainable energy source in the country and to utilize the potential of biogas in the country. The overall objective of the first phase of the National Biodigester Programme is 'The dissemination of domestic biodigesters as an indigenous, sustainable energy source through the development of a commercial, market oriented, biodigester sector in selected provinces of Cambodia'. The program aims to support the construction of 17,500 biodigesters in at least 6 provinces over the period of 2006 to 2009. To gain insights and feedbacks on the impacts of their activities to date, NBP commissioned the Cambodia Institute of Development Study (CIDS) to carry out a Biodigester User Survey in January 2007. The purpose of the survey is to evaluate the effects of domestic biodigester installations, as supported by the program, on 100 households in 3 provinces in Cambodia- Kampong Cham, Kandal and Svay Rieng.

  13. European Institutions?

    NARCIS (Netherlands)

    Meacham, Darian

    2016-01-01

    The aim of this article is to sketch a phenomenological theory of political institutions and to apply it to some objections and questions raised by Pierre Manent about the project of the European Union and more specifically the question of “European Construction”, i.e. what is the aim of the Europea

  14. Institution Morphisms

    Science.gov (United States)

    Goguen, Joseph; Rosu, Grigore; Norvig, Peter (Technical Monitor)

    2001-01-01

    Institutions formalize the intuitive notion of logical system, including both syntax and semantics. A surprising number of different notions of morphisim have been suggested for forming categories with institutions as objects, and a surprising variety of names have been proposed for them. One goal of this paper is to suggest a terminology that is both uniform and informative to replace the current rather chaotic nomenclature. Another goal is to investigate the properties and interrelations of these notions. Following brief expositions of indexed categories, twisted relations, and Kan extensions, we demonstrate and then exploit the duality between institution morphisms in the original sense of Goguen and Burstall, and the 'plain maps' of Meseguer, obtaining simple uniform proofs of completeness and cocompleteness for both resulting categories; because of this duality, we prefer the name 'comorphism' over 'plain map.' We next consider 'theoroidal' morphisms and comorphisims, which generalize signatures to theories, finding that the 'maps' of Meseguer are theoroidal comorphisms, while theoroidal morphisms are a new concept. We then introduce 'forward' and 'semi-natural' morphisms, and appendices discuss institutions for hidden algebra, universal algebra, partial equational logic, and a variant of order sorted algebra supporting partiality.

  15. Institutional Paralysis

    Science.gov (United States)

    Yarmolinsky, Adam

    1975-01-01

    Institutional paralysis of higher education is the result of the disjunction between faculty and administration; the disjunction between substantive planning and bugetary decision-making; the disjunction between departmental structures and functional areas of university concern; and the disjunction between the theory of direct democracy and its…

  16. User evaluation in practice

    DEFF Research Database (Denmark)

    Krogstrup, Hanne Kathrine

    2004-01-01

    The BIKVA-model (brugerinddragelse i kvalitetsvurdering) or in english UPQA (User Participation in Quality Assessment) are presented......The BIKVA-model (brugerinddragelse i kvalitetsvurdering) or in english UPQA (User Participation in Quality Assessment) are presented...

  17. User Privacy and Empowerment:

    DEFF Research Database (Denmark)

    Dhotre, Prashant Shantaram; Olesen, Henning; Khajuria, Samant

    2017-01-01

    of personal information and its manage-ment. Thus, empowering users and enhancing awareness are essential to compre-hending the value of secrecy. This paper also introduced latest advances in the domain of privacy issues like User Managed Access (UMA) can state suitable requirements for user empowerment...... and will cater to redefine the trustworthy relationship between service providers and users. Subsequently, this paper con-cludes with suggestions for providing empowerment to the user and developing user-centric, transparent business models.......Today, the service providers are capable of assembling a huge measure of user information using Big data techniques. For service providers, user infor-mation has become a vital asset. The present business models are attentive to collect extensive users’ information to extract useful knowledge...

  18. Water markets between Mexican water user associations

    NARCIS (Netherlands)

    Kloezen, W.H.

    1998-01-01

    Internationally, introducing water markets is regarded as a strong alternative institutional arrangement for managing irrigation water more effectively. Also in Mexico, the National Water Law of 1992 allows individual farmers as well as water user associations (WUA) to trade water. Although farmer

  19. Water markets between Mexican water user associations

    NARCIS (Netherlands)

    Kloezen, W.H.

    1998-01-01

    Internationally, introducing water markets is regarded as a strong alternative institutional arrangement for managing irrigation water more effectively. Also in Mexico, the National Water Law of 1992 allows individual farmers as well as water user associations (WUA) to trade water. Although farmer t

  20. Transparent User Authentication

    CERN Document Server

    Clarke, Nathan

    2011-01-01

    This groundbreaking text examines the problem of user authentication from a completely new viewpoint. Rather than describing the requirements, technologies and implementation issues of designing point-of-entry authentication, the book introduces and investigates the technological requirements of implementing transparent user authentication -- where authentication credentials are captured during a user's normal interaction with a system. This approach would transform user authentication from a binary point-of-entry decision to a continuous identity confidence measure. Topics and features: discu

  1. User Requirements for Wireless

    DEFF Research Database (Denmark)

    technologies or software has been developed. A variety of user requirements are provided illustrating the effect of changing the targeted user group with respect to age,; to the context and the different technologies or software as well as to the difference in viewpoint on ways of involving users...

  2. Directory of computer users in nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    Henne, R.L.; Erickson, J.J.; McClain, W.J.; Kirch, D.L.

    1977-01-01

    The directory is composed of two major divisions, a Users' section and a Vendors' section. The Users' section consists of detailed installation descriptions and indexes to these descriptions. A typical description contains the name, address, type, and size of the institution as well as names of persons to contact. Following the hardware descriptions are listed the type of studies for which the computers are utilized, including the languages used, the method of output and an estimate of how often the study is performed. The Vendors' section contains short descriptions of current commercially available nuclear medicine systems as supplied by the vendors themselves. In order to reduce the amount of obsolete data and to include new institutions in future updates of the directory, a user questionnaire is included. (HLW)

  3. CaMath user`s guide

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Ben-chin; Daly, B.

    1994-07-13

    CaMath is an external Mathematica package which can be loaded into Mathematica by a user. CaMath consists of a special set of channel access functions which provides the Mathematica users with easy and flexible access of channel information across the IOC networks. It also provides a complete set of process variable event monitoring functions. The available functions for CaMath, their functionality, and their syntax are described herein. This document also gives examples how a Mathematica user can interface to channel access devices. It is assumed that the user is already familiar with using Mathematica. Few examples of Mathematica module of using CaMath functions are also given in this document.

  4. DOSFAC2 user`s guide

    Energy Technology Data Exchange (ETDEWEB)

    Young, M.L.; Chanin, D.

    1997-12-01

    This document describes the DOSFAC2 code, which is used for generating dose-to-source conversion factors for the MACCS2 code. DOSFAC2 is a revised and updated version of the DOSFAC code that was distributed with version 1.5.11 of the MACCS code. included are (1) an overview and background of DOSFAC2, (2) a summary of two new functional capabilities, and (3) a user`s guide. 20 refs., 5 tabs.

  5. User interface design considerations

    DEFF Research Database (Denmark)

    Andersen, Simon Engedal; Jakobsen, Arne; Rasmussen, Bjarne D.

    1999-01-01

    When designing a user interface for a simulation model there are several important issues to consider: Who is the target user group, and which a priori information can be expected. What questions do the users want answers to and what questions are answered using a specific model?When developing...... the user interface of EESCoolTools these issues led to a series of simulation tools each with a specific purpose and a carefully selected set of input and output variables. To allow a more wide range of questions to be answered by the same model, the user can change between different sets of input...... and output variables. This feature requires special attention when designing the user interface and a special approach for controlling the user selection of input and output variables are developed. To obtain a consistent system description the different input variables are grouped corresponding...

  6. International user studies

    DEFF Research Database (Denmark)

    Nielsen, Lene; Madsen, Sabine; Jensen, Iben;

    in Sydhavnen, and it is funded by InfinIT. Based on a qualitative interview study with 15 user researchers from 11 different companies, we have investigated how companies collect and present data about users on international markets. Key findings are: Companies do not collect data about end users in all....../region. The preferred data collection method is field studies. If possible, user researchers choose to go to the field themselves to gain rich insights and to control the data collection process. The main insights companies gain from international user studies are (1) that there are many similarities among end users...... across nationalities and (2) that it often is more important to focus on and take differences in market conditions into account than national culture per se. Companies are in the process of finding out how best to present the insights about international end users to their employees. However, so far...

  7. Fueling the Future with Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    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. Institutional Awareness

    DEFF Research Database (Denmark)

    Ahlvik, Carina; Boxenbaum, Eva

    Drawing on dual-process theory and mindfulness research this article sets out to shed light on the conditions that need to be met to create “a reflexive shift in consciousness” argued to be a key foundational mechanism for agency in institutional theory. Although past research has identified...... different exogenous triggers to evoke shifts in consciousness, such as conflicting logics or socio-economic shocks, we argue that a reflexive shift in consciousness can also be cultivated by developing mindfulness. We develop a typology to depict conditions that need to be met to enable a reflexive shift...

  9. Institutional Investors

    DEFF Research Database (Denmark)

    Birkmose, Hanne Søndergaard; Strand, Therese

    Research Question/Issue: Institutional investors are facing increased pressure and threats of legislation from the European Union to abandon passive ownership strategies. This study investigates the prerequisites for – and potential dissimilarities in the practice of, active ownership among......, as such a setup transfers power from the board to the owners. Presumably, this reduces the impact of free rider and collective action problems, and increases the shareholders’ inclination to make proposals, which is also what we find. Theoretical/Academic Implications: We contribute to literature by investigating...

  10. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.

  11. Family genome browser: visualizing genomes with pedigree information.

    Science.gov (United States)

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Institute news

    Science.gov (United States)

    1999-11-01

    Joining the team A new member of staff has recently joined the Institute of Physics Education Department (Schools and Colleges) team. (Dr) Steven Chapman will have managerial responsibility for physics education issues in the 11 - 16 age range, particularly on the policy side. He will work closely with Mary Wood, who spends much of her time out and about doing the practical things to support physics education pre-16. Catherine Wilson will be spending more of her time working to support the Post-16 Physics Initiative but retains overall responsibility for the department. Steven graduated in Physics and Astronomy and then went on to do his doctorate at Sussex University. He stayed in the research field for a while, including a period at NPL. Then, having decided to train as a teacher, he taught for the last five years, most recently at a brand new school in Sutton where he was Head of Physics. Physics update Dates for `Physics Update' courses in 2000, intended for practising science teachers, are as follows: 1 - 3 April: Malvern College 9 - 10 June: Stirling University 8 - 10 July: York University 8 - 10 December: Oxford University The deadline for applications for the course to be held on 11 - 13 December 1999 at the School of Physics, Exeter University, is 12 November, so any late enquiries should be sent to Leila Solomon at The Institute of Physics, 76 Portland Place, London W1N 3DH (tel: 020 7470 4821) right away. Name that teacher! Late nominations are still welcome for the Teachers of Physics/Teachers of Primary Science awards for the year 2000. Closing date for nominations is `the last week in November'. Further details can be obtained from Catherine Wilson or Barbara Hill in the Institute's Education Department. Forward and back! The Education Group's one-day meeting on 13 November is accepting bookings until almost the last minute, so don't delay your application! The day is entitled `Post-16 physics: Looking forward, learning from the past' and it aims to

  13. myGenomeBrowser: building and sharing your own genome browser.

    Science.gov (United States)

    Carrere, Sébastien; Gouzy, Jérôme

    2017-04-15

    myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data. myGenomeBrowser is freely available at https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser and includes tutorial screencasts. Source code and installation instructions can be found at https://framagit.org/BBRIC/myGenomeBrowser . myGenomeBrowser is open-source and mainly implemented in Perl, JavaScript, Apache and Docker. sebastien.carrere@inra.fr.

  14. eGenomics: Cataloguing Our Complete Genome Collection III

    Directory of Open Access Journals (Sweden)

    Dawn Field

    2007-01-01

    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  15. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  16. Nonaffiliated Users in Academic Libraries: Using W.D. Ross's Ethical Pluralism to Make Sense of the Tough Questions

    Science.gov (United States)

    Lenker, Mark; Kocevar-Weidinger, Elizabeth

    2010-01-01

    Though the academic library's primary mission is to serve the students, faculty, and staff of its parent institution, would-be users not officially associated with the institution frequently call upon the library to provide services and/or resources. Requests by these nonaffiliated users (sometimes called community users) pose a moral quandary for…

  17. Measuring user engagement

    CERN Document Server

    Lalmas, Mounia; Yom-Tov, Elad

    2014-01-01

    User engagement refers to the quality of the user experience that emphasizes the positive aspects of interacting with an online application and, in particular, the desire to use that application longer and repeatedly. User engagement is a key concept in the design of online applications (whether for desktop, tablet or mobile), motivated by the observation that successful applications are not just used, but are engaged with. Users invest time, attention, and emotion in their use of technology, and seek to satisfy pragmatic and hedonic needs. Measurement is critical for evaluating whether online

  18. The User Reconfigured

    DEFF Research Database (Denmark)

    Bardzell, Jeffrey; Bardzell, Shaowen

    2015-01-01

    Foundational to HCI is the notion of “the user.” Whether a cognitive processor, social actor, consumer, or even a non- user, the user in HCI has always been as much a technical construct as actual people using systems. We explore an emerging formulation of the user—the subjectivity of in- formation......, and activism. We argue that subjectivi- ties of information clarifies the relationships between de- sign choices and embodied experiences, ways that designers design users and not just products, and ways to cultivate and transform, rather than merely support, human agency....

  19. Strategies and tools for whole genome alignments

    Energy Technology Data Exchange (ETDEWEB)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  20. Demonstrator 1: User Interface and User Functions

    DEFF Research Database (Denmark)

    Gram, Christian

    1999-01-01

    Describes the user interface and its functionality in a prototype system used for a virtual seminar session. The functionality is restricted to what is needed for a distributed seminar discussion among not too many people. The system is designed to work with the participants distributed at several...

  1. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  2. GenColors-based comparative genome databases for small eukaryotic genomes.

    Science.gov (United States)

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

  3. The UCSC Cancer Genomics Browser: update 2011.

    Science.gov (United States)

    Sanborn, J Zachary; Benz, Stephen C; Craft, Brian; Szeto, Christopher; Kober, Kord M; Meyer, Laurence; Vaske, Charles J; Goldman, Mary; Smith, Kayla E; Kuhn, Robert M; Karolchik, Donna; Kent, W James; Stuart, Joshua M; Haussler, David; Zhu, Jingchun

    2011-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

  4. Contact | Office of Cancer Genomics

    Science.gov (United States)

    For more information about the Office of Cancer Genomics, please contact: Office of Cancer Genomics National Cancer Institute 31 Center Drive, 10A07 Bethesda, Maryland 20892-2580 Phone: (301) 451-8027 Fax: (301) 480-4368 Email: ocg@mail.nih.gov *Please note that this site will not function properly in Internet Explorer unless you completely turn off the Compatibility View*

  5. User programmable virtualized networks

    NARCIS (Netherlands)

    Meijer, R.J.; Strijkers, R.J.; Gommans, L.; Laat, C.de

    2006-01-01

    This paper introduces the concept of a User Programmable Virtualized Network, which allows networks to deliver application specific services using network element components that developers can program as part of a users application. The use of special tokens in data or control packets is the basis

  6. Additional user needs

    Energy Technology Data Exchange (ETDEWEB)

    Rorschach, H.E.; Hayter, J.B.

    1986-08-15

    This paper summarizes the conclusions of a discussion group on users' needs held at the Workshop on an Advanced Steady-State Neutron Facility. The discussion was devoted to reactor characteristics, special facilities and siting considerations suggested by user needs.

  7. EMI New User Communities

    CERN Document Server

    Riedel, M

    2013-01-01

    This document provides pieces of information about new user communities that directly or indirectly take advantage of EMI Products. Each user community is described via one specific EMI product use case to understand and communicate the current usage of EMI Products in practice.

  8. User Frustrations as Opportunities

    Directory of Open Access Journals (Sweden)

    Michael Weiss

    2012-04-01

    Full Text Available User frustrations are an excellent source of new product ideas. Starting with this observation, this article describes an approach that entrepreneurs can use to discover business opportunities. Opportunity discovery starts with a problem that the user has, but may not be able to articulate. User-centered design techniques can help elicit those latent needs. The entrepreneur should then try to understand how users are solving their problem today, before proposing a solution that draws on the unique skills and technical capabilities available to the entrepreneur. Finally, an in-depth understanding of the user allows the entrepreneur to hone in on the points of difference and resonance that are the foundation of a strong customer value proposition.

  9. Lead User Innovation

    DEFF Research Database (Denmark)

    Brem, Alexander; Larsen, Henry

    2015-01-01

    , deliver and capture the value of an innovatively new device together. From the perspective of the lead user, we show antecedents and effects of social interaction between organizational actors and the lead user on the development of social capital, especially trust and shared imagination. The second case......User innovation and especially the integration of lead users is a key topic in the innovation management literature of recent years. This paper contributes by providing a rare perspective into what easily could be seen as innovation failure, shown from two perspectives. We show how a lack of shared...... imagination hampers participation and kills innovation between interdependent stakeholders at the threshold between invention and innovation in practice. We present a first case in the fun-sport industry where an external lead user and diverse firm representatives in different functions fail to create...

  10. International user studies

    DEFF Research Database (Denmark)

    Nielsen, Lene; Madsen, Sabine; Jensen, Iben

    across nationalities and (2) that it often is more important to focus on and take differences in market conditions into account than national culture per se. Companies are in the process of finding out how best to present the insights about international end users to their employees. However, so far...... a company’s general attitude and approach to (1) international markets and (2) user studies. Lastly, we present the theoretical ideas and concepts about culture that has informed the research....... in Sydhavnen, and it is funded by InfinIT. Based on a qualitative interview study with 15 user researchers from 11 different companies, we have investigated how companies collect and present data about users on international markets. Key findings are: Companies do not collect data about end users in all...

  11. User participation in implementation

    DEFF Research Database (Denmark)

    Fleron, Benedicte; Rasmussen, Rasmus; Simonsen, Jesper

    2012-01-01

    Systems development has been claimed to benefit from user participation, yet user participation in implementation activities may be more common and is a growing focus of participatory-design work. We investigate the effect of the extensive user participation in the implementation of a clinical...... system by empirically analyzing how management, participating staff, and non-participating staff view the implementation process with respect to areas that have previously been linked to user participation such as system quality, emergent interactions, and psychological buy-in. The participating staff...... experienced more uncertainty and frustration than management and non-participating staff, especially concerning how to run an implementation process and how to understand and utilize the configuration possibilities of the system. This suggests that user participation in implementation introduces a need...

  12. The PANTHER User Experience

    Energy Technology Data Exchange (ETDEWEB)

    Coram, Jamie L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Morrow, James D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Perkins, David Nikolaus [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    This document describes the PANTHER R&D Application, a proof-of-concept user interface application developed under the PANTHER Grand Challenge LDRD. The purpose of the application is to explore interaction models for graph analytics, drive algorithmic improvements from an end-user point of view, and support demonstration of PANTHER technologies to potential customers. The R&D Application implements a graph-centric interaction model that exposes analysts to the algorithms contained within the GeoGraphy graph analytics library. Users define geospatial-temporal semantic graph queries by constructing search templates based on nodes, edges, and the constraints among them. Users then analyze the results of the queries using both geo-spatial and temporal visualizations. Development of this application has made user experience an explicit driver for project and algorithmic level decisions that will affect how analysts one day make use of PANTHER technologies.

  13. Instituting Commoning

    Directory of Open Access Journals (Sweden)

    . STEALTH.unlimited

    2015-06-01

    Full Text Available Starting from the origins of the notion of management, this paper explores how commons governance is constituted by the earlier influential research of Elinor Ostrom, and pursues this with reference to scholars such as Saki Bailey, who emphasises that the choice of regulatory frame is ultimately a political one. We then argue that commons have to be ‘instituted’ in an open manner in order to remain accessible. This demands a set of scripts, rules or agreements that keep the process of commoning in place, and, simultaneously, keep commoning in a constant process of reproduction. We examine this tension and look at the shift in understanding about what ‘institutions of the commons’ have entailed in practice over the course of the last century and a half. Finally, we return to the political dimension to touch upon the question of whether, with the disappearance of the welfare state, a coherent concept of society can emerge from the current upsurge of commons initiatives.

  14. User`s guide to MIDAS

    Energy Technology Data Exchange (ETDEWEB)

    Tisue, S.A.; Williams, N.B.; Huber, C.C. [Argonne National Lab., IL (United States). Decision and Information Sciences Div.; Chun, K.C. [Argonne National Lab., IL (United States). Environmental Assessment Div.

    1995-12-01

    Welcome to the MIDAS User`s Guide. This document describes the goals of the Munitions Items Disposition Action System (MIDAS) program and documents the MIDAS software. The main text first describes the equipment and software you need to run MIDAS and tells how to install and start it. It lists the contents of the database and explains how it is organized. Finally, it tells how to perform various functions, such as locating, entering, viewing, deleting, changing, transferring, and printing both textual and graphical data. Images of the actual computer screens accompany these explanations and guidelines. Appendix A contains a glossary of names for the various abbreviations, codes, and chemicals; Appendix B is a list of modem names; Appendix C provides a database dictionary and rules for entering data; and Appendix D describes procedures for troubleshooting problems associated with connecting to the MIDAS server and using MIDAS.

  15. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

    Science.gov (United States)

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

    2014-01-01

    The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

  16. Aztec user`s guide. Version 1

    Energy Technology Data Exchange (ETDEWEB)

    Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

    1995-10-01

    Aztec is an iterative library that greatly simplifies the parallelization process when solving the linear systems of equations Ax = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. Aztec is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparse unstructured matrices for parallel solution. Once the distributed matrix is created, computation can be performed on any of the parallel machines running Aztec: nCUBE 2, IBM SP2 and Intel Paragon, MPI platforms as well as standard serial and vector platforms. Aztec includes a number of Krylov iterative methods such as conjugate gradient (CG), generalized minimum residual (GMRES) and stabilized biconjugate gradient (BICGSTAB) to solve systems of equations. These Krylov methods are used in conjunction with various preconditioners such as polynomial or domain decomposition methods using LU or incomplete LU factorizations within subdomains. Although the matrix A can be general, the package has been designed for matrices arising from the approximation of partial differential equations (PDEs). In particular, the Aztec package is oriented toward systems arising from PDE applications.

  17. Simplifying the Use of Pharmacogenomics in Clinical Practice: Building the Genomic Prescribing System.

    Science.gov (United States)

    Danahey, Keith; Borden, Brittany A; Furner, Brian; Yukman, Patrick; Hussain, Sheena; Saner, Donald; Volchenboum, Samuel L; Ratain, Mark J; O'Donnell, Peter H

    2017-09-26

    A barrier to the use of genomic information during prescribing is the limited number of software solutions that combine a user-friendly interface with complex medical data. We built and designed an online, secure, electronic custom interface termed the Genomic Prescribing System (GPS). Actionable pharmacogenomic (PGx) information was reviewed, collected, and stored in the back-end of GPS to enable creation of customized drug- and variant-specific clinical decision support (CDS) summaries. The database architecture utilized the star schema to store information. Patient raw genomic data underwent transformation via custom-designed algorithms to enable gene and phenotype-level associations. Multiple external data sets (PubMed, The Systematized Nomenclature of Medicine (SNOMED), National Drug File - Reference Terminology (ND-FRT), and a publically-available PGx knowledgebase) were integrated to facilitate the delivery of patient, drug, disease, and genomic information. Institutional security infrastructure was leveraged to securely store patient genomic and clinical data on a HIPAA-compliant server farm. As of May 17, 2016, the GPS back-end housed 257 CDS encompassing 112 genetic variants, 42 genes, and 46 PGx-actionable drugs. The GPS user interface presented patient-specific CDS alongside a recognizable traffic light symbol (green/yellow/red), denoting PGx risk for each genomic result. The number of traffic lights per visit increased with the corresponding increase in the number of available PGx-annotated drugs over time. An integrated drug and disease search functionality, links to primary literature sources, and potential alternative PGx drugs were indicated. The system, which was initially used as stand-alone CDS software within our clinical environment, was then integrated with the institutional electronic medical record for enhanced usability. There have been nearly 2000 logins in 43 months since inception, with usage exceeding 56 logins per month and system up

  18. Game user experience evaluation

    CERN Document Server

    Bernhaupt, Regina

    2015-01-01

    Evaluating interactive systems for their user experience (UX) is a standard approach in industry and research today. This book explores the areas of game design and development and Human Computer Interaction (HCI) as ways to understand the various contributing aspects of the overall gaming experience. Fully updated, extended and revised this book is based upon the original publication Evaluating User Experience in Games, and provides updated methods and approaches ranging from user- orientated methods to game specific approaches. New and emerging methods and areas explored include physiologi

  19. Designing for user engagement

    CERN Document Server

    Geisler, Cheryl

    2013-01-01

    Designing for User Engagement on the Web: 10 Basic Principles is concerned with making user experience engaging. The cascade of social web applications we are now familiar with - blogs, consumer reviews, wikis, and social networking - are all engaging experiences. But engagement is an increasingly common goal in business and productivity environments as well. This book provides a foundation for all those seeking to design engaging user experiences rich in communication and interaction. Combining a handbook on basic principles with case studies, it provides readers with a ric

  20. Safety for Users

    CERN Document Server

    HR Department

    2008-01-01

    CERN welcomes more than 8000 Users every year. The PH Department as host to these scientific associates requires the highest safety standards. The PH Safety Office has published a Safety Flyer for Users. Important safety topics and procedures are presented. Although the Flyer is intended primarily to provide safety information for Users, the PH Safety Office invites all those on the CERN sites to keep a copy of the flyer as it gives guidance in matters of safety and explains what to do in the event of an emergency. Link: http://ph-dep.web.cern.ch/ph-dep/Safety/SafetyOffice.html PH-Safety Office PH Department

  1. Safety for Users

    CERN Document Server

    HR Department

    2008-01-01

    CERN welcomes more than 8000 Users every year. The PH Department as host to these scientific associates requires the highest safety standards. The PH Safety Office has published a safety flyer for Users. Important safety topics and procedures are presented. Although the flyer is intended primarily to provide safety information for Users, the PH Safety Office invites all those on the CERN sites to keep a copy of the flyer as it gives guidance in matters of safety and explains what to do in the event of an emergency. The flyer is available at: http://ph-dep.web.cern.ch/ph-dep/Safety/SafetyOffice.html PH-Safety Office PH Department

  2. Distributed User Interfaces

    CERN Document Server

    Gallud, Jose A; Penichet, Victor M R

    2011-01-01

    The recent advances in display technologies and mobile devices is having an important effect on the way users interact with all kinds of devices (computers, mobile devices, laptops, tablets, and so on). These are opening up new possibilities for interaction, including the distribution of the UI (User Interface) amongst different devices, and implies that the UI can be split and composed, moved, copied or cloned among devices running the same or different operating systems. These new ways of manipulating the UI are considered under the emerging topic of Distributed User Interfaces (DUIs). DUIs

  3. 76 FR 45814 - Animal Generic Drug User Fee Rates and Payment Procedures for Fiscal Year 2012

    Science.gov (United States)

    2011-08-01

    ... INFORMATION CONTACT: Visit FDA's Web site at http://www.fda.gov/ForIndustry/UserFees/AnimalGenericDrugUserFee.... Background Section 741 of the FD&C Act (21 U.S.C. 379j-21) establishes three different kinds of user fees: (1.... Contact your bank or financial institution regarding the amount of the fees that need to be paid...

  4. The User Perspective in Performance Auditing--A Case Study of Norway

    Science.gov (United States)

    Arthur, Arnfrid; Rydland, Lars Tore; Amundsen, Kristin

    2012-01-01

    The user perspective is an important contextual factor for Supreme Audit Institutions (SAIs). This article provides examples from performance audits in Norway and explores why the user perspective has become important in performance audit practices. It shows that user satisfaction can be employed as a key performance indicator of effectiveness of…

  5. Genome Modeling System: A Knowledge Management Platform for Genomics.

    Directory of Open Access Journals (Sweden)

    Malachi Griffith

    2015-07-01

    Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

  6. The users centered design of a new digital fluorometer

    Energy Technology Data Exchange (ETDEWEB)

    Farias, Marcos S.; Santos, Isaac J.A.L. dos; Grecco, Claudio H.S.; Pedrosa, Paulo S.; Colthurst, Carlos M.; Szabo, Andre P. [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)], e-mail: msantana@ien.gov.br, e-mail: luquetti@ien.gov.br, e-mail: grecco@ien.gov.br, e-mail: pedrosa@ien.gov.br, e-mail: mcdonald@ien.gov.br, e-mail: szabo@ien.gov.br

    2009-07-01

    The fluorometer is the equipment used in chemical analysis laboratories, research institutes and nuclear fuel cycle companies. This equipment measures an unknown amount of uranium in ores, rivers, etc. The fluorometer functioning is based on the uranium fluorescence when submitted to the ultraviolet radiation incidence. The fluorescence is measured by an electronic optic system with optics filters, photomultiplier tube, and a current amplifier. The user centered design involves the user in the product development in all phases of the design process. Users are not simply consulted at the beginning of the design process and evaluated the system at the end; they are treated as partners throughout the design process. The user centered design emphasizes the needs and abilities of the users and improves the usability of the equipment. The activity centered design emphasizes the development of the equipment with a deep understanding of the users activities and of the current work practices of the users. The aim of this paper is to present a methodological framework that contributes to the design and evaluation of a new digital fluorometer towards an approach related to the users and their activities. This methodological framework includes users-based testing, interviews, questionnaires, human factors standards and guidelines, the users activity analysis and users satisfaction questionnaire. (author)

  7. The users centered design of a new digital fluorometer

    Energy Technology Data Exchange (ETDEWEB)

    Farias, Marcos S.; Santos, Isaac J.A.L. dos; Gomes, Luciene B.C.; Colthurst, Carlos M.; Szabo, Andre P.; Souza, Alvaro S.F. [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)], E-mail: msantana@ien.gov.br, E-mail: luquetti@ien.gov.br, E-mail: luciene@ien.gov.br, E-mail: mcdonald@ien.gov.br, E-mail: szabo@ien.gov.br, E-mail: alvaro@ien.gov.br

    2007-07-01

    The fluorometer is an equipment used in chemical analysis laboratories, research institutes and nuclear fuel cycle companies. This equipment measures an unknown amount of uranium in ores, rivers, etc. The fluorometer functioning is based on the uranium fluorescence when submitted to the ultraviolet radiation incidence. The fluorescence is measured by an electronic optic system with optics filters, photomultiplier tube, and a current amplifier. The user centered design involves the user in the product development in all phases of the design process. Users are not simply consulted at the beginning of the design process and evaluated the system at the end; they are treated as partners throughout the design process. The user centered design emphasizes the needs and abilities of the users and improves the usability of the equipment. The activity centered design emphasizes the development of the equipment with a deep understanding of the users activities and of the current work practices of the users. The aim of this paper is to present a methodological framework that contributes to the design and evaluation of a new digital fluorometer towards an approach related to the users and their activities. This methodological framework includes users-based testing, interviews, questionnaires, human factors standards and guidelines, the users activity analysis and users satisfaction questionnaire. (author)

  8. ARM User Survey Report

    Energy Technology Data Exchange (ETDEWEB)

    Roeder, LR

    2010-06-22

    The objective of this survey was to obtain user feedback to, among other things, determine how to organize the exponentially growing data within the Atmospheric Radiation Measurement (ARM) Climate Research Facility, and identify users’ preferred data analysis system. The survey findings appear to have met this objective, having received approximately 300 responses that give insight into the type of work users perform, usage of the data, percentage of data analysis users might perform on an ARM-hosted computing resource, downloading volume level where users begin having reservations, opinion about usage if given more powerful computing resources (including ability to manipulate data), types of tools that would be most beneficial to them, preferred programming language and data analysis system, level of importance for certain types of capabilities, and finally, level of interest in participating in a code-sharing community.

  9. The User Reconfigured

    DEFF Research Database (Denmark)

    Bardzell, Jeffrey; Bardzell, Shaowen

    2015-01-01

    , and activism. We argue that subjectivi- ties of information clarifies the relationships between de- sign choices and embodied experiences, ways that designers design users and not just products, and ways to cultivate and transform, rather than merely support, human agency.......—by laying out what it means and why research- ers are being drawn to it. We then use it to guide a case study of a relatively marginal use of computing—digitally mediated sexuality—to holistically explore design in rela- tion to embodiment, tactual experience, sociability, power, ideology, selfhood......Foundational to HCI is the notion of “the user.” Whether a cognitive processor, social actor, consumer, or even a non- user, the user in HCI has always been as much a technical construct as actual people using systems. We explore an emerging formulation of the user—the subjectivity of in- formation...

  10. Interactive Office user's manual

    Science.gov (United States)

    Montgomery, Edward E.; Lowers, Benjamin; Nabors, Terri L.

    1990-01-01

    Given here is a user's manual for Interactive Office (IO), an executive office tool for organization and planning, written specifically for Macintosh. IO is a paperless management tool to automate a related group of individuals into one productive system.

  11. User Interface History

    DEFF Research Database (Denmark)

    Jørgensen, Anker Helms; Myers, Brad A

    2008-01-01

    User Interfaces have been around as long as computers have existed, even well before the field of Human-Computer Interaction was established. Over the years, some papers on the history of Human-Computer Interaction and User Interfaces have appeared, primarily focusing on the graphical interface era...... and early visionaries such as Bush, Engelbart and Kay. With the User Interface being a decisive factor in the proliferation of computers in society and since it has become a cultural phenomenon, it is time to paint a more comprehensive picture of its history. This SIG will investigate the possibilities...... of  launching a concerted effort towards creating a History of User Interfaces. ...

  12. "Playing" with our users

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2014-01-01

    was from the amazing Dr Anthony Lewis Brooks (aka Tony) who has conceived the concepts GameAbilitation, ArtAbilitation, and Ludic Engagement Designs for All. While presenting some of his work on GameAbilitation and ArtAbilitation he brought up the subject of conducting research with users with disabilities......, about what happens to our users when research is over, funds are gone and the curtain of experiments has fallen. Dr Brooks presented the case of a young user who while unable to move and communicate had to part with the test device that provided him with interactive playful experience. We’ve all been...... confined in a house. For researchers that work with people with disabilities and in my case with playful interactions and positive immersive experience, we might have to think harder when we write project proposals or sketch our methodology. Devices, software and experience should be available to the users...

  13. FAST User Guide

    Science.gov (United States)

    Walatka, Pamela P.; Clucas, Jean; McCabe, R. Kevin; Plessel, Todd; Potter, R.; Cooper, D. M. (Technical Monitor)

    1994-01-01

    The Flow Analysis Software Toolkit, FAST, is a software environment for visualizing data. FAST is a collection of separate programs (modules) that run simultaneously and allow the user to examine the results of numerical and experimental simulations. The user can load data files, perform calculations on the data, visualize the results of these calculations, construct scenes of 3D graphical objects, and plot, animate and record the scenes. Computational Fluid Dynamics (CFD) visualization is the primary intended use of FAST, but FAST can also assist in the analysis of other types of data. FAST combines the capabilities of such programs as PLOT3D, RIP, SURF, and GAS into one environment with modules that share data. Sharing data between modules eliminates the drudgery of transferring data between programs. All the modules in the FAST environment have a consistent, highly interactive graphical user interface. Most commands are entered by pointing and'clicking. The modular construction of FAST makes it flexible and extensible. The environment can be custom configured and new modules can be developed and added as needed. The following modules have been developed for FAST: VIEWER, FILE IO, CALCULATOR, SURFER, TOPOLOGY, PLOTTER, TITLER, TRACER, ARCGRAPH, GQ, SURFERU, SHOTET, and ISOLEVU. A utility is also included to make the inclusion of user defined modules in the FAST environment easy. The VIEWER module is the central control for the FAST environment. From VIEWER, the user can-change object attributes, interactively position objects in three-dimensional space, define and save scenes, create animations, spawn new FAST modules, add additional view windows, and save and execute command scripts. The FAST User Guide uses text and FAST MAPS (graphical representations of the entire user interface) to guide the user through the use of FAST. Chapters include: Maps, Overview, Tips, Getting Started Tutorial, a separate chapter for each module, file formats, and system

  14. VOLTTRON: User Guide

    Energy Technology Data Exchange (ETDEWEB)

    Lutes, Robert G.; Katipamula, Srinivas; Akyol, Bora A.; Tenney, Nathan D.; Haack, Jereme N.; Monson, Kyle E.; Carpenter, Brandon J.

    2014-04-24

    This document is a user guide for the deployment of the Transactional Network platform and agent/application development within the VOLTTRON. The intent of this user guide is to provide a description of the functionality of the Transactional Network Platform. This document describes how to deploy the platform, including installation, use, guidance, and limitations. It also describes how additional features can be added to enhance its current functionality.

  15. SILMUSCEN and CLIGEN User`s Guide

    Energy Technology Data Exchange (ETDEWEB)

    Carter, T.; Tuomenvirta, H. [Finnish Meteorological Inst., Helsinki (Finland); Posch, M. [Water and Environment Research Inst., Helsinki (Finland)

    1995-12-31

    This User`s Guide has been prepared to provide recommendations for the selection and application of climatic scenarios in the Finnish Research Programme on Climate Change (SILMU). These scenarios are required for conducting impact studies in SILMU. They should reflect the current range of estimates of future climate in the Finnish region. In addition, they should be consistent with other projections of importance in impact studies, such as future atmospheric composition and sea level. Section 2 provides some background information about the types of scenarios required in SILMU and Section 3 offers a general description of the scenarios. In Section 4 there is some advice on applying sensitivity studies to complement the use of scenarios. Section 5 explains the installation of the SILMUSCEN program and Section 6 guides the user through some examples to illustrate how SILMUSCEN can be used. Section 7 offers some recommendations on which scenarios to adopt for different impact assessments. In order to ensure some compatibility between impact studies in SILMU, it is very important that the recommendations in this section are followed as far as possible. Section 8 addresses important omissions from the computer program and suggests procedures to adopt in their absence. Section 9 explores alternative methods of specifying the baseline climate, and shows how scenario adjustments to the baseline can be made. in Section 10, the stochastic weather generator, CLIGEN, is described and its use illustrated by means of examples. Finally, possible refinements of the programs are outlined in Section 11, along with contact names and addresses for obtaining further information. (36 refs.)

  16. Poster: the macaque genome.

    Science.gov (United States)

    2007-04-13

    The rhesus macaque (Macaca mulatta) facilitates an extraordinary range of biomedical and basic research, and the publication of the genome only makes it a more powerful model for studies of human disease; moreover, the macaque's position relative to humans and chimpanzees affords the opportunity to learn about the processes that have shaped the last 25 million years of primate evolution. To allow users to explore these themes of the macaque genome, Science has created a special interactive version of the poster published in the print edition of the 13 April 2007 issue. The interactive version includes additional text and exploration, as well as embedded video featuring seven scientists discussing the importance of the macaque and its genome sequence in studies of biomedicine and evolution. We have also created an accompanying teaching resource, including a lesson plan aimed at teachers of advanced high school life science students, for exploring what a comparison of the macaque and human genomes can tell us about human biology and evolution. These items are free to all site visitors.

  17. Metadata: A user`s view

    Energy Technology Data Exchange (ETDEWEB)

    Bretherton, F.P. [Univ. of Wisconsin, Madison, WI (United States); Singley, P.T. [Oak Ridge National Lab., TN (United States)

    1994-12-31

    An analysis is presented of the uses of metadata from four aspects of database operations: (1) search, query, retrieval, (2) ingest, quality control, processing, (3) application to application transfer; (4) storage, archive. Typical degrees of database functionality ranging from simple file retrieval to interdisciplinary global query with metadatabase-user dialog and involving many distributed autonomous databases, are ranked in approximate order of increasing sophistication of the required knowledge representation. An architecture is outlined for implementing such functionality in many different disciplinary domains utilizing a variety of off the shelf database management subsystems and processor software, each specialized to a different abstract data model.

  18. Hanford inventory program user`s manual

    Energy Technology Data Exchange (ETDEWEB)

    Hinkelman, K.C.

    1994-09-12

    Provides users with instructions and information about accessing and operating the Hanford Inventory Program (HIP) system. The Hanford Inventory Program is an integrated control system that provides a single source for the management and control of equipment, parts, and material warehoused by Westinghouse Hanford Company in various site-wide locations. The inventory is comprised of spare parts and equipment, shop stock, special tools, essential materials, and convenience storage items. The HIP replaced the following systems; ACA, ASP, PICS, FSP, WSR, STP, and RBO. In addition, HIP manages the catalog maintenance function for the General Supplies inventory stocked in the 1164 building and managed by WIMS.

  19. Cancer Genome Anatomy Project | Office of Cancer Genomics

    Science.gov (United States)

    The National Cancer Institute (NCI) Cancer Genome Anatomy Project (CGAP) is an online resource designed to provide the research community access to biological tissue characterization data. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov.

  20. Small-Scale Bioenergy Alternatives for Industry, Farm, and Institutions : A User`s Perspective.

    Energy Technology Data Exchange (ETDEWEB)

    Folk, Richard [ed.] [Idaho Univ., Moscow, ID (United States). Dept. of Forest Products

    1991-12-31

    This report presents research on biomass as an energy source. Topics include: bioenergy development and application; bioenergy combustion technology; and bioenergy from agricultural, forest, and urban resources. There are a total of 57 individual reports included. Individual reports are processed separately for the databases.

  1. CyanoBase: the cyanobacteria genome database update 2010.

    Science.gov (United States)

    Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

    2010-01-01

    CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

  2. StellaBase: The Nematostella vectensis Genomics Database

    OpenAIRE

    James C Sullivan; Ryan, Joseph F; Watson, James A.; Webb, Jeramy; Mullikin, James C; Rokhsar, Daniel; Finnerty, John R

    2005-01-01

    StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model organism that has already proven useful for addressing fundamental questions in developmental evolution and evolutionary genomics. StellaBase allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions...

  3. Building International Genomics Collaboration for Global Health Security.

    Science.gov (United States)

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

    2015-01-01

    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.

  4. Building International Genomics Collaboration for Global Health Security

    Directory of Open Access Journals (Sweden)

    Helen H Cui

    2015-12-01

    Full Text Available 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.

  5. Defense Institution Building in Africa: An Assessment

    Science.gov (United States)

    2016-01-01

    demo- cratically responsible defence institutions.”1 NATO, until recently, was the main user of the term. As a result, most of the literature on DIB...respecting good governance; abiding by the princi- ples of gender equality and women’s empowerment ; and ensuring coor- dination of SSR assistance.21 Other key

  6. Genomics: Implementatie, toepassing en toekomst

    NARCIS (Netherlands)

    Pennings JLA; Hoebee B; TOX

    2007-01-01

    Genomics - the large scale analysis of hereditary information encoded in the DNA - has been implemented at the National Institute for Public Health and the Environment (RIVM) in the Netherlands. In the near future other large-scale technologies will become important for the RIVM, including proteomic

  7. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  8. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  9. Electronic Library of Embrapa Cerrados: user study

    Directory of Open Access Journals (Sweden)

    Maria Elisabeth Salviati

    2015-09-01

    Full Text Available Introduction: This paper presents the results of research conducted with Electronic Library users – website, created in 2004 by Embrapa Cerrados, that organizes, stores, and provides full text of the technical scientific production published by the Institution. Objective: To explore the user profile and to make an accurate assessment of the website. Methodology: Data collection of demographic aspects; habits; and search features: navigation, loading time of pages, help, layout and terminology by an online survey. Analysis by SPSS software - Statistical Package for the Social Sciences. Results: The main users are students and agronomists, young people up to 30 years old, coming from the Federal District, belonging to universities and high schools wishing to update knowledge. After, appear the users of public agencies; private companies; Embrapa; agribusiness; federal government; schools; associations and non-governmental organizations; rural extension; cooperatives and syndicates. These users have no difficulties to use the service. Conclusions: The service works well, but some suggestions are useful to improve it. In addition, little demand coming from farms, ranches, rural extension services, cooperatives and syndicates indicates the need to design new products and services oriented to such public.

  10. Fueling Future with Algal Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-07-05

    Algae constitute a major component of fundamental eukaryotic diversity, 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 algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils of secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.

  11. [Dialogical leadership in hospitals institutions].

    Science.gov (United States)

    Amestoy, Simone Coelho; Trindade, Letícia de Lima; Waterkemper, Roberta; Heidman, Ivonete Teresinha Schülter; Boehs, Astrid Egged; Backes, Vânia Marli Schubert

    2010-01-01

    The aim of this study is make a theorical-reflection about the importance of using dialogical leadership in hospital institutions through Freirean referencial. The dialogical leadership pattern differs from the coercive and autocratic methods, for being reasoned on the establishment of an efficient communicational process, able to stimulate autonomy, co-responsibility and appreciation of each member from nurse team. The dialogical leadership, unlike the directive one, is a management instrument, that pursuits to minimize the conflicts and stimulate the formation of healthy interpersonal relationships, which can contribute to the improvement of organizational atmosphere and quality care provided to health services users.

  12. Evaluating User Participation and User Influence in an Enterprise System

    Science.gov (United States)

    Gibbs, Martin D.

    2010-01-01

    Does user influence have an impact on the data quality of an information systems development project? What decision making should users have? How can users effectively be engaged in the process? What is success? User participation is considered to be a critical success factor for Enterprise Resource Planning (ERP) projects, yet there is little…

  13. Evaluating User Participation and User Influence in an Enterprise System

    Science.gov (United States)

    Gibbs, Martin D.

    2010-01-01

    Does user influence have an impact on the data quality of an information systems development project? What decision making should users have? How can users effectively be engaged in the process? What is success? User participation is considered to be a critical success factor for Enterprise Resource Planning (ERP) projects, yet there is little…

  14. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    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

  15. Institutions, Institutional Change, Language, and Searle

    NARCIS (Netherlands)

    W.A. Dolfsma (Wilfred); R. McMaster; J. Finch

    2005-01-01

    textabstractThis paper endeavours to contribute to the growing institutionalist literature on the conception of the institution. We draw from John Davis’ (2003) analysis of the individual in posing the questions: what differentiates institutions, and how can changing institutions be identified thro

  16. The UCSC Cancer Genomics Browser: update 2013.

    Science.gov (United States)

    Goldman, Mary; Craft, Brian; Swatloski, Teresa; Ellrott, Kyle; Cline, Melissa; Diekhans, Mark; Ma, Singer; Wilks, Chris; Stuart, Josh; Haussler, David; Zhu, Jingchun

    2013-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information. The browser provides whole-genome to base-pair level views of several different types of genomics data, including some next-generation sequencing platforms. The ability to view multiple datasets together allows users to make comparisons across different data and cancer types. Biological pathways, collections of genes, genomic or clinical information can be used to sort, aggregate and zoom into a group of samples. We currently display an expanding set of data from various sources, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and Stand Up To Cancer. New features include a completely redesigned user interface with an interactive tutorial and updated documentation. We have also added data downloads, additional clinical heatmap features, and an updated Tumor Image Browser based on Google Maps. New security features allow authenticated users access to private datasets hosted by several different consortia through the public website.

  17. Skittle: A 2-Dimensional Genome Visualization Tool

    Directory of Open Access Journals (Sweden)

    Sanford John C

    2009-12-01

    Full Text Available Abstract Background It is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information - regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled Skittle. Results This program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a "repeat map" which comprehensively displays all local repeating units, based upon analysis of all possible local alignments. Skittle includes a smooth-zooming interface which allows the user to analyze genomic patterns at any scale. Skittle is especially useful in identifying and analyzing tandem repeats, including repeats not normally detectable by other methods. However, Skittle is also more generally useful for analysis of any genomic data, allowing users to correlate published annotations and observable visual patterns, and allowing for sequence and construct quality control. Conclusions Preliminary observations using Skittle reveal intriguing genomic patterns not otherwise obvious, including structured variations inside tandem repeats. The striking visual patterns revealed by Skittle appear to be useful for hypothesis development, and have already led the authors to theorize that imperfect tandem repeats could act as information carriers, and may form tertiary structures within the interphase nucleus.

  18. GRSAC Users Manual

    Energy Technology Data Exchange (ETDEWEB)

    Ball, S.J.; Nypaver, D.J.

    1999-02-01

    An interactive workstation-based simulation code (GRSAC) for studying postulated severe accidents in gas-cooled reactors has been developed to accommodate user-generated input with ''smart front-end'' checking. Code features includes on- and off-line plotting, on-line help and documentation, and an automated sensitivity study option. The code and its predecessors have been validated using comparisons with a variety of experimental data and similar codes. GRSAC model features include a three-dimensional representation of the core thermal hydraulics, and optional ATWS (anticipated transients without scram) capabilities. The user manual includes a detailed description of the code features, and includes four case studies which guide the user through four different examples of the major uses of GRSAC: an accident case; an initial conditions setup and run; a sensitivity study; and the setup of a new reactor model.

  19. Engaging with users

    DEFF Research Database (Denmark)

    Riisberg, Vibeke; Bang, Anne Louise

    to change the education of future designers. This is an emerging field at a number of design schools across the world, among these Design School Kolding in Denmark. In this paper we discuss ways in which we as design educators can teach fashion and textile students ways to engage with users during...... the creative process. To a large degree it is not common to engage direct with users in fashion and textile design. However, we see an increasing interest in this subject among the design students and also in recent research within fashion and textiles. We therefore argue that there is a need for participatory...... with the biggest sense organ – our skin. Thus, the aim of our research is to develop new dialogue tools for teaching fashion and textile students in order to stimulate new ways of thinking and engaging with users. By developing and employing participatory design methods in the field of fashion and textiles, we...

  20. End User Evaluations

    Science.gov (United States)

    Jay, Caroline; Lunn, Darren; Michailidou, Eleni

    As new technologies emerge, and Web sites become increasingly sophisticated, ensuring they remain accessible to disabled and small-screen users is a major challenge. While guidelines and automated evaluation tools are useful for informing some aspects of Web site design, numerous studies have demonstrated that they provide no guarantee that the site is genuinely accessible. The only reliable way to evaluate the accessibility of a site is to study the intended users interacting with it. This chapter outlines the processes that can be used throughout the design life cycle to ensure Web accessibility, describing their strengths and weaknesses, and discussing the practical and ethical considerations that they entail. The chapter also considers an important emerging trend in user evaluations: combining data from studies of “standard” Web use with data describing existing accessibility issues, to drive accessibility solutions forward.

  1. Water Institutions and Management in Cape Verde

    Directory of Open Access Journals (Sweden)

    Miguel Suarez Bosa

    2015-05-01

    Full Text Available The water-management model used in Cape Verde for irrigation water is a singular one involving both public and private institutions. The institutional framework adopted since independence (1975 includes influences of both Portuguese colonial occupation and African culture. Water is a common-pool resource, which can take the form of communal, private or state property, or not be subject to any form of ownership. Thus, this case study enables us to compare theories about managing. From a neo-liberal point of view, the common administration of resources of this kind is inefficient, but for one school of the institutional theory, solutions can come “from within”; in other words, from user groups themselves, who can co-operate, once they have defined commitments. Research based on surveys and interviews with private sector administrators leads to the conclusion that user association management is successful, whereas, individual management can lead to squandering.

  2. 77 FR 6812 - National Institute of Nursing Research; Notice of Closed Meeting

    Science.gov (United States)

    2012-02-09

    ... HUMAN SERVICES National Institutes of Health National Institute of Nursing Research; Notice of Closed... of Committee: National Institute of Nursing Research Special Emphasis Panel Genomic Advances to Wound...: Tamizchelvi Thyagarajan, Ph.D., Scientific Review Officer, National Institute of Nursing Research,...

  3. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  4. GLAST User Support

    Science.gov (United States)

    Band, David L.; Science Support Center, GLAST

    2006-12-01

    The Gamma-ray Large Area Space Telescope (GLAST) mission will provide the user community with many scientific opportunities. The mission's interface with the user community is the GLAST Science Support Center (GSSC). Yearly guest investigator (GI) cycles will support research related to GLAST. After the first year GIs may propose pointed observations; however, as a consequence of the large field-of-view of GLAST's instruments, pointed observations will rarely have an advantage over the default survey mode. Data, analysis software and documentation will be provided through the GSSC website (http://glast.gsfc.nasa.gov/ssc/); the website also includes a library of scientific results, and a helpdesk.

  5. User Centered Design

    DEFF Research Database (Denmark)

    Egbert, Maria; Matthews, Ben

    2012-01-01

    The interdisciplinary approach of User Centered Design is presented here with a focus on innovation in the design and use of hearing technologies as well as on the potential of innovation in interaction. This approach is geared towards developing new products, systems, technologies and practices...... based on an understanding of why so few persons with hearing loss use the highly advanced hearing technologies. In integrating Conversation Analysis (“CA”), audiology and User Centered Design, three disciplines which are collaborating together for the first time, we are addressing the following...

  6. EPRINT ARCHIVE USER SURVEY

    CERN Multimedia

    2001-01-01

    University of Southampton invites the CERN community to participate in a survey Professor Stevan Harnad is conducting on current users and non-users of Eprint Archives. http://www.eprints.org/survey/ The findings will be used to suggest potential enhancements of the services as well as to get a deeper understanding of the very rapid developments in the on-line dissemination and use of scientific and scholarly research. (The survey is anonymous. Revealing your identity is optional and it will be kept confidential.)

  7. RADTRAN 5 user guide.

    Energy Technology Data Exchange (ETDEWEB)

    Kanipe, Frances L.; Neuhauser, Karen Sieglinde

    2003-07-01

    This User Guide for the RADTRAN 5 computer code for transportation risk analysis describes basic risk concepts and provides the user with step-by-step directions for creating input files by means of either the RADDOG input file generator software or a text editor. It also contains information on how to interpret RADTRAN 5 output, how to obtain and use several types of important input data, and how to select appropriate analysis methods. Appendices include a glossary of terms, a listing of error messages, data-plotting information, images of RADDOG screens, and a table of all data in the internal radionuclide library.

  8. TRANS-USERS

    DEFF Research Database (Denmark)

    to redesign production and business processes to accommodate for users' requirements (Maisons MACCHI), and the client as driver of innovation on the construction and renovation of the low budget hotel brand Formule 1 of ACCOR Hotels. In the third part, the discussion and conclusion addresses three interlinked...... in Denmark, Sweden and France. The five case studies are: The industrialised home building concept BoKlok, a web based product configurator for kitchens by HTH, the innovative potential of the dual role of employees as both user and employee in Rockwool, the application of quality management systems...

  9. The OSIRIS user guide

    CERN Document Server

    Telling, M T F

    2003-01-01

    This user guide contains all the information necessary to perform a successful neutron scattering experiment on the OSIRIS spectrometer at ISIS, RAL, UK. Since OSIRIS is a continually evolving and improving instrument some information contained within this manual may become redundant. However, the basic instrument operating procedures should remain essentially unchanged. While updated manuals will be produced when appropriate, the most comprehensive source of information concerning OSIRIS is the Instrument Scientist/Local Contact. It would be appreciated, however, if this user guide were the first point of call should problems arise

  10. TIA Software User's Manual

    Science.gov (United States)

    Cramer, K. Elliott; Syed, Hazari I.

    1995-01-01

    This user's manual describes the installation and operation of TIA, the Thermal-Imaging acquisition and processing Application, developed by the Nondestructive Evaluation Sciences Branch at NASA Langley Research Center, Hampton, Virginia. TIA is a user friendly graphical interface application for the Macintosh 2 and higher series computers. The software has been developed to interface with the Perceptics/Westinghouse Pixelpipe(TM) and PixelStore(TM) NuBus cards and the GW Instruments MacADIOS(TM) input-output (I/O) card for the Macintosh for imaging thermal data. The software is also capable of performing generic image-processing functions.

  11. "Playing" with our users

    DEFF Research Database (Denmark)

    Brooks, Anthony Lewis

    2014-01-01

    . Unfortunately if donated in the school they are rarely being used by the students. In the case of virtual reality or artistic installations it is extremely difficult to provide such equipment to users. Last but not least we are not sure how the software will be used and if the experience will continue...... after the conduct of the research. If not due to restrictions, user should at least continue to be part of the research’s debrief and next steps. While I was in Nottingham I realised that sometimes our research, our playful educational experience, our DIY VR helmet, our beta, glitchy, research-only game...

  12. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

    Science.gov (United States)

    Smith, David Roy

    2016-06-23

    Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal.

  13. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  14. Perspectives on User Satisfaction Surveys.

    Science.gov (United States)

    Cullen, Rowena

    2001-01-01

    Discusses academic libraries, digital environments, increasing competition, the relationship between service quality and user satisfaction, and user surveys. Describes the SERVQUAL model that measures service quality and user satisfaction in academic libraries; considers gaps between user expectations and managers' perceptions of user…

  15. Personal lifelong user model clouds

    DEFF Research Database (Denmark)

    Dolog, Peter; Kay, Judy; Kummerfeld, Bob

    This paper explores an architecture for very long term user modelling, based upon personal user model clouds. These ensure that the individual's applications can access their model whenever it is needed. At the same time, the user can control the use of their user model. So, they can ensure...

  16. Bacterial genome reengineering.

    Science.gov (United States)

    Zhou, Jindan; Rudd, Kenneth E

    2011-01-01

    The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer design tool with a model organism database increases the level of quality control. Computer-assisted design of gene primer pairs relies upon having highly accurate genomic DNA sequence information that exactly matches the DNA of the cells being used in the laboratory to ensure predictable DNA hybridizations. It is equally crucial to have confidence that the predicted start codons define the locations of genes accurately. Annotations in the EcoGene database are queried by PrimerPair to eliminate pseudogenes, IS elements, and other problematic genes before the design process starts. These projects progressively familiarize users with the EcoGene content, scope, and application interfaces that are useful for genome reengineering projects. The first protocol leads to the design of a pair of primer sequences that were used to clone and express a single gene. The N-terminal protein sequence was experimentally verified and the protein was detected in the periplasm. This is followed by instructions to design PCR primer pairs for cloning gene fragments encoding 50 periplasmic proteins without their signal peptides. The design process begins with the user simply designating one pair of forward and reverse primer endpoint positions relative to all start and stop codon positions. The gene name, genomic coordinates, and primer DNA sequences are reported to the user. When making chromosomal deletions, the integrity of the provisional primer design is checked to see whether it will generate any unwanted double deletions with adjacent genes. The bad designs are recalculated and replacement primers are provided alongside the

  17. Identity of Institution and Institutional Design

    Directory of Open Access Journals (Sweden)

    F. Bahar Ülker Kaya

    2006-05-01

    Full Text Available Corporate identity is planning and reşecting memorable, personal, characteristic pecularities of an institution and the ability that separates it from others. Corporate identity is in interaction with the corporate culture and corporate image. It is an entity formed by the philosophy of the institution, institutional communication, behavior and planning. Institutional planning formed by the planning of production and communication and architectural/ interior architectural planning, is the most significant element that constitutes the visual identity of an institution. While forming architectural and interior architectural planning of institutions, establishing places that will clearly reşect the corporate identity is gaining importance. In the perception of visual identity of institutions, planning elements such as; colour, texture, material and form are more significant than others.

  18. The YH database: the first Asian diploid genome database

    DEFF Research Database (Denmark)

    Li, Guoqing; Ma, Lijia; Song, Chao

    2009-01-01

    The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse......, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView. The relationships between phenotype and genotype can be searched by location, dbSNP ID, HGMD ID, gene symbol and disease name. A BLAST web service is also provided for the purpose of aligning query sequence against YH...... genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org.cn....

  19. The YH database: the first Asian diploid genome database.

    Science.gov (United States)

    Li, Guoqing; Ma, Lijia; Song, Chao; Yang, Zhentao; Wang, Xiulan; Huang, Hui; Li, Yingrui; Li, Ruiqiang; Zhang, Xiuqing; Yang, Huanming; Wang, Jian; Wang, Jun

    2009-01-01

    The YH database is a server that allows the user to easily browse and download data from the first Asian diploid genome. The aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data. Powered by GBrowse, we illustrate here the genome sequences, SNPs, and sequencing reads in the MapView. The relationships between phenotype and genotype can be searched by location, dbSNP ID, HGMD ID, gene symbol and disease name. A BLAST web service is also provided for the purpose of aligning query sequence against YH genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org.cn.

  20. GIPSy: Genomic island prediction software.

    Science.gov (United States)

    Soares, Siomar C; Geyik, Hakan; Ramos, Rommel T J; de Sá, Pablo H C G; Barbosa, Eudes G V; Baumbach, Jan; Figueiredo, Henrique C P; Miyoshi, Anderson; Tauch, Andreas; Silva, Artur; Azevedo, Vasco

    2016-08-20

    Bacteria are highly diverse organisms that are able to adapt to a broad range of environments and hosts due to their high genomic plasticity. Horizontal gene transfer plays a pivotal role in this genome plasticity and in evolution by leaps through the incorporation of large blocks of genome sequences, ordinarily known as genomic islands (GEIs). GEIs may harbor genes encoding virulence, metabolism, antibiotic resistance and symbiosis-related functions, namely pathogenicity islands (PAIs), metabolic islands (MIs), resistance islands (RIs) and symbiotic islands (SIs). Although many software for the prediction of GEIs exist, they only focus on PAI prediction and present other limitations, such as complicated installation and inconvenient user interfaces. Here, we present GIPSy, the genomic island prediction software, a standalone and user-friendly software for the prediction of GEIs, built on our previously developed pathogenicity island prediction software (PIPS). We also present four application cases in which we crosslink data from literature to PAIs, MIs, RIs and SIs predicted by GIPSy. Briefly, GIPSy correctly predicted the following previously described GEIs: 13 PAIs larger than 30kb in Escherichia coli CFT073; 1 MI for Burkholderia pseudomallei K96243, which seems to be a miscellaneous island; 1 RI of Acinetobacter baumannii AYE, named AbaR1; and, 1 SI of Mesorhizobium loti MAFF303099 presenting a mosaic structure. GIPSy is the first life-style-specific genomic island prediction software to perform analyses of PAIs, MIs, RIs and SIs, opening a door for a better understanding of bacterial genome plasticity and the adaptation to new traits.

  1. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  2. BrucellaBase: Genome information resource.

    Science.gov (United States)

    Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Khader, L K M Abdul; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2016-09-01

    Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html.

  3. Patient-professional interactions in mental health institutions in Denmark

    DEFF Research Database (Denmark)

    Ringer, Agnes

    by discursive and narrative approaches, the aim of the study is to shed light on how the professionals and users construct patient identities. How are the users and the professionals positioned in their interactions? How are concepts such as psychiatric diagnosis and mental illness negotiated within...... the institution? How are possibilities for participation and service user involvement negotiated? Finally, the study wishes to understand what the encounters with the professionals and the practices of the institution may mean for the users’ self-understandings and subjectivity....

  4. OASIS User Manual

    CERN Document Server

    Bojtar, L

    2009-01-01

    The OASIS system has been operational for years now. After a long development the project has reached a state where the number of features it provides exceeds largely what most of its users knows about. The author felt it was time to write a user manual explaining all the functionality of the viewer application. This document is a user manual, concentrating on the functionality of the viewer from the user’s point of view. There are already documents available on the project’s web site about the technical aspects at http://project-oasis.web.cern.ch/project-oasis/presentations.htm . There was an attempt to produce a tutorial on the viewer, but it didn’t get much further than the table of contents, that however is well thought. The structure of this user manual follows the same principle, the basic and most often used features are grouped together. Advanced or less often used features are described in a separate chapter. There is a second organizational principle, features belong to different levels: chann...

  5. Users Office - Removal

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    As of 8 December 2010 and until the end of February 2011, the Users Office will move from Bldg. 60. New Location : Bldg. 510-R-033 Opening Hours: Monday, Tuesday, Thursday, Friday : 08.30 – 12.30 Monday to Friday: 14.00 – 16.00 Closed Wednesday mornings.

  6. Educating the Music User

    Science.gov (United States)

    Adams, Mark C.

    2016-01-01

    To better serve students' evolving needs in music, music educators must connect classroom learning with how students use and interact with music in their daily lives. One way to accomplish this is by approaching classrooms with the music user in mind, which can open new possibilities for meaningful music making and remove students from the…

  7. Power User Interface

    Science.gov (United States)

    Pfister, Robin; McMahon, Joe

    2006-01-01

    Power User Interface 5.0 (PUI) is a system of middleware, written for expert users in the Earth-science community, PUI enables expedited ordering of data granules on the basis of specific granule-identifying information that the users already know or can assemble. PUI also enables expert users to perform quick searches for orderablegranule information for use in preparing orders. PUI 5.0 is available in two versions (note: PUI 6.0 has command-line mode only): a Web-based application program and a UNIX command-line- mode client program. Both versions include modules that perform data-granule-ordering functions in conjunction with external systems. The Web-based version works with Earth Observing System Clearing House (ECHO) metadata catalog and order-entry services and with an open-source order-service broker server component, called the Mercury Shopping Cart, that is provided separately by Oak Ridge National Laboratory through the Department of Energy. The command-line version works with the ECHO metadata and order-entry process service. Both versions of PUI ultimately use ECHO to process an order to be sent to a data provider. Ordered data are provided through means outside the PUI software system.

  8. Educating the Music User

    Science.gov (United States)

    Adams, Mark C.

    2016-01-01

    To better serve students' evolving needs in music, music educators must connect classroom learning with how students use and interact with music in their daily lives. One way to accomplish this is by approaching classrooms with the music user in mind, which can open new possibilities for meaningful music making and remove students from the…

  9. TO STORES USERS

    CERN Multimedia

    SPL Division

    2001-01-01

    Stores users are informed that the Stores (Central, Emergency window, Raw materials, Chemical products and Prévessin Self service stores) will be closed on Friday, 7 December owing to migration of the Stores computers to Windows 2000. Thank you for your understanding.

  10. The User Interface.

    Science.gov (United States)

    Lindeman, Martha J.; And Others

    1989-01-01

    The first of three articles on the design of user interfaces for information retrieval systems discusses the need to examine types of display, prompting, and input as separate entities. The second examines the use of artificial intelligence in creating natural language interfaces, and the third outlines standards for case studies in human computer…

  11. Users, Bystanders and Agents

    DEFF Research Database (Denmark)

    Krummheuer, Antonia Lina

    2015-01-01

    Human-agent interaction (HAI), especially in the field of embodied conversational agents (ECA), is mainly construed as dyadic communication between a human user and a virtual agent. This is despite the fact that many application scenarios for future ECAs involve the presence of others. This paper...

  12. Museums and cultural institutions as spaces for Cultural Citizenship

    DEFF Research Database (Denmark)

    Bernhardt, Nana; Sattrup, Lise

    2014-01-01

    How can museums and cultural institutions make a stronger impact as democratic educational institutions; as places where knowledge is not just something that is presented and put at the disposal of visitors, but actually created through interaction between museums and users? How can active partic...

  13. Usability Testing of User Manuals

    DEFF Research Database (Denmark)

    Møller, Margrethe H.

    2013-01-01

    Many guidelines and several standards exist for the development of good user manuals. But even though technical writers comply with all guidelines, problems will typically arise when users apply the manual in practice. Therefore, it is useful to have real users test the manual before it is publis...... it is published. This article discusses user tests in the form of think-aloud tests, with examples from the research project ”User Manuals for older adults"....

  14. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  15. SHARP User Manual

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Y. Q. [Argonne National Lab. (ANL), Argonne, IL (United States); Shemon, E. R. [Argonne National Lab. (ANL), Argonne, IL (United States); Thomas, J. W. [Argonne National Lab. (ANL), Argonne, IL (United States); Mahadevan, Vijay S. [Argonne National Lab. (ANL), Argonne, IL (United States); Rahaman, Ronald O. [Argonne National Lab. (ANL), Argonne, IL (United States); Solberg, Jerome [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-03-31

    SHARP is an advanced modeling and simulation toolkit for the analysis of nuclear reactors. It is comprised of several components including physical modeling tools, tools to integrate the physics codes for multi-physics analyses, and a set of tools to couple the codes within the MOAB framework. Physics modules currently include the neutronics code PROTEUS, the thermal-hydraulics code Nek5000, and the structural mechanics code Diablo. This manual focuses on performing multi-physics calculations with the SHARP ToolKit. Manuals for the three individual physics modules are available with the SHARP distribution to help the user to either carry out the primary multi-physics calculation with basic knowledge or perform further advanced development with in-depth knowledge of these codes. This manual provides step-by-step instructions on employing SHARP, including how to download and install the code, how to build the drivers for a test case, how to perform a calculation and how to visualize the results. Since SHARP has some specific library and environment dependencies, it is highly recommended that the user read this manual prior to installing SHARP. Verification tests cases are included to check proper installation of each module. It is suggested that the new user should first follow the step-by-step instructions provided for a test problem in this manual to understand the basic procedure of using SHARP before using SHARP for his/her own analysis. Both reference output and scripts are provided along with the test cases in order to verify correct installation and execution of the SHARP package. At the end of this manual, detailed instructions are provided on how to create a new test case so that user can perform novel multi-physics calculations with SHARP. Frequently asked questions are listed at the end of this manual to help the user to troubleshoot issues.

  16. GenomePixelizer--a visualization program for comparative genomics within and between species.

    Science.gov (United States)

    Kozik, A; Kochetkova, E; Michelmore, R

    2002-02-01

    GenomePixelizer is a visualization tool that generates custom images of the physical or genetic positions of specified sets of genes in whole genomes or parts of genomes. Multiple sets of genes can be shown simultaneously with user-defined characteristics displayed. It allows the analysis of duplication events within and between species based on sequence similarities. The program is written in Tcl/Tk and works on any platform that supports the Tcl/Tk toolkit. GenomePixelizer generates HTML ImageMap tags for each gene in the image allowing links to databases. Images can be saved and presented on web pages.

  17. Observing the user experience a practitioner's guide to user research

    CERN Document Server

    Kuniavsky, Mike; Goodman, Elizabeth

    2012-01-01

    The gap between who designers and developers imagine their users are, and who those users really are can be the biggest problem with product development. Observing the User Experience will help you bridge that gap to understand what your users want and need from your product, and whether they'll be able to use what you've created. Filled with real-world experience and a wealth of practical information, this book presents a complete toolbox of techniques to help designers and developers see through the eyes of their users. It provides in-depth coverage of 13 user experience research techniques

  18. What are Institutional Logics

    DEFF Research Database (Denmark)

    Berg Johansen, Christina; Waldorff, Susanne Boch

    This study presents new insights into the explanatory power of the institutional logics perspective. With outset in a discussion of seminal theory texts, we identify two fundamental topics that frame institutional logics: overarching institutional orders guides by institutional logics, as well...

  19. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  20. IT User Community Survey

    CERN Document Server

    Peter Jones (IT-CDA-WF)

    2016-01-01

    IT-CDA is gathering information to more accurately form a snapshot of the CERN IT user community and we would appreciate you taking time to complete the following survey.   We want to use this survey to better understand how the user community uses their devices and our services, and how the delivery of those services could be improved. You will need to authenticate to complete the survey. However please note that your responses are confidential and will be compiled together and analysed as a group. You can also volunteer to offer additional information if you so wish. This survey should take no longer than 5 minutes. Thanks in advance for your collaboration.

  1. Trilinos users guide.

    Energy Technology Data Exchange (ETDEWEB)

    Willenbring, James M.; Heroux, Michael Allen

    2003-08-01

    The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries. A new software capability is introduced into Trilinos as a package. A Trilinos package is an integral unit usually developed by a small team of experts in a particular algorithms area such as algebraic preconditioners, nonlinear solvers, etc. The Trilinos Users Guide is a resource for new and existing Trilinos users. Topics covered include how to configure and build Trilinos, what is required to integrate an existing package into Trilinos and examples of how those requirements can be met, as well as what tools and services are available to Trilinos packages. Also discussed are some common practices that are followed by many Trilinos package developers. Finally, a snapshot of current Trilinos packages and their interoperability status is provided, along with a list of supported computer platforms.

  2. Portraying User Interface History

    DEFF Research Database (Denmark)

    Jørgensen, Anker Helms

    2008-01-01

    in that they largely address prevailing UI techno­logies, and thirdly history from above in that they focus on the great deeds of the visionaries. The paper then compares this state-of-art in UI history to the much more mature fields history of computing and history of technology. Based hereon, some speculations......The user interface is coming of age. Papers adressing UI history have appeared in fair amounts in the last 25 years. Most of them address particular aspects such as an in­novative interface paradigm or the contribution of a visionary or a research lab. Contrasting this, papers addres­sing UI...... history at large have been sparse. However, a small spate of publications appeared recently, so a reasonable number of papers are available. Hence this work-in-progress paints a portrait of the current history of user interfaces at large. The paper first describes a theoretical framework recruited from...

  3. Information for stores users

    CERN Multimedia

    Logistics Group - FI Department

    2005-01-01

    The Farnell catalogue can now be accessed from the Material Request form on EDH in addition to the CERN Stores catalogue. Users can order Farnell equipment as well as standard Stores equipment at the same time using a single document, the EDH Materials Request form. The Materials Request form offers users items from both the internal 'Stores' catalogue and the external 'Farnell' catalogue, all of which may be ordered on the same form. The system automatically forwards orders for standard Stores equipment to the CERN Stores and those for Farnell equipment to Farnell. The delivery time is 48 hours in both cases. Requests for materials are routed for approval in accordance with the standard EDH routing procedures. Logistics Group FI Department

  4. Information for stores users

    CERN Multimedia

    2005-01-01

    The Farnell catalogue can now be accessed from the Material Request form on EDH in addition to the CERN Stores catalogue. Users can order Farnell equipment as well as standard Stores equipment at the same time using a single document, the EDH Materials Request form. The Materials Request form offers users items from both the internal 'Stores' catalogue and the external 'Farnell' catalogue, all of which may be ordered on the same form. The system automatically forwards orders for standard Stores equipment to the CERN Stores and those for Farnell equipment to Farnell. The delivery time is 48 hours in both cases. Requests for materials are routed for approval in accordance with the standard EDH routing procedures. Logistics Group FI Department

  5. Internet user behaviour

    Directory of Open Access Journals (Sweden)

    Radbâță, A.

    2011-01-01

    Full Text Available Internet is a useful tool for everybody in a technologically advanced world. As Internet appears and develops, it creates a totally new network environment. The development of commerce on the Internet based on virtual communities has become one of the most successful business models in the world. After analyzing the concept of internet, the e-commerce market and its marketing mix and the benefits and limitations of the Internet, we have presented a few studies on Internet user behaviour. Furthermore, the paper looks at a representative sample of Romanian internet users. The results reveal that the Romanians are using the Internet especially for information gathering, e-mail, entertainment and social networking.

  6. Outside users payload model

    Science.gov (United States)

    1985-01-01

    The outside users payload model which is a continuation of documents and replaces and supersedes the July 1984 edition is presented. The time period covered by this model is 1985 through 2000. The following sections are included: (1) definition of the scope of the model; (2) discussion of the methodology used; (3) overview of total demand; (4) summary of the estimated market segmentation by launch vehicle; (5) summary of the estimated market segmentation by user type; (6) details of the STS market forecast; (7) summary of transponder trends; (8) model overview by mission category; and (9) detailed mission models. All known non-NASA, non-DOD reimbursable payloads forecast to be flown by non-Soviet-block countries are included in this model with the exception of Spacelab payloads and small self contained payloads. Certain DOD-sponsored or cosponsored payloads are included if they are reimbursable launches.

  7. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

    Science.gov (United States)

    Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

    2016-01-01

    PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

  8. MP users guide

    CERN Document Server

    Brent, Richard P

    2010-01-01

    MP is a package of ANSI Standard Fortran (ANS X3.9-1966) subroutines for performing multiple-precision floating-point arithmetic and evaluating elementary and special functions. The subroutines are machine independent and the precision is arbitrary, subject to storage limitations. The User's Guide describes the routines and their calling sequences, example and test programs, use of the Augment precompiler, and gives installation instructions for the package.

  9. 16. ESRF users meeting

    Energy Technology Data Exchange (ETDEWEB)

    Coraux, J.; Renevier, H.; Favre-Nicolin, V.; Daudin, B.; Proietti, M.G.; Renaud, G.; Fowler, B.; Mercer, D.L.; Omar, A.H.; Thompson, P.; Markovic, N.M.; Stamenkovic, V.; Lucas, C.A.; Andrejczuk, A.; Kwiatkowska, J.; Dobrzynski, L.; Zukowski, E.; Bellin, Ch.; Loupias, G.; Shukla, A.; Buslaps, Th.; Stankov, S.; Sladecek, M.; Slezak, T.; Korecki, J.; Spiridis, N.; Sepiol, B.; Vogl, G.; Chumakov, A.; Ruffer, R.; Hermann, R.P.; Grandjean, F.; Schweika, W.; Long, G.J.; Leupold, O.; Belrhall, H.; Caserotto, H.; Dauvergne, F.; Geoffroy, L.; Guljarro, M.; Launer, L.; Levault, B.; Walsh, M.; Beckers, M.; Schell, N.; Martins, R.M.S.; Mucklich, A.; Moller, W.; Silva, R.J.C.; Mahesh, K.K.; Braz Fernandes, F.M.; Tejas, Parikh; Neil, Fellows; Durodola, J.; Slawinski, W.; Przenioslo, R.; Sosnowska, I.; Suard, E

    2006-07-01

    This document gathers the posters that were presented during the poster session of this workshop. These posters highlight the results obtained by ESRF'users in different fields such as surface structure, Compton scattering studies, localized vibrational modes in thermoelectric materials, Ni-Ti thin films, residual stresses in superconducting wires, and changes in crystal and magnetic structure of NdFeO{sub 3}.

  10. Personal lifelong user model clouds

    DEFF Research Database (Denmark)

    Dolog, Peter; Kay, Judy; Kummerfeld, Bob

    This paper explores an architecture for very long term user modelling, based upon personal user model clouds. These ensure that the individual's applications can access their model whenever it is needed. At the same time, the user can control the use of their user model. So, they can ensure...... it is accessed only when and where they wish, by applications that they wish. We consider the challenges of representing user models so that they can be reused by multiple applications. We indicate potential synergies between distributed and centralised user modelling architectures, proposing an architecture...

  11. Institutional Logics in Action

    DEFF Research Database (Denmark)

    Lounsbury, Michael; Boxenbaum, Eva

    2013-01-01

    This double volume presents state-of-the-art research and thinking on the dynamics of actors and institutional logics. In the introduction, we briefly sketch the roots and branches of institutional logics scholarship before turning to the new buds of research on the topic of how actors engage ins...... prolific stream of research on institutional logics by deepening our insight into the active use of institutional logics in organizational action and interaction, including the institutional effects of such (inter)actions....

  12. Entrepreneurship as institutional change

    DEFF Research Database (Denmark)

    Bjerregaard, Toke; Lauring, Jakob

    2012-01-01

    between and exploit the multiple, potentially contradictory institutional logics of the different spheres in which they operate. While much research has elucidated how institutional entrepreneurs effect change, this study illustrates how effective entrepreneurs managing and exploiting institutional...... contradictions engage simultaneously in practices of maintaining and changing institutions to establish a balance between the poles on which their ventures depend. We illustrate this by two cases of small-scale entrepreneurship bridging institutional contradictions from an ethnographic study conducted under...

  13. User Communities i Innovationsprocessen

    DEFF Research Database (Denmark)

    Brix, Jacob; Sejer Jakobsen, Henning; Jordansen, Inger

    to workshops uden fysisk tilstedeværelse af deltagerne med internettet som kommunikationskanal (online user communities via Skype & blogs). Empirien stammer fra BDI projektet Handivision1, hvor målgruppen og brugergruppen primært har været personer med fysiske funktionsnedsættelser. Vores analyse indikerer...... for at virke uvidende sammenlignet med andre meddeltagere. 3. At mødes fysisk under en innovationsworkshop har betydning for måden hvorpå deltagerne bliver inspireret af - og lærer af hinanden samt deres evnen til at blive konkrete 4. Online user communities, som styres af en konsulterende leder, resulterer i...... stor udstrækning i problemorienterede forslag og ideer, hvor dynamikken deltagerne imellem er svær at opretholde 5. Online user communities, der ikke styres eller ledes i processen, resulterer i større udstrækning end ved mere styrede forløb i problemerkendelse frem for forslag og ideer til nytænkning....

  14. Users in Persistant Action

    DEFF Research Database (Denmark)

    Christiansen, John K.; Gasparin, Marta; Varnes, Claus J.

    2012-01-01

    years before a 15 years-old- boy wanted the 1.5 litres back to the market, even though Coca-Cola resisted, he managed by the hybrid collective to struggle with Coca-Cola and convince them to re-introduce the 1.5 litres volume by various interessment devices, including buy-cot to frame the power relation......This study adds to the concept of lead users by investigating the role users´ post launch. The case of the 1.5 litre Urge bottle in Norway shows that what constitutes a ‘lead’ becomes an effect of the product displaced in a hybrid collective in time and space. The hybrid collective is an assumption...... in which realities are constructed in contrast to the assumption of diffusion in society, where reality is given and determined. The theory lead users is closely related to the product life cycle in the diffusion perspective, as they both progress linearly. The 1.5 litres was removed from the market 8...

  15. Genome Improvement at JGI-HAGSC

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. User interface inspection methods a user-centered design method

    CERN Document Server

    Wilson, Chauncey

    2014-01-01

    User Interface Inspection Methods succinctly covers five inspection methods: heuristic evaluation, perspective-based user interface inspection, cognitive walkthrough, pluralistic walkthrough, and formal usability inspections. Heuristic evaluation is perhaps the best-known inspection method, requiring a group of evaluators to review a product against a set of general principles. The perspective-based user interface inspection is based on the principle that different perspectives will find different problems in a user interface. In the related persona-based inspection, colleagues assume the

  17. Workflow User Interfaces Patterns

    Directory of Open Access Journals (Sweden)

    Jean Vanderdonckt

    2012-03-01

    Full Text Available Este trabajo presenta una colección de patrones de diseño de interfaces de usuario para sistemas de información para el flujo de trabajo; la colección incluye cuarenta y tres patrones clasificados en siete categorías identificados a partir de la lógica del ciclo de vida de la tarea sobre la base de la oferta y la asignación de tareas a los responsables de realizarlas (i. e. recursos humanos durante el flujo de trabajo. Cada patrón de la interfaz de usuario de flujo de trabajo (WUIP, por sus siglas en inglés se caracteriza por las propiedades expresadas en el lenguaje PLML para expresar patrones y complementado por otros atributos y modelos que se adjuntan a dicho modelo: la interfaz de usuario abstracta y el modelo de tareas correspondiente. Estos modelos se especifican en un lenguaje de descripción de interfaces de usuario. Todos los WUIPs se almacenan en una biblioteca y se pueden recuperar a través de un editor de flujo de trabajo que vincula a cada patrón de asignación de trabajo a su WUIP correspondiente.A collection of user interface design patterns for workflow information systems is presented that contains forty three resource patterns classified in seven categories. These categories and their corresponding patterns have been logically identified from the task life cycle based on offering and allocation operations. Each Workflow User Interface Pattern (WUIP is characterized by properties expressed in the PLML markup language for expressing patterns and augmented by additional attributes and models attached to the pattern: the abstract user interface and the corresponding task model. These models are specified in a User Interface Description Language. All WUIPs are stored in a library and can be retrieved within a workflow editor that links each workflow pattern to its corresponding WUIP, thus giving rise to a user interface for each workflow pattern.

  18. User constraints for reliable user-defined smart home scenarios

    DEFF Research Database (Denmark)

    Le Guilly, Thibaut; Nielsen, Michael Kvist; Pedersen, Thomas

    2016-01-01

    of constraints restricting the control commands that can be used inside user-defined scenarios. The system is based on timed automata model checking abstracted by event condition action rules. A prototype was implemented, including a user interface to interact with the user. The usability of the system...

  19. Adding and Removing Web Area Users, and Changing User Roles

    Science.gov (United States)

    Webmasters can add users to a web area, and assign or change roles, which define the actions a user is able to take in the web area. Non-webmasters must use a request form to add users and change roles.

  20. Solar energy storage researchers information user study

    Energy Technology Data Exchange (ETDEWEB)

    Belew, W.W.; Wood, B.L.; Marle, T.L.; Reinhardt, C.L.

    1981-03-01

    The results of a series of telephone interviews with groups of users of information on solar energy storage are described. In the current study only high-priority groups were examined. Results from 2 groups of researchers are analyzed: DOE-Funded Researchers and Non-DOE-Funded Researchers. The data will be used as input to the determination of information products and services the Solar Energy Research Institute, the Solar Energy Information Data Bank Network, and the entire information outreach community should be preparing and disseminating.

  1. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  2. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  3. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  4. Directory of computer users in nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, J.J.; Gurney, J.; McClain, W.J. (eds.)

    1979-09-01

    The Directory of Computer Users in Nuclear Medicine consists primarily of detailed descriptions and indexes to these descriptions. A typical Installation Description contains the name, address, type, and size of the institution and the names of persons within the institution who can be contacted for further information. If the department has access to a central computer facility for data analysis or timesharing, the type of equipment available and the method of access to that central computer is included. The dedicated data processing equipment used by the department in its nuclear medicine studies is described, including the peripherals, languages used, modes of data collection, and other pertinent information. Following the hardware descriptions are listed the types of studies for which the data processing equipment is used, including the language(s) used, the method of output, and an estimate of the frequency of the particular study. An Installation Index and an Organ Studies Index are also included. (PCS)

  5. Automatic annotation of organellar genomes with DOGMA

    Energy Technology Data Exchange (ETDEWEB)

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  6. Mapping the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles R.

    1989-06-01

    The following pages aim to lay a foundation for understanding the excitement surrounding the ''human genome project,'' as well as to convey a flavor of the ongoing efforts and plans at the Human Genome Center at the Lawrence Berkeley Laboratory. Our own work, of course, is only part of a broad international effort that will dramatically enhance our understanding of human molecular genetics before the end of this century. In this country, the bulk of the effort will be carried out under the auspices of the Department of Energy and the National Institutes of Health, but significant contributions have already been made both by nonprofit private foundations and by private corporation. The respective roles of the DOE and the NIH are being coordinated by an inter-agency committee, the aims of which are to emphasize the strengths of each agency, to facilitate cooperation, and to avoid unnecessary duplication of effort. The NIH, for example, will continue its crucial work in medical genetics and in mapping the genomes of nonhuman species. The DOE, on the other hand, has unique experience in managing large projects, and its national laboratories are repositories of expertise in physics, engineering, and computer science, as well as the life sciences. The tools and techniques the project will ultimately rely on are thus likely to be developed in multidisciplinary efforts at laboratories like LBL. Accordingly, we at LBL take great pride in this enterprise -- an enterprise that will eventually transform our understanding of ourselves.

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. User producer interaction in context

    NARCIS (Netherlands)

    Nahuis, R.; Moors, E.H.M.; Smits, R.E.H.M.

    2012-01-01

    User producer interaction (UPI) increases chances for successful innovations. It is not always clear, however, what type of interaction is necessary in a particular context. This article identifies seven different types of UPI: constructing linkages, broadening, characterizing users, upstream

  9. Accessible Capacity of Secondary Users

    CERN Document Server

    Ma, Xiao; Lin, Lei; Bai, Baoming

    2010-01-01

    A new problem formulation is presented for the Gaussian interference channels (GIFC) with two pairs of users, which are distinguished as primary users and secondary users, respectively. The primary users employ a pair of encoder and decoder that were originally designed to satisfy a given error performance requirement under the assumption that no interference exists from other users. In the case when the secondary users attempt to access the same medium, we are interested in the maximum transmission rate (defined as {\\em accessible capacity}) at which secondary users can communicate reliably without affecting the error performance requirement by the primary users under the constraint that the primary encoder (not the decoder) is kept unchanged. By modeling the primary encoder as a generalized trellis code (GTC), we are then able to treat the secondary link as a finite state channel (FSC). The relation of the accessible capacity to the capacity region of the GIFC is revealed. Upper and lower bounds on the acce...

  10. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  11. Missing Links--User Needs vs. Producers' Offerings.

    Science.gov (United States)

    Fahy, Sarah

    There are a variety of reasons which prevent users from making the most of information products. The practitioner must keep current with the myriad of information sources available and try to stay aware of changes in coverage. This paper categorizes the types of data in a large financial institution as follows: press sources, mergers and…

  12. User Control Problems and Taking User Empowerment Further

    Science.gov (United States)

    Rodrigues, Rowena

    User control in identity management is beset with a number of problems, as outlined in this paper. It is argued that akin to traditional contexts, greater user control will result in greater user liability, which is demonstrated with the help of digital and non-digital examples. In this context, there is a critical need for greater user empowerment. This could be achieved in two ways-first, facilitating user awareness of identity management technologies, their scope and effects and second, through the implementation of proposed control-liability notices.

  13. User Behaviours Associated with Password Security and Management

    Directory of Open Access Journals (Sweden)

    Kay Bryant

    2006-11-01

    Full Text Available Control mechanisms established on the boundary of an information system are an important preliminary step to minimising losses from security breaches. The primary function of such controls is to restrict the use of information systems and resources to authorized users. Password-based systems remain the predominant method of user authentication despite the many sophisticated and viable security alternatives that have emerged from research and development. However, the literature shows that passwords are often compromised through the poor security and management practices of users. This paper examines user password composition and security practices for email accounts. The results of a survey that examines user practice in creating and using passwords are reported. The results show that many users know about the risks of hackers, viruses and so on and take preliminary steps to combat them such as having passwords longer than eight characters. However, this appears to be as far as many users are willing to accede to the probability that their information and computing resources can be compromised. This paper makes some recommendations for the education of users in creating and maintaining their passwords. The responsibility for these educational programs can be shared between governments, organisations, educational institutions at all levels, and software vendors.

  14. [The treatment received by public health services users in Mexico].

    Science.gov (United States)

    Puentes Rosas, Esteban; Gómez Dantés, Octavio; Garrido Latorre, Francisco

    2006-06-01

    To document the fact that differences in the treatment received by health services users in Mexico are mainly dependent on the type of provider, regardless of the users' socioeconomic status. The data were obtained by means of a survey of 18 018 users who visited 73 health services in 13 states within Mexico. They were asked to grade the way the institution had performed in seven of the eight domains that define appropriate user treatment (autonomy, confidentiality, communication, respectful manner, condition of basic facilities, access to social assistance networks, and free user choice). The questionnaire included some vignettes to help determine user expectations. A composite ordinal probit model was applied; the perception of quality in connection with each of the appropriate treatment domains was the independent variable, whereas gender, educational level, age, type of provider, and user expectations were used as control variables. The type of provider was the main factor that determined users' perceptions regarding the treatment they received when visiting health services in Mexico. Institutions belonging to the social security system performed the worst, while the services provided under the program targeting the rural population (IMSS Oportunidades) received the highest scores. Overall, the domain that was most highly ranked was respectful manner, whereas the lowest score was given to the ability to choose the provider. Men felt they had been able to communicate better than women, while respectful manner, communication, and social support showed a significant negative association with educational level (P < 0.05). Differences were noted in the way different public health service providers in Mexico treat their users, regardless of the latter's socioeconomic status. Social security system providers showed the greatest deficiencies in this respect. Respectful manner was the domain that received the highest scores in the case of all providers. Organizational

  15. Making sense of enterprise systems in institutions

    DEFF Research Database (Denmark)

    Svejvig, Per; Jensen, Tina Blegind

    2013-01-01

    Whereas previous research provides a number of accounts of failure prone enterprise system (ES) implementations, empirical evidence of the re-implementation of an accounting system in a Scandinavian high-tech company shows how the system became highly integrated, accepted by its users, and well......-aligned to the work processes. To learn from this case study, we investigate the interactive and dynamic relationships among the enterprise system, people and institutional properties. We investigate the institutional structures and the sensemaking processes at play to identify how the idea of an efficient accounting...

  16. Measuring user experience : what's new?

    NARCIS (Netherlands)

    Cremers, A.H.M.; Smets, N.; Vermeeren, A.; Kort, J.

    2007-01-01

    This paper proposes a short overview of characteristics of different user evaluation methods and a research framework to systematically compare these different methods. Comparisons will be carried out in the context of Freeband user experience studies. Results will provide more insight into how user

  17. Measuring user experience : what's new?

    NARCIS (Netherlands)

    Cremers, A.H.M.; Smets, N.; Vermeeren, A.; Kort, J.

    2007-01-01

    This paper proposes a short overview of characteristics of different user evaluation methods and a research framework to systematically compare these different methods. Comparisons will be carried out in the context of Freeband user experience studies. Results will provide more insight into how user

  18. What drives Users' Website Registration?

    NARCIS (Netherlands)

    T. Li (Ting); P.A. Pavlou (Paul)

    2013-01-01

    textabstractUser registration is an important prerequisite for the success of many websites by enabling users to gain access to domain information and personalized content. It is not always desirable for users, however, because they need to disclose personal information. This paper examines what dri

  19. Evaluation from a user perspective

    DEFF Research Database (Denmark)

    Krogstrup, Hanne Kathrine

    2004-01-01

    Over the last decade, user participation has been placed on the agenda in many contexts and also in relation to evaluation. The reasons for user participation in evaluation are based om several overlapping arguments. In this contexts four arguments for user participation are discussed: a control ...... argument, a democratic argument, a knowledge argument and an emancipatory argument...

  20. Binary Classification Method of Social Network Users

    Directory of Open Access Journals (Sweden)

    I. A. Poryadin

    2017-01-01

    Full Text Available The subject of research is a binary classification method of social network users based on the data analysis they have placed. Relevance of the task to gain information about a person by examining the content of his/her pages in social networks is exemplified. The most common approach to its solution is a visual browsing. The order of the regional authority in our country illustrates that its using in school education is needed. The article shows restrictions on the visual browsing of pupil’s pages in social networks as a tool for the teacher and the school psychologist and justifies that a process of social network users’ data analysis should be automated. Explores publications, which describe such data acquisition, processing, and analysis methods and considers their advantages and disadvantages. The article also gives arguments to support a proposal to study the classification method of social network users. One such method is credit scoring, which is used in banks and credit institutions to assess the solvency of clients. Based on the high efficiency of the method there is a proposal for significant expansion of its using in other areas of society. The possibility to use logistic regression as the mathematical apparatus of the proposed method of binary classification has been justified. Such an approach enables taking into account the different types of data extracted from social networks. Among them: the personal user data, information about hobbies, friends, graphic and text information, behaviour characteristics. The article describes a number of existing methods of data transformation that can be applied to solve the problem. An experiment of binary gender-based classification of social network users is described. A logistic model obtained for this example includes multiple logical variables obtained by transforming the user surnames. This experiment confirms the feasibility of the proposed method. Further work is to define a system

  1. MOSS user's manual

    Science.gov (United States)

    Salmen, Larry; Gropper, James; Hamill, John; Gentry, Barbara

    1978-01-01

    The Map Overlay and Statistical System (MOSS) Users' Manual is specialized document has been designed for trained users of the MOSS interactive graphics software. Those totally unfamiliar with MOSS or Geographic Information Systems are referred elsewhere as described below: -- If you know nothing about MOSS or what it can do for you, and you wish introductory information on MOSS, or you want to deign an application and data entry process compatible with MOSS, or you want "hands-on" training, contact the WELUT Team Leader at the address below for a "hands-on" GIS training session. -- If you have been introduced to MOSS, have your application defined, data entered, and want to know how to use MOSS, start reading at Section 1 of this Manual. --If you are interested in the MOSS data structure, refer to Section 2 of this Manual. --If you have some experience in using MOSS and want to refer to the general types of MOSS commands, read Section 3 of this Manual. --If you are an experience MOSS user and want details on individual MOSS commands, refer to Section 4.3 of this Manual. --If you are interested in the Federation of Rocky Mountain States -- WELUT 02 Project contractual background results, turn to Appendices D and E of this Manual. MOSS has been operation for less than 3 months, and has received limited operational testing at the date of this printing (October 1978). Undiscovered software limitations and bugs may yet appear. All such bugs as well as documentation errors, obscurities, and inadequacies should be reported to: Team Leader

  2. Data Management for High-Throughput Genomics

    CERN Document Server

    Roehm, Uwe

    2009-01-01

    Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be automatically processed and made available to scientists for further analysis. This paper explores the potential and the limitations of using relational database systems as the data processing platform for high-throughput genomics. In particular, we are interested in the storage management for high-throughput sequence data and in leveraging SQL and user-defined functions for data analysis inside a database system. We give an overview of a database design for high-throughput genomics, how we used a SQL Server database in some unconventional ways to prototype this scenario, and we will discuss some initial findings about the scalability and performance of such a more database-centric approach.

  3. Cliffs User Manual

    CERN Document Server

    Tolkova, Elena

    2014-01-01

    Cliffs is an open-source relative of MOST (Method Of Splitting Tsunamis) numerical model, implemented as described in (Tolkova, 2014, Pure and Appl. Geophys., 171(9), 2289-2314). Cliffs features: Shallow-Water approximation with an option to manipulate numerical dispersion; Use of Cartesian or spherical (lon/lat) coordinates; 1D and 2D configurations; Structured co-located grid with (optionally) varying spacing; Runup on land; Initial conditions or boundary forcing; Grid nesting with one-way coupling; Parallelized with OpenMP; NetCDF format of input/output data. This user manual accompanies Cliffs code distribution.

  4. 15. ESRF users meeting

    Energy Technology Data Exchange (ETDEWEB)

    Fotis C, Kafatos; Ulrich, K.U.; Weib, S.; Rossberg, A.; Scheinost, A.C.; Foerstendorf, H.; Zanker, H.; Meyerheim, H.L.; Sander, D.; Popescu, R.; Kirschner, J.; Robach, O.; Ferrer, S.; Lyman, P.F.; Shneerson, V.L.; Fung, R.; Harder, R.J.; Parihar, S.S.; Johnson-Steigelman, H.T.; Lu, E.D.; Saldin, D.K.; Eastwood, D.S.; Atkinson, D.; Tanner, B.K.; Hase, T.P.A.; Van Kampen, M.; Hjorvarsson, B.; Brown, S.; Thompson, P.; Konovalov, O.; Saint-Martin, E.; Daillant, J.; Luzet, D.; Szlachetko, J.; Barrett, R.; Berset, M.; Dousse, J.C.; Fennane, K.; Hoszowska, J.; Kubala-Kukus, A.; Pajek, M.; Szlachetko, M.; Monaco, A.; Chumakov, A.; Crichton, W.; Van Buerck, I.; Wortmann, G.; Meyer, A.; Ponkratz, U.; Ruffer, R.; Sakurai, Y.; Hiraoka, N.; Itou, M.; Buslaps, T.; Honkimki, V.; Maeno, Y.; Collart, E.; Shukla, A.; Rueff, J.P.; Leininger, Ph.; Ishii, H.; Cai, Y.; Cheong, S.W.; Martins, R.M.S.; Schell, N.; Beckers, M.; Silva, R.; Braz Fernandes, F.M.; Acapito, F.; Seta, M. de; Capelini, G.; Giorgi, M.; Schorr, G.; Geandier, G.; Alves Marques, M.; Barros Marquesa, M.I. de; Cabaco, M.I.; Gaspara, A.M.; Marques, M.P.M.; Amado, A.M.; Amorim da Costa, A.M.; Bruneseaux, F.; Weisbecker, P.; Brandao, M.J.; Aeby-Gautier, E.; Simmonds, H.; Lei, C.; Das, A.; Trolley, D.; Thomas, H.E.; Macdonald, J.E.; Wiegart, L.; Tolan, M.; Struth, B.; Petukhov, A.V.; Thijssen, J.H.J.; Hart, D.C.; Imhof, A.; Van Blaaderen, A.; Dolbnya, I.P.; Snigirev, A.; Mossaid, A.; Snigireva, I.; Reconditi, M.; Brunello, E

    2005-07-01

    This document gathers the posters presented on the one day and a half long plenary meeting workshop. This meeting workshop is a privileged forum where ESRF users can exchange their views on the latest scientific and technical development involving synchrotron radiation. One poster deals with the investigation of colloid composition and uranium bond structure to see whether the migration of contaminants from abandoned mines could be stimulated or attenuated by colloids. Another poster is dedicated to the investigation of the uranium speciation in covered mine tailings by a combination of micro-spectroscopic and wet chemical approaches. 2 posters deal with the contribution of synchrotron radiation to radiotherapy.

  5. User-Driven CHAOS

    DEFF Research Database (Denmark)

    Lykke, Marianne; Lund, Haakon; Skov, Mette

    2016-01-01

    CHAOS (Cultural Heritage Archive Open System) provides streaming access to more than 500.000 broad-casts by the Danish Broadcast Corporation from 1931 and onwards. The archive is part of the LARM project with the purpose of enabling researchers to search, annotate, and interact with recordings....... To optimally sup-port the researchers a user-centred approach was taken to develop the platform and related metadata scheme. Based on the requirements a three level metadata scheme was developed: (1) core archival metadata, (2) LARM metadata, and (3) project-specific metadata. The paper analyses how.......fm’s strength in providing streaming access to a large, shared corpus of broadcasts....

  6. User Ethnography as Theatre

    DEFF Research Database (Denmark)

    Torguet, Rosa; Friis, Preben; Buur, Jacob

    2013-01-01

    This paper discusses the potential of using theatre with professional actors to convey the outcome of ethnographic user studies to industry or academia. Framed in the ongoing discussion within design ethnography of how representations can support the communication of ethnographic findings more...... effectively. The use of theatre within innovation processes can help facilitate the provoking role that an ethnography often plays when presented to organizations. Live performances were used as part of a participatory innovation project in the field of indoor climate with industry partners and academic...

  7. XTV users guide

    Energy Technology Data Exchange (ETDEWEB)

    Dearing, J.F.; Johns, R.C. [Los Alamos National Lab., NM (United States). Technology and Safety Assessment Div.

    1996-09-01

    XTV is an X-Windows based Graphical User Interface for viewing results of Transient Reactor Analysis Code (TRAC) calculations. It provides static and animated color mapped visualizations of both thermal-hydraulic and heat conduction components in a TRAC model of a nuclear power plant, as well as both on-screen and hard copy two-dimensional plot capabilities. XTV is the successor to TRAP, the former TRAC postprocessor using the proprietary DISSPLA graphics library. This manual describes Version 2.0, which requires TRAC version 5.4.20 or later for full visualization capabilities.

  8. Raspberry Pi user guide

    CERN Document Server

    Upton, Eben

    2013-01-01

    The essential guide to getting started with the Raspberry Pi ® The Raspberry Pi has been a success beyond the dream of its creators. Their goal, to encourage a new generation of computer programmers who understand how computers work, is well under way. Raspberry Pi User Guide 2e is the newest edition of the runaway bestseller written by the Pi's co-creator, Eben Upton, and tech writer Gareth Halfacree. It contains everything you need to know to get the Pi up and running, including how to: Connect a keyboard, mouse, monitor and other peripheralsInstall software and configure your Raspberry

  9. Raspberry Pi user guide

    CERN Document Server

    Halfacree, Gareth

    2012-01-01

    Make the most out of the world’s first truly compact computer It's the size of a credit card, it can be charged like a smartphone, it runs on open-source Linux, and it holds the promise of bringing programming and playing to millions at low cost. And now you can learn how to use this amazing computer from its co-creator, Eben Upton, in Raspberry Pi User Guide. Cowritten with Gareth Halfacree, this guide gets you up and running on Raspberry Pi, whether you're an educator, hacker, hobbyist, or kid. Learn how to connect your Pi to other hardware, install software, write basic programs, an

  10. User and technical documentation

    Science.gov (United States)

    1988-01-01

    The program LP1 calculates outbound and return trajectories between low earth orbit (LEO) and libration point no. 1 (L1). Libration points (LP) are defined as locations in space that orbit the Earth such that they are always stationary with respect to the Earth-Moon line. L1 is located behind the Moon such that the pull of the Earth and Moon together just cancel the centrifugal acceleration associated with the libration point's orbit. The input required from the user to define the flight is described. The contents of the six reports produced as outputs are presented. Also included are the instructions needed to execute the program.

  11. Information for Stores users

    CERN Multimedia

    FI Department

    2008-01-01

    The DISTRELEC catalogue (IT) is now available in EDH in addition to the CERN Stores catalogue and the catalogues of existing suppliers. Using an EDH materials request form, users can now order DISTRELEC equipment from amongst the following product groups: peripherals, multimedia, PC components, data media, communication and data cables and adapters. Non-authorised materials will be clearly indicated. As a reminder, the system automatically manages the distribution of standard Stores equipment and punch out equipment ordered on the same request form. In both cases, delivery will take a maximum of 48 hours. The approval of the EDH document will follow the usual EDH routing procedures. Logistics Group FI Department

  12. Information for stores users

    CERN Multimedia

    2006-01-01

    The Radiospares Catalogue is now accessible from the Material Request page on EDH in the same way as the CERN Stores Catalogue. This means that users can order Radiospares equipment by completing an EDH Materials Request form. N.B.: The system will automatically forward orders for standard Stores equipment to the CERN Stores and those for Radiospares equipment to Radiospares. In both cases the delivery time will be a maximum of 48 hours. Requests for materials will be routed for approval in accordance with the standard EDH routing procedures. Logistics Group FI Department

  13. Information for stores users

    CERN Multimedia

    2007-01-01

    From next week, the SFS UNIMARKET (tooling) catalogue will be accessible using the Material Request form on EDH in addition to the CERN Stores catalogue and those of existing suppliers. Users will now be able to place orders from the SFS catalogue using the Material Request form on EDH. Note: The system automatically forwards orders for standard Stores equipment and those for SFS equipment, placed using the same Material Request form, to the CERN Stores and SFS respectively. In both cases, the maximum delivery time will be 48 hours. Requests for equipment will be routed for approval in accordance with standard EDH routing procedures. Logistics Group FI Department

  14. INFORMATION FOR STORES USERS

    CERN Multimedia

    2007-01-01

    From next week, the SFS UNIMARKET (tooling) catalogue will be accessible using the Material Request form on EDH in addition to the CERN Stores catalogue and those of existing suppliers. Users will now be able to place orders from the SFS catalogue using the Material Request form on EDH. Note: The system automatically forwards orders for standard Stores equipment and those for SFS equipment, placed using the same Material Request form, to the CERN Stores and SFS respectively. In both cases, the maximum delivery time will be 48 hours. Requests for equipment will be routed for approval in accordance with standard EDH routing procedures. Logistics Group FI Department

  15. Percept User Manual.

    Energy Technology Data Exchange (ETDEWEB)

    Carnes, Brian [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Kennon, Stephen Ray [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-05-01

    This document is the main user guide for the Sierra/Percept capabilities including the mesh_adapt and mesh_transfer tools. Basic capabilities for uniform mesh refinement (UMR) and mesh transfers are discussed. Examples are used to provide illustration. Future versions of this manual will include more advanced features such as geometry and mesh smoothing. Additionally, all the options for the mesh_adapt code will be described in detail. Capabilities for local adaptivity in the context of offline adaptivity will also be included. This page intentionally left blank.

  16. XMGR5 users manual

    Energy Technology Data Exchange (ETDEWEB)

    Jones, K.R.; Fisher, J.E.

    1997-03-01

    ACE/gr is XY plotting tool for workstations or X-terminals using X. A few of its features are: User defined scaling, tick marks, labels, symbols, line styles, colors. Batch mode for unattended plotting. Read and write parameters used during a session. Polynomial regression, splines, running averages, DFT/FFT, cross/auto-correlation. Hardcopy support for PostScript, HP-GL, and FrameMaker.mif format. While ACE/gr has a convenient point-and-click interface, most parameter settings and operations are available through a command line interface (found in Files/Commands).

  17. Information for stores users

    CERN Multimedia

    2006-01-01

    The Radiospares Catalogue is now accessible from the Material Request page on EDH in the same way as the CERN Stores Catalogue. This means that users can order Radiospares equipment by completing an EDH Materials Request form. N.B.: The system will automatically forward orders for standard Stores equipment to the CERN Stores and those for Radiospares equipment to Radiospares. In both cases the delivery time will be a maximum of 48 hours. Requests for materials will be routed for approval in accordance with the standard EDH routing procedures. Logistics Group FI Department

  18. CDS User survey

    CERN Multimedia

    CERN Document Service

    2011-01-01

      The CERN Document Server is launching a user survey in order to collect information relative to its search engine, submission interfaces, collaborative features and content organisation. With the view of re-shaping its collections and interfaces and to better integrate with the new INSPIRE platform that serves all HEP literature, CERN Document Server team invites you to take part in the survey. Your input is essential to provide us with useful information before setting up the new service and improve your interactions with CDS. Thanks for participating !  

  19. Incident users of antipsychotics

    DEFF Research Database (Denmark)

    Baandrup, Lone; Kruse, Marie

    2016-01-01

    PURPOSE: In Denmark, as well as in many other countries, consumption of antipsychotics is on the rise, partly due to increasing off-label use. The aim of this study was to analyze and quantify the extent of off-label use and polypharmacy in incident users of antipsychotic medication, and to examine...... polypharmacy (HR 1.38; 95 % CI 1.32-1.45), whereas antipsychotic discontinuation was associated with decreased hospitalization risk in most off-label conditions. CONCLUSIONS: The brief duration of most antipsychotic prescriptions suggests that antipsychotics are prescribed more liberally than recommended...

  20. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  1. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  2. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  3. A socially inclusive approach to user participation in higher education.

    Science.gov (United States)

    Simons, Lucy; Tee, Steve; Lathlean, Judith; Burgess, Abigail; Herbert, Lesley; Gibson, Colin

    2007-05-01

    This paper is a report of a study to evaluate the development of an innovative Service User Academic post in mental health nursing in relation to student learning and good employment practice in terms of social inclusion. Institutions providing professional mental health education are usually expected to demonstrate user involvement in the design, delivery and evaluation of their educational programmes to ensure that user voices are central to the development of clinical practice. Involvement can take many forms but not everyone values user knowledge as equal to other sources of knowledge. This can lead to users feeling exploited, rather than fully integrated in healthcare professional education processes. Development of the post discussed in this paper was stimulated and informed by an innovative example from Australia. An observational case study of the development and practice of a Service User Academic post was undertaken in 2005. Participants were purposively sampled and included the User Academic, six members of a user and carer reference group, 10 educators and 35 students. Data were collected by group discussions and interviews. Data analysis was based on the framework approach. The evaluation revealed tangible benefits for the students and the wider academic community. Most important was the powerful role model the Service User Academic provided for students. The post proved an effective method to promote service user participation and began to integrate service user perspectives within the educational process. However, the attempts to achieve socially inclusive practices were inhibited by organizational factors. The expectations of the role and unintended discriminatory behaviours had an impact on achieving full integration of the role. Furthermore, shortcomings in the support arrangements were revealed. The search for an optimum model of involvement may prove elusive, but the need to research and debate different strategies, to avoid tokenism and

  4. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  5. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  6. GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.

    Science.gov (United States)

    Altermann, Eric; Lu, Jingli; McCulloch, Alan

    2017-01-01

    Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.

  7. Performance improvement of per-user threshold based multiuser switched scheduling system

    KAUST Repository

    Nam, Haewoon

    2013-01-01

    SUMMARY This letter proposes a multiuser switched scheduling scheme with per-user threshold and post user selection and provides a generic analytical framework for determining the optimal feedback thresholds. The proposed scheme applies an individual feedback threshold for each user rather than a single common threshold for all users to achieve some capacity gain due to the flexibility of threshold selection as well as a lower scheduling outage probability. In addition, since scheduling outage may occur with a non-negligible probability, the proposed scheme employs post user selection in order to further improve the ergodic capacity, where the user with the highest potential for a higher channel quality than other users is selected. Numerical and simulation results show that the capacity gain by post user selection is significant when random sequence is used. Copyright © 2013 The Institute of Electronics, Information and Communication Engineers.

  8. Ethnobotany genomics research: Status and future prospects

    Directory of Open Access Journals (Sweden)

    Franky Varah

    2015-01-01

    Full Text Available The present study is an attempt to analyze the world publication of ethnobotany genomics by using "DNA barcoding" and "DNA barcoding plants" as keywords. Some of the parameters used for the analysis include the publication output, countries′ performance, the institutions involved, subject areas, authors, and journals distribution. The Scopus International Database is used for this purpose. An evaluating indicator, citations and h-index are applied to characterize the ethnobotany genomic publication output. It is interesting to note that over the past decade, there has been a notable growth in publication output. Moreover, there has been a significant increase in the participation from a number of countries as well as institutions, subject categories, journals, authors, and collaborations. The increasing significance of ethnobotany genomics was analyzed by ranking countries, institutions, subject categories, journals, authors and collaborations in terms the total number of publication, their citations and h-index.

  9. User Types in Online Applications

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2011-08-01

    Full Text Available Online applications are presented in the context of information society. Online applications characteristics are analyzed. Quality characteristics are presented in relation to online applications users. Types of users for AVIO application are presented. Use cases for AVIO application are identified. The limitations of AVIO application are defined. Types of users in online applications are identified. The threedimensional matrix of access to the online application resources is built. The user type-oriented database is structured. Access management of the fields related to the database tables is analyzed. The classification of online applications users is done.

  10. TRLAN User Guide

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kesheng; Simon, H.

    1999-03-09

    TRLAN is a program designed to find a small number of extreme eigenvalues and their corresponding eigenvectors of a real symmetric matrix. Denote the matrix as A, the eigenvalue as {lambda}, and the corresponding eigenvector as x, they are defined by the following equation, Ax = {lambda}x. There are a number of different implementations of the Lanczos algorithm available. Why another one? Our main motivation is to develop a specialized version that only target the case where one wants both eigenvalues and eigenvectors of a large real symmetric eigenvalue problems that can not use the shift-and-invert scheme. In this case the standard non-restarted Lanczos algorithm requires one to store a large number of Lanczos vectors which can cause storage problem and make each iteration of the method very expensive. The underlying algorithm of TRLAN is a dynamic thick-restart Lanczos algorithm. Like all restarted methods, the user can choose how many vectors can be generated at once. Typically, th e user chooses a moderate size so that all Lanczos vectors can be stored in core. This allows the restarted methods to execute efficiently. This implementation of the thick-restart Lanczos method also uses the latest restarting technique, it is very effective in reducing the time required to compute a desired solutions compared to similar restarted Lanczos schemes, e.g., ARPACK.

  11. Photovoltaics information user study

    Energy Technology Data Exchange (ETDEWEB)

    Belew, W.W.; Wood, B.L.; Marie, T.L.; Reinhardt, C.L.

    1980-10-01

    The results of a series of telephone interviews with groups of users of information on photovoltaics (PV) are described. These results, part of a larger study on many different solar technologies, identify types of information each group needed and the best ways to get information to each group. The report is 1 of 10 discussing study results. The overall study provides baseline data about information needs in the solar community. It covers these technological areas: photovoltaics, passive solar heating and cooling, active solar heating and cooling, biomass energy, solar thermal electric power, solar industrial and agricultural process heat, wind energy, ocean energy, and advanced energy storage. An earlier study identified the information user groups in the solar community and the priority (to accelerate solar energy commercialization) of getting information to each group. In the current study only high-priority groups were examined. Results from seven PV groups respondents are analyzed in this report: DOE-Funded Researchers, Non-DOE-Funded Researchers, Researchers Working for Manufacturers, Representatives of Other Manufacturers, Representatives of Utilities, Electric Power Engineers, and Educators.

  12. Nephrolithiasis in topiramate users.

    Science.gov (United States)

    Maalouf, Naim M; Langston, Joshua P; Van Ness, Paul C; Moe, Orson W; Sakhaee, Khashayar

    2011-08-01

    Topiramate is a neuromodulatory agent increasingly prescribed for a number of neurological and non-neurological indications. Topiramate-treated patients are at risk for nephrolithiasis due to hypocitraturia and high urine pH. However, the prevalence of symptomatic stone disease in TPM users is generally perceived to be low. This study was undertaken to assess in topiramate-treated patients the prevalence of symptomatic nephrolithiasis (by history) and of asymptomatic nephrolithiasis by computed tomography (CT) scan. Topiramate users were identified from a database of patients with neurological disorders at a single university hospital. Among 75 topiramate-treated adult patients with a median daily dose of 300 mg and median treatment duration of 48 months, the prevalence of symptomatic nephrolithiasis was 10.7%. In a subset of topiramate-treated patients and no history of symptomatic stone disease, the prevalence of asymptomatic nephrolithiasis detected by CT scan was 20%. The prevalence of symptomatic nephrolithiasis with long-term topiramate use is higher than reported in short-term studies. Furthermore, clinical prevalence is underestimated due to asymptomatic nephrolithiasis.

  13. Electronic Commerce user manual

    Energy Technology Data Exchange (ETDEWEB)

    1992-04-10

    This User Manual supports the Electronic Commerce Standard System. The Electronic Commerce Standard System is being developed for the Department of Defense of the Technology Information Systems Program at the Lawrence Livermore National Laboratory, operated by the University of California for the Department of Energy. The Electronic Commerce Standard System, or EC as it is known, provides the capability for organizations to conduct business electronically instead of through paper transactions. Electronic Commerce and Computer Aided Acquisition and Logistics Support, are two major projects under the DoD`s Corporate Information Management program, whose objective is to make DoD business transactions faster and less costly by using computer networks instead of paper forms and postage. EC runs on computers that use the UNIX operating system and provides a standard set of applications and tools that are bound together by a common command and menu system. These applications and tools may vary according to the requirements of the customer or location and may be customized to meet the specific needs of an organization. Local applications can be integrated into the menu system under the Special Databases & Applications option on the EC main menu. These local applications will be documented in the appendices of this manual. This integration capability provides users with a common environment of standard and customized applications.

  14. Electronic Commerce user manual

    Energy Technology Data Exchange (ETDEWEB)

    1992-04-10

    This User Manual supports the Electronic Commerce Standard System. The Electronic Commerce Standard System is being developed for the Department of Defense of the Technology Information Systems Program at the Lawrence Livermore National Laboratory, operated by the University of California for the Department of Energy. The Electronic Commerce Standard System, or EC as it is known, provides the capability for organizations to conduct business electronically instead of through paper transactions. Electronic Commerce and Computer Aided Acquisition and Logistics Support, are two major projects under the DoD's Corporate Information Management program, whose objective is to make DoD business transactions faster and less costly by using computer networks instead of paper forms and postage. EC runs on computers that use the UNIX operating system and provides a standard set of applications and tools that are bound together by a common command and menu system. These applications and tools may vary according to the requirements of the customer or location and may be customized to meet the specific needs of an organization. Local applications can be integrated into the menu system under the Special Databases Applications option on the EC main menu. These local applications will be documented in the appendices of this manual. This integration capability provides users with a common environment of standard and customized applications.

  15. FPG Child Development Institute

    Science.gov (United States)

    ... Development, Teaching, and Learning The Frank Porter Graham Child Development Institute will partner with Zero to Three to ... 25 September 21, 2017 More Frank Porter Graham Child Development Institute The University of North Carolina at Chapel ...

  16. Proteomics Data on UCSC Genome Browser - Office of Cancer Clinical Proteomics Research

    Science.gov (United States)

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data.

  17. Canadian institute honours Hawking

    Science.gov (United States)

    Durrani, Matin

    2009-11-01

    The Perimeter Institute for Theoretical Physics in Waterloo, Canada, has announced that a major new extension to its campus will be known as the Stephen Hawking Centre. The extension, which is currently being built, is due to open in 2011 and will double the size of the institute. It will also provide a home for the institute's Masters students, the first of whom joined the Perimeter Institute this autumn as part of its Perimeter Scholars international programme.

  18. Public Libraries, Museums and User Participation - An outline of a research projeckt

    DEFF Research Database (Denmark)

    Jochumsen, Henrik; Rasmussen, Casper Hvenegaard

    2013-01-01

    The aim of this paper is to sketch a research project on user participation in public libraries and museums. For several years’ user participation, participatory culture and user driven innovation have been “buzzwords” in the ongoing development of cultural institutions in general and in museums...... and libraries in particular. From a cultural policy perspective research in this area is therefore of great importance. Taking our point of departure in respectively the public library and the local cultural history museum in the city of Roskilde we introduce to the current relevance of the subject...... of the research project. The case of Roskilde is particularly illustrative as it not only contains user participation, libraries and museums but also illustrate how the development of user participation actually blurs the borders of the two institutions. After a definition of the concept of user participation...

  19. Public Libraries, Museums and User Participation - An outline of a research projeckt

    DEFF Research Database (Denmark)

    Jochumsen, Henrik; Rasmussen, Casper Hvenegaard

    2013-01-01

    The aim of this paper is to sketch a research project on user participation in public libraries and museums. For several years’ user participation, participatory culture and user driven innovation have been “buzzwords” in the ongoing development of cultural institutions in general and in museums...... and libraries in particular. From a cultural policy perspective research in this area is therefore of great importance. Taking our point of departure in respectively the public library and the local cultural history museum in the city of Roskilde we introduce to the current relevance of the subject...... of the research project. The case of Roskilde is particularly illustrative as it not only contains user participation, libraries and museums but also illustrate how the development of user participation actually blurs the borders of the two institutions. After a definition of the concept of user participation...

  20. EPOS Seismology services and their users

    Science.gov (United States)

    Haslinger, Florian; Dupont, Aurelien; Michelini, Alberto; Rietbrock, Andreas; Sleeman, Reinoud; Wiemer, Stefan; Basili, Roberto; Bossu, Rémy; Cakti, Eser; Cotton, Fabrice; Crawford, Wayne; Crowley, Helen; Danciu, Laurentiu; Diaz, Jordi; Garth, Tom; Locati, Mario; Luzi, Lucia; Pitilakis, Kyriazis; Roumelioti, Zafeiria; Strollo, Angelo

    2017-04-01

    The construction of seismological community services for the European Plate Observing System Research Infrastructure (EPOS) is by now well under way. A significant number of services are already operational, largely based on those existing at established institutions or collaborations like ORFEUS, EMSC, AHEAD and EFEHR, and more are being added to be ready for internal validation by late 2017. In this presentation we focus on a number of issues related to the interaction of the community of users with the services provided by the seismological part of the EPOS research infrastructure. How users interact with a service (and how satisfied they are with this interaction) is viewed as one important component of the validation of a service within EPOS, and certainly is key to the uptake of a service and from that also it's attributed value. Within EPOS Seismology, the following aspects of user interaction have already surfaced: - user identification (and potential tracking) versus ease-of-access and openness Requesting users to identify themselves when accessing a service provides various advantages to providers and users (e.g. quantifying & qualifying the service use, customization of services and interfaces, handling access rights and quotas), but may impact the ease of access and also shy away users who don't wish to be identified for whatever reason. - service availability versus cost There is a clear and prominent connection between the availability of a service, both regarding uptime and capacity, and its operational cost (IT systems and personnel), and it is often not clear where to draw the line (and based on which considerations). In connection to that, how to best utilize third-party IT infrastructures (either commercial or public), and what the long-term cost implications of that might be, is equally open. - licensing and attribution The issue of intellectual property and associated licensing policies for data, products and services is only recently gaining

  1. Furthering critical institutionalism

    NARCIS (Netherlands)

    Cleaver, Frances; Koning, De Jessica

    2015-01-01

    This special issue furthers the study of natural resource management from a critical institutional perspective. Critical institutionalism (CI) is a contemporary body of thought that explores how institutions dynamically mediate relationships between people, natural resources and society. It focus

  2. Multinationals and Institutional Competitiveness

    DEFF Research Database (Denmark)

    Hull Kristensen, Peer; Morgan, Glenn

    This article discusses how institutional competitiveness and multinationals are mutually enriching concepts. Seen from the perspective of Multinationals, institutional competitiveness becomes expressed at two levels. At the level of corporate HQs institutional competitiveness proves itself...... competitiveness of Liberal Market Economies and Coordinated Markets Economies under the current competitive regime....

  3. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome.

    Science.gov (United States)

    Wang, Yi; Liu, Xianju; Ren, Chong; Zhong, Gan-Yuan; Yang, Long; Li, Shaohua; Liang, Zhenchang

    2016-04-21

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species. In this study, we identified and characterized five types of CRISPR/Cas9 target sites in the widely cultivated grape species Vitis vinifera and developed a user-friendly database for editing grape genomes in the future. A total of 35,767,960 potential CRISPR/Cas9 target sites were identified from grape genomes in this study. Among them, 22,597,817 target sites were mapped to specific genomic locations and 7,269,788 were found to be highly specific. Protospacers and PAMs were found to distribute uniformly and abundantly in the grape genomes. They were present in all the structural elements of genes with the coding region having the highest abundance. Five PAM types, TGG, AGG, GGG, CGG and NGG, were observed. With the exception of the NGG type, they were abundantly present in the grape genomes. Synteny analysis of similar genes revealed that the synteny of protospacers matched the synteny of homologous genes. A user-friendly database containing protospacers and detailed information of the sites was developed and is available for public use at the Grape-CRISPR website ( http://biodb.sdau.edu.cn/gc/index.html ). Grape genomes harbour millions of potential CRISPR/Cas9 target sites. These sites are widely distributed among and within chromosomes with predominant abundance in the coding regions of genes. We developed a publicly-accessible Grape-CRISPR database for facilitating the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among

  4. Linking user-generated video annotations to the web of data

    NARCIS (Netherlands)

    Hildebrand, M.; Ossenbruggen, J.R. van

    2012-01-01

    In the audiovisual domain tagging games are explored as a method to collect user-generated metadata. For example, the Netherlands Institute for Sound and Vision deployed the video labelling game "Waisda?" to collect user tags for videos from their collection. These tags are potentially useful to imp

  5. Preparing Technical Communication Students to Function as User Advocates in a Self-Service Society

    Science.gov (United States)

    Cleary, Yvonne; Flammia, Madelyn

    2012-01-01

    The self-service nature of today's society means that technical communicators are needed more than ever before since users may find themselves struggling to make sense of online documentation with minimal support from the institutions that provide it. Certain demographics within the user population (older adults, disabled persons, non-native…

  6. Buying and selling crack: transactions at the retail level and the role of user-sellers

    NARCIS (Netherlands)

    Oteo Pérez, A.; Benschop, A.; Korf, D.J.

    2013-01-01

    To assess key characteristics of the retail crack market and the role of users as buyers and sellers, data from a survey inside and outside institutional setting among 1,039 crack users in the three largest Dutch cities were analyzed to explore their role in the crack market as buyers and sellers.

  7. Linking user-generated video annotations to the web of data

    NARCIS (Netherlands)

    M. Hildebrand (Michiel); J.R. van Ossenbruggen (Jacco)

    2012-01-01

    htmlabstractIn the audiovisual domain tagging games are explored as a method to collect user-generated metadata. For example, the Netherlands Institute for Sound and Vision deployed the video labelling game "Waisda?" to collect user tags for videos from their collection. These tags are potentially u

  8. Buying and selling crack: transactions at the retail level and the role of user-sellers

    NARCIS (Netherlands)

    A. Oteo Pérez; A. Benschop; D.J. Korf

    2013-01-01

    To assess key characteristics of the retail crack market and the role of users as buyers and sellers, data from a survey inside and outside institutional setting among 1,039 crack users in the three largest Dutch cities were analyzed to explore their role in the crack market as buyers and sellers. O

  9. Rivet user manual

    Science.gov (United States)

    Buckley, Andy; Butterworth, Jonathan; Grellscheid, David; Hoeth, Hendrik; Lönnblad, Leif; Monk, James; Schulz, Holger; Siegert, Frank

    2013-12-01

    This is the manual and user guide for the Rivet system for the validation and tuning of Monte Carlo event generators. As well as the core Rivet library, this manual describes the usage of the rivet program and the AGILe generator interface library. The depth and level of description is chosen for users of the system, starting with the basics of using validation code written by others, and then covering sufficient details to write new Rivet analyses and calculational components. Catalogue identifier: AEPS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPS_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571126 No. of bytes in distributed program, including test data, etc.: 4717522 Distribution format: tar.gz Programming language: C++, Python. Computer: PC running Linux, Mac. Operating system: Linux, Mac OS. RAM: 20 MB Classification: 11.9, 11.2. External routines: HepMC (https://savannah.cern.ch/projects/hepmc/), GSL (http://www.gnu.org/software/gsl/manual/gsl-ref.html), FastJet (http://fastjet.fr/), Python (http://www.python.org/), Swig (http://www.swig.org/), Boost (http://www.boostsoftware.com/), YAML (http://www.yaml.org/spec/1.2/spec.html) Nature of problem: Experimental measurements from high-energy particle colliders should be defined and stored in a general framework such that it is simple to compare theory predictions to them. Rivet is such a framework, and contains at the same time a large collection of existing measurements. Solution method: Rivet is based on HepMC events, a standardised output format provided by many theory simulation tools. Events are processed by Rivet to generate histograms for the requested list of analyses, incorporating all experimental phase space cuts and histogram definitions. Restrictions: Cannot calculate

  10. SIFT missense predictions for genomes.

    Science.gov (United States)

    Vaser, Robert; Adusumalli, Swarnaseetha; Leng, Sim Ngak; Sikic, Mile; Ng, Pauline C

    2016-01-01

    The SIFT (sorting intolerant from tolerant) algorithm helps bridge the gap between mutations and phenotypic variations by predicting whether an amino acid substitution is deleterious. SIFT has been used in disease, mutation and genetic studies, and a protocol for its use has been previously published with Nature Protocols. This updated protocol describes SIFT 4G (SIFT for genomes), which is a faster version of SIFT that enables practical computations on reference genomes. Users can get predictions for single-nucleotide variants from their organism of interest using the SIFT 4G annotator with SIFT 4G's precomputed databases. The scope of genomic predictions is expanded, with predictions available for more than 200 organisms. Users can also run the SIFT 4G algorithm themselves. SIFT predictions can be retrieved for 6.7 million variants in 4 min once the database has been downloaded. If precomputed predictions are not available, the SIFT 4G algorithm can compute predictions at a rate of 2.6 s per protein sequence. SIFT 4G is available from http://sift-dna.org/sift4g.

  11. User Experience Dimensions

    DEFF Research Database (Denmark)

    Lykke, Marianne; Jantzen, Christian

    2016-01-01

    The present study develops a set of 10 dimensions based on a systematic understanding of the concept of experience as a holistic psychological. Seven of these are derived from a psychological conception of what experiencing and experiences are. Three supplementary dimensions spring from...... the observation that experiences apparently have become especially valuable phenomena in Western societies. The 10 dimensions are tried out in a field study at the Center for Art and Media (ZKM) in Germany with the purpose to study their applicability in the evaluation of interactive sound archives. 29 walk......-alongs were carried out with 58 museums visitors. Our analysis showed that it was possible to identify the 10 experience dimensions in the study material. Some dimensions were expressed more frequently than others. The distribution of expressed dimensions and the content of the user comments provided a clear...

  12. Information for stores users

    CERN Multimedia

    2006-01-01

    The Bossard catalogue is now accessible alongside the CERN Stores catalogue from the Material Request form on EDH. Users will thus be able to order Bossard equipment using the EDH Materials Request form. As a reminder, the system automatically forwards orders for standard Stores equipment to the CERN Stores and those for Bossard equipment to Bossard. In both cases the delivery time will be a maximum of 48 hours. Requests for materials will be routed for approval in accordance with the standard EDH routing procedures. Some items will remain available from the emergency desk in the event of urgent requests. These items will be visible in the Stores catalogue even if they cannot be purchased via the EDH material request form. Logistics Group FI Department

  13. INFORMATION FOR GAS USERS

    CERN Multimedia

    Logistics Group

    2001-01-01

    The contractor for the supply and distribution of pressurised gases has drawn our attention to the large number of gas bottles and banks being stored on the site for increasingly long periods. Users are reminded that the rental charges for gas bottles and banks are based on a progressive rate depending on their period of use. To assist CERN in its efforts to optimise its operations in this field, you are kindly requested : to return empty or unused containers to the official gas distribution points as soon as possible, to try to limit reserve stocks, bearing in mind that standardised gases can be delivered within 36 hours. This will result in a higher turnover rate and in increased safety and will improve the availability of the gases. For all further enquiries, please contact Gas.Store@cern.ch by e-mail or call 72265. Thank you for your co-operation.

  14. Communication to Linux users

    CERN Multimedia

    IT Department

    We would like to inform you that the aging “phone” Linux command will stop working: On lxplus on 30 November 2009, On lxbatch on 4 January 2010, and is replaced by the new “phonebook” command, currently available on SLC4 and SLC5 Linux. As the new “phonebook” command has different syntax and output formats from the “phone” command, please update and test all scripts currently using “phone” before the above dates. You can refer to the article published on the IT Service Status Board, under the Service Changes section. Please send any comments to it-dep-phonebook-feedback@cern.ch Best regards, IT-UDS User Support Section

  15. Information for gas users

    CERN Multimedia

    2003-01-01

    The contractor for the supply and distribution of pressurised gases has drawn our attention to the large number of gas bottles and banks being stored on the site for increasingly long periods. Users are reminded that the rental charges for gas bottles and banks are based on a progressive rate depending on their period of use. To assist CERN in its efforts to optimise its operations in this field, you are kindly requested: - to return empty or unused containers to the official gas distribution points as soon as possible - to try to limit reserve stocks, bearing in mind that standardised gases can be delivered within 36 hours. This will result in a higher turnover rate and in increased safety and will improve the availability of the gases. For all further enquiries, please contact "Gas store" by e-mail. Thank you for your co-operation. Logistics Group SPL Division

  16. INFORMATION FOR GAS USERS

    CERN Multimedia

    Logistics Group

    2001-01-01

    The contractor for the supply and distribution of pressurised gases has drawn our attention to the large number of gas bottles and banks being stored on the site for increasingly long periods. Users are reminded that the rental charges for gas bottles and banks are based on a progressive rate depending on their period of use. To assist CERN in its efforts to optimise its operations in this field, you are kindly requested : to return empty or unused containers to the official gas distribution points as soon as possible, to try to limit reserve stocks, bearing in mind that standardised gases can be delivered within 36 hours. This will result in a higher turnover rate and in increased safety and will improve the availability of the gases. For all further enquiries, please contact Gas.Store@cern.ch by e-mail or call 72265. Thank you for your co-operation.

  17. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  18. Furthering critical institutionalism

    Directory of Open Access Journals (Sweden)

    Frances Dalton Cleaver

    2015-03-01

    Full Text Available This special issue furthers the study of natural resource management from a critical institutional perspective. Critical institutionalism (CI is a contemporary body of thought that explores how institutions dynamically mediate relationships between people, natural resources and society. It focuses on the complexity of institutions entwined in everyday social life, their historical formation, the interplay between formal and informal, traditional and modern arrangements, and the power relations that animate them. In such perspectives a social justice lens is often used to scrutinise the outcomes of institutional processes. We argue here that critical institutional approaches have potentially much to offer commons scholarship, particularly through the explanatory power of the concept of bricolage for better understanding institutional change.  Critical institutional approaches, gathering momentum over the past 15 years or so, have excited considerable interest but the insights generated from different disciplinary perspectives remain insufficiently synthesised. Analyses emphasising complexity can be relatively illegible to policy-makers, a fact which lessens their reach. This special issue therefore aims to synthesise critical institutional ideas and so to lay the foundation for moving beyond the emergent stage to make meaningful academic and policy impact. In bringing together papers here we define and synthesise key themes of critical institutionalism, outline the concept of institutional bricolage and identity some key challenges facing this school of thought.

  19. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.

    Science.gov (United States)

    Elsik, Christine G; Unni, Deepak R; Diesh, Colin M; Tayal, Aditi; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies.

  20. IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Jung Kyongyong

    2009-04-01

    Full Text Available Abstract Background Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. Results The Insect Mitochondrial Genome Database (IMGD is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. Conclusion The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site http://www.imgd.org/.

  1. User Environment Tracking and Problem Detection with XALT

    Energy Technology Data Exchange (ETDEWEB)

    Agrawal, Kapil [ORNL; Fahey, Mark R [ORNL; McLay, Robert [Texas Advanced Computing Center; James, Doug [Texas Advanced Computing Center

    2014-01-01

    This work improves our understanding of individual users software needs, then leverages that understanding to help stakeholders conduct business in a more efficient, effective, and systematic way. The product, XALT, builds on work that is already improving the user experience and enhancing support programs for thousands of users on twelve supercomputers across the United States and Europe. XALT will instrument individual jobs on high-end computers to generate a picture of the compilers, libraries, and other software that users need to run their jobs successfully. It will highlight the products our researchers need and do not need, and alert users and support staff to the root causes of software configuration issues as soon as the problems occur. A key objective of this work is generating the information needed to improve efficiency and effectiveness for an extensive community of stakeholders including users, sponsoring institutions, support organizations, and development teams. Efficiency, effectiveness, and responsible stewardship each require a clear picture of users needs. XALT is an important step in the quest to achieve that clarity.

  2. PopGenome: an efficient Swiss army knife for population genomic analyses in R.

    Science.gov (United States)

    Pfeifer, Bastian; Wittelsbürger, Ulrich; Ramos-Onsins, Sebastian E; Lercher, Martin J

    2014-07-01

    Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess statistical significance based on coalescent simulations. PopGenome's integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. Developers can easily incorporate new analyses methods into the PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License.

  3. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Bansal Manju

    2011-07-01

    Full Text Available Abstract Background As more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics. Findings Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability in the vicinity of all annotated translation start sites (TLS. Conclusion PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/.

  4. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  5. User involvement in care work

    DEFF Research Database (Denmark)

    Dybbroe, Betina; Kamp, Annette

    effectiveness and shared responsibility for care pathways. While NPM position users as consumers making their free choice, the user involvement paradigm underlines the users’ active participation in the mastering of their problems and disease. Research is scarce on this theme, and has until now primarily......In recent years user involvement has become a paradigm for transforming the health and social care sector. This development–also labelled empowerment, co-creation, partnership, patient-centeredness - is seen as a means to reform organizations in ways that enhance quality, economic cost...... addressed the way this paradigm affects the users, in specific sectors. However user involvement also affects working life. It may imply change and redistribution of tasks and identities between users and professionals, and may also transform the relations of care. In this paper we explore the possible...

  6. Time, Attitude, and User Participation

    DEFF Research Database (Denmark)

    Pries-Heje, Lene

    2008-01-01

    , equivocation, resistance and rejection depending on three things: (1) the dynamic between user and consultants, (2) the dynamic between different user groups, and (3) the understanding of technical, organizational and socio-technical options. When relating the empirical findings to existing theory on user...... be that the perception of usefulness of the system in any given phase of the implementation is heavily dependent on preceding events—the process. A process model analysis identifies eight episodes and nine encounters in the case showing that the user’s attitude towards the ERP system changes between acceptance...... participation, it is argued that the changes could be explained as a slide from influential user participation toward pseudo participation and back to influential participation, and that user participation in the context of ERP implementations raises new issues regarding user participation. Thus further...

  7. From Institutional Change to Experimentalist Institutions

    DEFF Research Database (Denmark)

    Hull Kristensen, Peer; Morgan, Glenn

    2012-01-01

    Institutionalist theory has shown how work and employment relations are shaped by national contexts. Recent developments in these theories have been increasingly concerned with the issue of institutional change. This reflects a shift in the nature of the competitive environment of firms from...... lead firms to constant experimentation in work organization as they seek to position themselves within systems of production and innovation that are global in nature. This creates a pressure for institutional change to facilitate the process of firm-level experimentation; it also tends to create...... a pressure for new experimental forms of institutions that are themselves searching for ways to improve their relevance. This change calls for extending the study of industrial relations and employment systems in the current era to investigate how new dynamic complementarities among employees, managers...

  8. User interface for personal accounting

    OpenAIRE

    Femec, Vasilij

    2008-01-01

    This diploma work describes a method for user interface development for an application Bilanca that is intended for a review of personal financial flows. It is a simple application that subtracts outcome from income and shows the current financial state. The work begins with a detailed analysis of the best possible user interface options that give the most comfortable user experience. This is followed by the implementation in a Delphi environment. The results show that even a simple applicati...

  9. Profiting from innovative user communities

    DEFF Research Database (Denmark)

    Jeppesen, Lars Bo

    platforms. This article explains how manufacturers can profit from their abilities to organize and facilitate a process of innovation by user communities and capture the value of the innovations produced in such communities. When managed strategically, two distinct, but not mutually exclusive business......, a manufacturer can incorporate and commercialize the best complements found in the user communities. Keywords: innovation, modding, user communities, software platform, business model. JEL code(s): L21; L23; O31; O32...

  10. Library user metaphors and services

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav

    How do library professionals talk about and refer to library users, and how is this significant? In recent decades, the library profession has conceived of users in at least five different ways, viewing them alternatively as citizens, clients, customers, guests, or partners. This book argues...... that these user metaphors crucially inform librarians' interactions with the public, and, by extension, determine the quality and content of the services received. The ultimate aim of the book is to provide library professionals with insights and tools for avoiding common pitfalls associated with false...... or professionally inadequate conceptions of library users....

  11. Library user metaphors and services

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav

    How do library professionals talk about and refer to library users, and how is this significant? In recent decades, the library profession has conceived of users in at least five different ways, viewing them alternatively as citizens, clients, customers, guests, or partners. This book argues...... that these user metaphors crucially inform librarians' interactions with the public, and, by extension, determine the quality and content of the services received. The ultimate aim of the book is to provide library professionals with insights and tools for avoiding common pitfalls associated with false...... or professionally inadequate conceptions of library users....

  12. User acquaintance with mobile interfaces.

    Science.gov (United States)

    Ehrler, Frederic; Walesa, Magali; Sarrey, Evelyne; Wipfli, Rolf; Lovis, Christian

    2013-01-01

    Handheld technology finds slowly its place in the healthcare world. Some clinicians already use intensively dedicated mobile applications to consult clinical references. However, handheld technology hasn't still broadly embraced to the core of the healthcare business, the hospitals. The weak penetration of handheld technology in the hospitals can be partly explained by the caution of stakeholders that must be convinced about the efficiency of these tools before going forward. In a domain where temporal constraints are increasingly strong, caregivers cannot loose time on playing with gadgets. All users are not comfortable with tactile manipulations and the lack of dedicated peripheral complicates entering data for novices. Stakeholders must be convinced that caregivers will be able to master handheld devices. In this paper, we make the assumption that the proper design of an interface may influence users' performances to record information. We are also interested to find out whether users increase their efficiency when using handheld tools repeatedly. To answer these questions, we have set up a field study to compare users' performances on three different user interfaces while recording vital signs. Some user interfaces were familiar to users, and others were totally innovative. Results showed that users' familiarity with smartphone influences their performances and that users improve their performances by repeating a task.

  13. DIRAC: Secure web user interface

    Energy Technology Data Exchange (ETDEWEB)

    Casajus Ramo, A [University of Barcelona, Diagonal 647, ES-08028 Barcelona (Spain); Sapunov, M, E-mail: sapunov@in2p3.f [Centre de Physique des Particules de Marseille, 163 Av de Luminy Case 902 13288 Marseille (France)

    2010-04-01

    Traditionally the interaction between users and the Grid is done with command line tools. However, these tools are difficult to use by non-expert users providing minimal help and generating outputs not always easy to understand especially in case of errors. Graphical User Interfaces are typically limited to providing access to the monitoring or accounting information and concentrate on some particular aspects failing to cover the full spectrum of grid control tasks. To make the Grid more user friendly more complete graphical interfaces are needed. Within the DIRAC project we have attempted to construct a Web based User Interface that provides means not only for monitoring the system behavior but also allows to steer the main user activities on the grid. Using DIRAC's web interface a user can easily track jobs and data. It provides access to job information and allows performing actions on jobs such as killing or deleting. Data managers can define and monitor file transfer activity as well as check requests set by jobs. Production managers can define and follow large data productions and react if necessary by stopping or starting them. The Web Portal is build following all the grid security standards and using modern Web 2.0 technologies which allow to achieve the user experience similar to the desktop applications. Details of the DIRAC Web Portal architecture and User Interface will be presented and discussed.

  14. BGD: a database of bat genomes.

    Directory of Open Access Journals (Sweden)

    Jianfei Fang

    Full Text Available Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD. BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

  15. Fuzzy assessment of health information system users' security awareness.

    Science.gov (United States)

    Aydın, Özlem Müge; Chouseinoglou, Oumout

    2013-12-01

    Health information systems (HIS) are a specific area of information systems (IS), where critical patient data is stored and quality health service is only realized with the correct use and efficient dissemination of this data to health workers. Therefore, a balance needs to be established between the levels of security and flow of information on HIS. Instead of implementing higher levels and further mechanisms of control to increase the security of HIS, it is preferable to deal with the arguably weakest link on HIS chain with respect to security: HIS users. In order to provide solutions and approaches for transforming users to the first line of defense in HIS but also to employ capable and appropriate candidates from the pool of newly graduated students, it is important to assess and evaluate the security awareness levels and characteristics of these existing and future users. This study aims to provide a new perspective to understand the phenomenon of security awareness of HIS users with the use of fuzzy analysis, and to assess the present situation of current and future HIS users of a leading medical and educational institution of Turkey, with respect to their security characteristics based on four different security scales. The results of the fuzzy analysis, the guide on how to implement this fuzzy analysis to any health institution and how to read and interpret these results, together with the possible implications of these results to the organization are provided.

  16. TMAP7 User Manual

    Energy Technology Data Exchange (ETDEWEB)

    Glen R. Longhurst

    2006-09-01

    The TMAP Code was written at the Idaho National Engineering and Environmental Laboratory by Brad Merrill and James Jones in the late 1980s as a tool for safety analysis of systems involving tritium. Since then it has been upgraded to TMAP4 and has been used in numerous applications including experiments supporting fusion safety, predictions for advanced systems such as the International Thermonuclear Experimental Reactor (ITER), and estimates involving tritium production technologies. Its further upgrade to TMAP2000 and now to TMAP7 was accomplished in response to several needs. TMAP and TMAP4 had the capacity to deal with only a single trap for diffusing gaseous species in solid structures. TMAP7 includes up to three separate traps and up to 10 diffusing species. The original code had difficulty dealing with heteronuclear molecule formation such as HD and DT. That has been removed. Under pre-specified boundary enclosure conditions and solution-law dependent diffusion boundary conditions, such as Sieverts' law, TMAP7 automatically generates heteronuclear molecular partial pressures when solubilities and partial pressures of the homonuclear molecular species are provided for law-dependent diffusion boundary conditions. A further sophistication is the addition of non-diffusing surface species. Atoms such as oxygen or nitrogen or formation and decay or combination of hydroxyl radicals on metal surfaces are sometimes important in reactions with diffusing hydrogen isotopes but do not themselves diffuse appreciably in the material. TMAP7 will accommodate up to 30 such surface species, allowing the user to specify relationships between those surface concentrations and partial pressures of gaseous species above the surfaces or to form them dynamically by combining diffusion species or other surface species. Additionally, TMAP7 allows the user to include a surface binding energy and an adsorption barrier energy. The code includes asymmetrical diffusion between the surface

  17. TMAP7 User Manual

    Energy Technology Data Exchange (ETDEWEB)

    Glen R. Longhurst

    2008-12-01

    The TMAP Code was written at the Idaho National Engineering and Environmental Laboratory by Brad Merrill and James Jones in the late 1980s as a tool for safety analysis of systems involving tritium. Since then it was upgraded to TMAP4 and has been used in numerous applications including experiments supporting fusion safety, predictions for advanced systems such as the International Thermonuclear Experimental Reactor (ITER), and estimates involving tritium production technologies. Its further upgrade to TMAP2000 and now to TMAP7 was accomplished in response to several needs. TMAP and TMAP4 had the capacity to deal with only a single trap for diffusing gaseous species in solid structures. TMAP7 includes up to three separate traps and up to 10 diffusing species. The original code had difficulty dealing with heteronuclear molecule formation such as HD and DT under solution-law dependent diffusion boundary conditions. That difficulty has been overcome. TMAP7 automatically generates heteronuclear molecular partial pressures when solubilities and partial pressures of the homonuclear molecular species are provided for law-dependent diffusion boundary conditions. A further sophistication is the addition of non-diffusing surface species. Atoms such as oxygen or nitrogen or formation and decay or combination of hydroxyl radicals on metal surfaces are sometimes important in reactions with diffusing hydrogen isotopes but do not themselves diffuse appreciably in the material. TMAP7 will accommodate up to 30 such surface species, allowing the user to specify relationships between those surface concentrations and partial pressures of gaseous species above the surfaces or to form them dynamically by combining diffusion species or other surface species. Additionally, TMAP7 allows the user to include a surface binding energy and an adsorption barrier energy. The code includes asymmetrical diffusion between the surface sites and regular diffusion sites in the bulk. All of the

  18. Users or Students? Privacy in University MOOCS.

    Science.gov (United States)

    Jones, Meg Leta; Regner, Lucas

    2016-10-01

    Two terms, student privacy and Massive Open Online Courses, have received a significant amount of attention recently. Both represent interesting sites of change in entrenched structures, one educational and one legal. MOOCs represent something college courses have never been able to provide: universal access. Universities not wanting to miss the MOOC wave have started to build MOOC courses and integrate them into the university system in various ways. However, the design and scale of university MOOCs create tension for privacy laws intended to regulate information practices exercised by educational institutions. Are MOOCs part of the educational institutions these laws and policies aim to regulate? Are MOOC users students whose data are protected by aforementioned laws and policies? Many university researchers and faculty members are asked to participate as designers and instructors in MOOCs but may not know how to approach the issues proposed. While recent scholarship has addressed the disruptive nature of MOOCs, student privacy generally, and data privacy in the K-12 system, we provide an in-depth description and analysis of the MOOC phenomenon and the privacy laws and policies that guide and regulate educational institutions today. We offer privacy case studies of three major MOOC providers active in the market today to reveal inconsistencies among MOOC platform and the level and type of legal uncertainty surrounding them. Finally, we provide a list of organizational questions to pose internally to navigate the uncertainty presented to university MOOC teams.

  19. Eprints Institutional Repository Software: A Review

    Directory of Open Access Journals (Sweden)

    Mike R. Beazley

    2011-01-01

    Full Text Available Setting up an institutional repository (IR can be a daunting task. There are many software packages out there, some commercial, some open source, all of which offer different features and functionality. This article will provide some thoughts about one of these software packages: Eprints. Eprints was one of the first IR software packages to appear and has been available for 10 years. It is under continual development by its creators at the University of Southampton and the current version is v3.2.3. Eprints is open-source, meaning that anyone can download and make use of the software for free and the software can be modified however the user likes. This presents clear advantages for institutions will smaller budgets and also for institutions that have programmers on staff. Eprints requires some additional software to run: Linux, Apache, MySQL, and Perl. This software is all open-source and already present on the servers of many institutions. There is now a version of Eprints that will run on Windows servers as well, which will make the adoption of Eprints even easier for some. In brief, Eprints is an excellent choice for any institution looking to get an IR up and running quickly and easily. Installation is straightforward as is the initial configuration. Once the IR is up and running, users may upload documents and provide the necessary metadata for the records by filling out a simple web form. Embargoes on published documents are handled elegantly by the software, and the software links to the SHERPA/RoMEO database so authors can easily verify their rights regarding IR submissions. Eprints has some drawbacks, which will be discussed later in the review, but on the whole it is easy to recommend to anyone looking to start an IR. However, It is less clear that an institution with an existing IR based on another software package should migrate to Eprints.

  20. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Science.gov (United States)

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

    CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG) format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  1. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Directory of Open Access Journals (Sweden)

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  2. Non-professional user`s understanding of Geographic Information

    DEFF Research Database (Denmark)

    Arleth, Mette

    2003-01-01

    -based online services and comprehend the information contents? Using the Gi-based online services qualitatively in the participatory process obviously requires knowledge of the non-professional user`s understanding and use of GI. This paper discusses the needs for research into this field as well as relevant...... research methods....

  3. Secure Genomic Computation through Site-Wise Encryption.

    Science.gov (United States)

    Zhao, Yongan; Wang, XiaoFeng; Tang, Haixu

    2015-01-01

    Commercial clouds provide on-demand IT services for big-data analysis, which have become an attractive option for users who have no access to comparable infrastructure. However, utilizing these services for human genome analysis is highly risky, as human genomic data contains identifiable information of human individuals and their disease susceptibility. Therefore, currently, no computation on personal human genomic data is conducted on public clouds. To address this issue, here we present a site-wise encryption approach to encrypt whole human genome sequences, which can be subject to secure searching of genomic signatures on public clouds. We implemented this method within the Hadoop framework, and tested it on the case of searching disease markers retrieved from the ClinVar database against patients' genomic sequences. The secure search runs only one order of magnitude slower than the simple search without encryption, indicating our method is ready to be used for secure genomic computation on public clouds.

  4. Echo™ User Manual

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Dustin Yewell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-06-06

    Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reporting and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.

  5. LCS Users Manual

    Energy Technology Data Exchange (ETDEWEB)

    A.J. Redd; D.W. Ignat

    1998-02-01

    The Lower Hybrid Simulation Code (LSC) is a computational model of lower hybrid current drive in the presence of an electric field. Details of geometry, plasma profiles, and circuit equations are treated. Two-dimensional velocity space effects are approximated in a one-dimensional Fokker-Planck treatment. The LSC was originally written to be a module for lower hybrid current drive called by the Tokamak Simulation Code (TSC), which is a numerical model of an axisymmetric tokamak plasma and the associated control systems. The TSC simulates the time evolution of a free boundary plasma by solving the MHD equations on a rectangular computational grid. The MHD equations are coupled to the external circuits (representing poloidal field coils) through the boundary conditions. The code includes provisions for modeling the control system, external heating, and fusion heating. The LSC module can also be called by the TRANSP code. TRANSP represents the plasma with an axisymmetric, fixed-boundary model and focuses on calculation of plasma transport to determine transport coefficients from data on power inputs and parameters reached. This manual covers the basic material needed to use the LSC. If run in conjunction with TSC, the "TSC Users Manual" should be consulted. If run in conjunction with TRANSP, on-line documentation will be helpful. A theoretical background of the governing equations and numerical methods is given. Information on obtaining, compiling, and running the code is also provided.

  6. Users page feedback

    CERN Multimedia

    2010-01-01

    In October last year the Communication Group proposed an interim redesign of the users’ web pages in order to improve the visibility of key news items, events and announcements to the CERN community. The proposed update to the users' page (right), and the current version (left, behind) This proposed redesign was seen as a small step on the way to much wider reforms of the CERN web landscape proposed in the group’s web communication plan.   The results are available here. Some of the key points: - the balance between news / events / announcements and access to links on the users’ pages was not right - many people asked to see a reversal of the order so that links appeared first, news/events/announcements last; - many people felt that we should keep the primary function of the users’ pages as an index to other CERN websites; - many people found the sections of the front page to be poorly delineated; - people do not like scrolling; - there were performance...

  7. Multisensor user authentication

    Science.gov (United States)

    Colombi, John M.; Krepp, D.; Rogers, Steven K.; Ruck, Dennis W.; Oxley, Mark E.

    1993-09-01

    User recognition is examined using neural and conventional techniques for processing speech and face images. This article for the first time attempts to overcome this significant problem of distortions inherently captured over multiple sessions (days). Speaker recognition uses both Linear Predictive Coding (LPC) cepstral and auditory neural model representations with speaker dependent codebook designs. For facial imagery, recognition is developed on a neural network that consists of a single hidden layer multilayer perceptron backpropagation network using either the raw data as inputs or principal components of the raw data computed using the Karhunen-Loeve Transform as inputs. The data consists of 10 subjects; each subject recorded utterances and had images collected for 10 days. The utterances collected were 400 rich phonetic sentences (4 sec), 200 subject name recordings (3 sec), and 100 imposter name recordings (3 sec). Face data consists of over 2000, 32 X 32 pixel, 8 bit gray scale images of the 10 subjects. Each subsystem attains over 90% verification accuracy individually using test data gathered on days following the training data.

  8. Genome engineering with targetable nucleases.

    Science.gov (United States)

    Carroll, Dana

    2014-01-01

    Current technology enables the production of highly specific genome modifications with excellent efficiency and specificity. Key to this capability are targetable DNA cleavage reagents and cellular DNA repair pathways. The break made by these reagents can produce localized sequence changes through inaccurate nonhomologous end joining (NHEJ), often leading to gene inactivation. Alternatively, user-provided DNA can be used as a template for repair by homologous recombination (HR), leading to the introduction of desired sequence changes. This review describes three classes of targetable cleavage reagents: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas RNA-guided nucleases (RGNs). As a group, these reagents have been successfully used to modify genomic sequences in a wide variety of cells and organisms, including humans. This review discusses the properties, advantages, and limitations of each system, as well as the specific considerations required for their use in different biological systems.

  9. Institutions as Knowledge Capital

    DEFF Research Database (Denmark)

    Foss, Nicolai Juul; Garzarelli, Giampaolo

    The paper revisits the socioeconomic theory of the Austrian School economist Ludwig M. Lachmann. By showing that the common claim that Lachmann's idiosyncratic (read: eclectic and multidisciplinary) approach to economics entails nihilism is unfounded, it reaches the following conclusions. (1...... theory without simultaneously denying the policy approach of comparative institutional analysis. (90 words.)KeywordsComparative institutional analysis, coordination, expectations, institutionalevolution, interpretative institutionalism.JEL CodesB31, B52, B53, D80....

  10. Modeling Inefficient Institutions

    OpenAIRE

    2006-01-01

    Why do inefficient %uF818 non-growth enhancing %uF818 institutions emerge and persist? This paper develops a simple framework to provide some answers to this question. Political institutions determine the allocation of political power, and economic institutions determine the framework for policy-making and place constraints on various policies. Groups with political power, the elite, choose policies to increase their income and to directly or indirectly transfer resources from the rest of soc...

  11. The ILL millennium symposium and European user meeting

    Energy Technology Data Exchange (ETDEWEB)

    Carlile, C.J.; Frick, B.; Radaelli, P.G.; Alba-Simionesco, C.; Chauty, A.; Niss, K.; Casas, F.; Sokolov, A.; Lequeux, F.; Montes, H.; Harrison, A.; Schurtenberger, P.; Dubbers, D.; Frank, A.; Gudel, H.U.; Wagner, R.; Vettier, C.; Gahler, R.; Protassov, K.; Geltenbort, P.; Plonka, C.; Simpson, G.; Pinston, J.A.; Genevey, J.; Urban, W.; Scherillo, A.; Orlandi, R.; Smith, A.G.; Mana, G.; Abele, H.; Van der Grinten, M.; Steuwer, A.; Klotz, S.; Hamel, G.; Strassle, C.Th.; Kervananois, N.; Koza, M.M.; Nishiyama, Y.; Langan, P.; Wada, M.; Sugiyama, J.; Chanzy, H.; Gunter, M.M.; Lerch, M.; Boysen, H.; Korte, C.; Suard, E.; Blanco, J.A.; Fernandez-Rodriguez, J.; Brown, P.J.; Stunault, A.; Katsumata, K.; Lovesey, S.W.; Iga, F.; Michimura, S.; Kremer, R.K.; Banks, M.; Capogna, L.; Enderle, M.; Gibson, B.J.; McIntyre, G.J.; Ouladdiaf, B.; Pujol, S.; Raggazzoni, J.L.; Rheinstadter, M.; Schefer, J.; Boehm, M.; Roessli, B.; Wills, A.S.; Ouladdiaf, B.; Lelievre-Berna, E.; Goff, J.P.; Toader, A.M.; Skoulatos, M.; Enderle, M.; Stewart, J.R.; Murani, A.; Roger, M.; Shannon, N.; Kaul, E.E.; Geibel, C.; Simonet, V.; Lhotel, E.; Paulsen, C.; Ressouche, E.; Staub, U.; Amato, A.; Baines, C.; Petrakovskii, G.A.; Bramwell, S.; Fukuhara, N.; Ebert, J.; Lindner, D.; Dauvergne, M.T.; Hartlein, M.; Timmins, P.; Conti, E.; Svergun, D.; Budayova-Spano, M.; Bonnete, F.; El Hajji, M.; Blakeley, M.P.; Meilleur, F.; Castro, B.; Gabel, F.; Ferrand, M.; Chenal, A.; Forge, V.; Fragneto, G.; Haertlein, M.; Gillet, D.; Haertlein, M

    2006-07-01

    Five years ago the ILL (Institute Laue-Langevin) convened the first Millennium symposium in order to launch an ambitious modernization program of instruments and infrastructure known as the ILL Millennium Program. After 5 years of activity we have decided to run a second such symposium. The scientific program of this Millennium Symposium will address the following points: -) instrumental and scientific achievements made possible by the Millennium Program, -) trends in science and engineering and the implications for the ILL, -) scenarios for future instrumentation and user support facilities, and -) the scientific priorities of the user community. This document gathers the abstracts of 63 contributions and 73 posters.

  12. Institutional pressures and HRM: developing institutional fit

    NARCIS (Netherlands)

    Boon, C.; Paauwe, J.; Boselie, J.P.P.E.F.; den Hartog, D.N.

    2009-01-01

    Purpose – Research in strategic human resource management (HRM) has focused mainly on the effects of HRM practices or systems on organizational effectiveness. However, institutional theory argues that besides being financially successful, organizations also need legitimacy to survive. Owing to the t

  13. Fungal genome resources at NCBI.

    Science.gov (United States)

    Robbertse, B; Tatusova, T

    2011-09-01

    The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

  14. Figure 2 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Grouping and sorting genomic data in IGV. The IGV user interface displaying 202 glioblastoma samples from TCGA. Samples are grouped by tumor subtype (second annotation column) and data type (first annotation column) and sorted by copy number of the EGFR locus (middle column). Adapted from Figure 1; Robinson et al. 2011

  15. Figure 4 from Integrative Genomics Viewer: Visualizing Big Data | Office of Cancer Genomics

    Science.gov (United States)

    Gene-list view of genomic data. The gene-list view allows users to compare data across a set of loci. The data in this figure includes copy number, mutation, and clinical data from 202 glioblastoma samples from TCGA. Adapted from Figure 7; Thorvaldsdottir H et al. 2012

  16. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

    OpenAIRE

    Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Debra J. H. Mathews

    2015-01-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

  17. Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

    OpenAIRE

    Davidsen, Tanja; Madupu, Ramana; Sterk, Peter; Field, Dawn; Garrity, George; Gilbert, Jack; Glöckner, Frank Oliver; Hirschman, Lynette; Kolker, Eugene; Kottmann, Renzo; Kyrpides, Nikos; Meyer, Folker; Morrison, Norman; Schriml, Lynn; Tatusova, Tatiana

    2010-01-01

    This report summarizes the proceedings of the 9th workshop of the Genomic Standards Consortium (GSC), held at the J. Craig Venter Institute, Rockville, MD, USA. It was the first GSC workshop to have open registration and attracted over 90 participants. This workshop featured sessions that provided overviews of the full range of ongoing GSC projects. It included sessions on Standards in Genomic Sciences, the open access journal of the GSC, building standards for genome annotation, the M5 platf...

  18. Policies to Promote User Innovation

    DEFF Research Database (Denmark)

    Svensson, Peter; Hartmann, Rasmus Koss

    As it becomes apparent that users are an important source in innovation in society and in individual organizations, scholars are realizing that user-directed innovation policy may contribute to improving social welfare. How such policy might be designed, however, is uncertain, as are the costs an...

  19. User-Centered Design Gymkhana

    OpenAIRE

    Garreta Domingo, Muriel; Almirall Hill, Magí; Mor Pera, Enric

    2007-01-01

    The User-centered design (UCD) Gymkhana is a tool for human-computer interaction practitioners to demonstrate through a game the key user-centered design methods and how they interrelate in the design process.The target audiences are other organizational departments unfamiliar with UCD but whose work is related to the definition, cretaion, and update of a product service.

  20. Scientific customer needs - NASA user

    Science.gov (United States)

    Black, David C.

    1987-01-01

    Some requirements for scientific users of the Space Station are considered. The use of testbeds to evaluate design concepts for information systems, and for interfacing between designers and builders of systems is examined. The need for an information system that provides an effective interaction between ground-based users and their space-based equipment is discussed.