WorldWideScience

Sample records for browser database update

  1. The UCSC Genome Browser database: 2017 update.

    Science.gov (United States)

    Tyner, Cath; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Eisenhart, Christopher; Fischer, Clayton M; Gibson, David; Gonzalez, Jairo Navarro; Guruvadoo, Luvina; Haeussler, Maximilian; Heitner, Steve; Hinrichs, Angie S; Karolchik, Donna; Lee, Brian T; Lee, Christopher M; Nejad, Parisa; Raney, Brian J; Rosenbloom, Kate R; Speir, Matthew L; Villarreal, Chris; Vivian, John; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

    2017-01-04

    Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. The UCSC genome browser database: update 2007

    DEFF Research Database (Denmark)

    Kuhn, R M; Karolchik, D; Zweig, A S

    2006-01-01

    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

  3. The UCSC Genome Browser Database: 2008 update

    DEFF Research Database (Denmark)

    Karolchik, D; Kuhn, R M; Baertsch, R

    2007-01-01

    The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrat...

  4. The UCSC Genome Browser Database: update 2006

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  5. The UCSC Genome Browser database: 2018 update.

    Science.gov (United States)

    Casper, Jonathan; Zweig, Ann S; Villarreal, Chris; Tyner, Cath; Speir, Matthew L; Rosenbloom, Kate R; Raney, Brian J; Lee, Christopher M; Lee, Brian T; Karolchik, Donna; Hinrichs, Angie S; Haeussler, Maximilian; Guruvadoo, Luvina; Navarro Gonzalez, Jairo; Gibson, David; Fiddes, Ian T; Eisenhart, Christopher; Diekhans, Mark; Clawson, Hiram; Barber, Galt P; Armstrong, Joel; Haussler, David; Kuhn, Robert M; Kent, W James

    2017-11-02

    The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Web Browser Security Update Effectiveness

    Science.gov (United States)

    Duebendorfer, Thomas; Frei, Stefan

    We analyze the effectiveness of different Web browser update mechanisms on various operating systems; from Google Chrome's silent update mechanism to Opera's update requiring a full re-installation. We use anonymized logs from Google's world wide distributed Web servers. An analysis of the logged HTTP user-agent strings that Web browsers report when requesting any Web page is used to measure the daily browser version shares in active use. To the best of our knowledge, this is the first global scale measurement of Web browser update effectiveness comparing four different Web browser update strategies including Google Chrome. Our measurements prove that silent updates and little dependency on the underlying operating system are most effective to get users of Web browsers to surf the Web with the latest browser version.

  7. JPL Small Body Database Browser

    Data.gov (United States)

    National Aeronautics and Space Administration — The JPL Small-Body Database Browser provides data for all known asteroids and many comets. Newly discovered objects and their orbits are added on a daily basis....

  8. A genome browser database for rice ( Oryza sativa ) and Chinese ...

    African Journals Online (AJOL)

    We have constructed an integrated genome browser database for sequence analysis of rice (Oryza sativa) and Chinese cabbage (Brassica rapa) genomes. The genome browser for Arabidopsis (Arabidopsis thaliana) was included to provide the comparative analysis with Chinese cabbage. The genome browser of rice ...

  9. A genome browser database for rice (Oryza sativa) and Chinese ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... 2National Institute of Horticultural and Herbal Science (NIHHS), Naju 520-821, Korea. 3High-Tech ... We have constructed an integrated genome browser database for sequence analysis of rice (Oryza ... Chinese cabbage genomes, users can obtain information using comparative genomics methods and.

  10. GBshape: a genome browser database for DNA shape annotations.

    Science.gov (United States)

    Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J; Parker, Stephen C J; Nuzhdin, Sergey V; Tullius, Thomas D; Rohs, Remo

    2015-01-01

    Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. The Pain Genes Database: An interactive web browser of pain-related transgenic knockout studies.

    Science.gov (United States)

    Lacroix-Fralish, Michael L; Ledoux, Jean B; Mogil, Jeffrey S

    2007-09-01

    The transgenic knockout mouse is one of the most important tools of modern biology, and commonly employed by pain researchers to examine the function of genes of interest. Over 400 papers, at a current rate of >60 papers per year, have been published to date describing a statistically significant behavioral pain "phenotype" resulting from the null mutation of a single gene. The standard literature review format is incapable of providing a sufficiently broad and up-to-date overview of the field. We have therefore constructed the Pain Genes Database, an interactive, web-based data browser designed to allow easy access to and analysis of the published pain-related phenotypes of mutant mice (over 200 different mutants at the date of submission). Manuscripts describing results of pain-relevant knockout studies were identified via Medline search. Manuscripts were included in the database if they described the testing of a spontaneous or genetically engineered mutant mouse with null expression of a single gene on a behavioral assay of acute or tonic nociception, injury- or stimulus-induced hypersensitivity (i.e., allodynia or hyperalgesia), or drug- or stress-induced inhibition of nociception (i.e., analgesia), and reported at least one statistically significant difference between the mutant mice and their simultaneously tested wildtype controls. The database features two levels of exploration, one allowing the identification of genes by name, acronym, genomic position or "summary" phenotype, and the other allowing in-depth browsing, paper-by-paper, of specific phenotypes and test parameters. Links to genetic databases and Medline abstracts are provided for each gene and paper. It is our intention to update the database continually based on weekly Medline searches. This database should provide pain researchers with a useful and easy-to-use tool for the generation of novel hypotheses regarding the roles of genes and their protein products in pain processing and modulation

  12. Wind turbine reliability database update.

    Energy Technology Data Exchange (ETDEWEB)

    Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.; Veers, Paul S.

    2009-03-01

    This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

  13. Updating a cracked database

    NARCIS (Netherlands)

    S. Idreos (Stratos); M.L. Kersten (Martin); S. Manegold (Stefan)

    2007-01-01

    textabstractA cracked database is a datastore continuously reorganized based on operations being executed. For each query, the data of interest is physically reclustered to speed-up future access to the same, overlapping or even disjoint data. This way, a cracking DBMS self-organizes and adapts

  14. Update History of This Database - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Update History of This Database Date Update contents 2017/03/13 SKIP Stemcell Database... English archive site is opened. 2013/03/29 SKIP Stemcell Database ( https://www.skip.med.k...eio.ac.jp/SKIPSearch/top?lang=en ) is opened. About This Database Database Description Download License Update History of This Databa...se Site Policy | Contact Us Update History of This Database - SKIP Stemcell Database | LSDB Archive ...

  15. Update History of This Database - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Update History of This Database Date Update contents 2017/02/27 Arabidopsis Phenome Data...base English archive site is opened. - Arabidopsis Phenome Database (http://jphenom...e.info/?page_id=95) is opened. About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Update History of This Database - Arabidopsis Phenome Database | LSDB Archive ...

  16. Update History of This Database - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Yeast Interacting Proteins Database Update History of This Database Date Update contents 201... Download License Update History of This Database Site Policy | Contact Us Update Histor

  17. Update History of This Database - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Update History of This Database Date Update contents 2014/05/07 The co...ntact information is corrected. The features and manner of utilization of the database are corrected. 2014/02/04 Trypanosomes Databas...e English archive site is opened. 2011/04/04 Trypanosomes Database ( http://www.tan...paku.org/tdb/ ) is opened. About This Database Database Description Download Lice...nse Update History of This Database Site Policy | Contact Us Update History of This Database - Trypanosomes Database | LSDB Archive ...

  18. Update History of This Database - Society Catalog | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Society Catalog Update History of This Database Date Update contents 2013/05/13 The original.... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Society Catalog | LSDB Archive ...

  19. Update History of This Database - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us TMFunction Update History of This Database Date Update contents 2017/01/23 TMFunction Englis... Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - TMFunction | LSDB Archive ...

  20. Update History of This Database - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Taxonomy Icon Update History of This Database Date Update contents 2013/06/19 Taxonomy Icon ...About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Taxonomy Icon | LSDB Archive ...

  1. Update History of This Database - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Gclust Server Update History of This Database Update History of This Database Date Update co...o.ac.jp/ ) is released. About This Database Database Description Download License Update History of This Dat...abase Site Policy | Contact Us Update History of This Database - Gclust Server | LSDB Archive ...

  2. Update History of This Database - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us MicrobeDB.jp Update History of This Database Date Update contents 2017/06/29 Archive V2 is r...ion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - MicrobeDB.jp | LSDB Archive ...

  3. Update History of This Database - RGP physicalmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RGP physicalmap Update History of This Database Date Update contents 2015/07/07 RGP physical...escription Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RGP physicalmap | LSDB Archive ...

  4. Update History of This Database - Metabolonote | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Metabol...onote Update History of This Database Date Update contents 2016/06/22 Metabolonote En...glish archive site is opened. 2012/12/28 Metabolonote ( http://webs2.kazusa.or.jp/metabolonote/ ) is opened.... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Metabolonote | LSDB Archive ...

  5. Update History of This Database - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us SSBD Update History of This Database Date Update contents 2016/07/25 SSBD English archive si...tion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - SSBD | LSDB Archive ... ...te is opened. 2013/09/03 SSBD ( http://ssbd.qbic.riken.jp/ ) is opened. About This Database Database Descrip

  6. Update History of This Database - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us SAHG Update History of This Database Date Update contents 2016/05/09 SAHG English archive si...te is opened. 2009/10 SAHG ( http://bird.cbrc.jp/sahg ) is opened. About This Database Database Description ...Download License Update History of This Database Site Policy | Contact Us Update History of This Database - SAHG | LSDB Archive ...

  7. Update History of This Database - DMPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DMPD Update History of This Database Date Update contents 2010/03/29 DMPD English archive si....jp/macrophage/ ) is released. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - DMPD | LSDB Archive ...

  8. Update History of This Database - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RMOS Update History of This Database Date Update contents 2015/10/27 RMOS English archive si...12 RMOS (http://cdna01.dna.affrc.go.jp/RMOS/) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - RMOS | LSDB Archive ...

  9. Update History of This Database - RGP gmap98 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RGP gmap98 Update History of This Database Date Update contents 2015/02/12 RGP gmap98 Englis...ap98/geneticmap98.html) is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - RGP gmap98 | LSDB Archive ...

  10. Update History of This Database - Togo Picture Gallery | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Togo Picture Gallery Update History of This Database Date Update contents 2017/05/16 Togo Pi...cs.html ) is opened. About This Database Database Description Download License Update History of This Databa...se Site Policy | Contact Us Update History of This Database - Togo Picture Gallery | LSDB Archive ...

  11. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj - Ortholog DB Update History of This Database Date Update contents 2017/03/07 PGDBj Or...log-db.html ) is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ...

  12. Update History of This Database - NBDC NikkajiRDF | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us NBDC NikkajiRDF Update History of This Database Date Update contents 2017/02/17 Archive vers...iweb.jst.go.jp/ ) is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - NBDC NikkajiRDF | LSDB Archive ...

  13. Update History of This Database - RGP gmap2000 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RGP gmap2000 Update History of This Database Date Update contents 2015/03/10 RGP gmap2000 En...icmap2000/index.html) is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - RGP gmap2000 | LSDB Archive ...

  14. Update History of This Database - RGP estmap2001 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RGP estmap2001 Update History of This Database Date Update contents 2015/04/02 RGP estmap200...stmap2001/index.html) is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - RGP estmap2001 | LSDB Archive ...

  15. Update History of This Database - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Open TG-GATEs Update History of This Database Date Update contents 2015/10/01 URLs of the da...nload License Update History of This Database Site Policy | Contact Us Update History of This Database - Open TG-GATEs | LSDB Archive ... .../02/25 Open TG-GATEs( http://toxico.nibio.go.jp/ ) is released. About This Database Database Description Dow

  16. Update History of This Database - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RPSD Update History of This Database Date Update contents 2015/10/16 The original website is...005/02/14 Last update at RPSD (http://structure.rice.dna.affrc.go.jp/plant/index.html). About This Database Database... Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RPSD | LSDB Archive ...

  17. Update History of This Database - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PSCDB Update History of This Database Date Update contents 2016/11/30 PSCDB English archive ...abase Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - PSCDB | LSDB Archive ... ...site is opened. 2011/11/13 PSCDB ( http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/ ) is opened. About This Dat

  18. Update History of This Database - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us GRIPDB Update History of This Database Date Update contents 2017/07/19 GRIPDB English archiv...base Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - GRIPDB | LSDB Archive ... ...e site is opened. 2009/01/30 GRIPDB (http://grip.cbrc.jp/GDB/index.html) is opened. About This Database Data

  19. Update History of This Database - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Dicty_cDB Update History of This Database Date Update contents 2015/01/09 The original websi...ase Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Dicty_cDB | LSDB Archive ... ...te information was updated. 2010/03/29 Dicty_cDB English archive site is opened. 2009/8 Data is updated. 199...6/12 Dicty_cDB(http://dictycdb.biol.tsukuba.ac.jp/cDNA/database.html) is released. About This Database Datab

  20. Update History of This Database - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us tRNADB-CE Update History of This Database Date Update contents 2014/08/25 Contact address, D.../trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/index.cgi ) is released. About This Database Database Description ...Download License Update History of This Database Site Policy | Contact Us Update History of This Database - tRNADB-CE | LSDB Archive ... ... Updated The data is updated to the latest version which is equivalent to the data version 6.1 of the origin

  1. Update History of This Database - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RED Update History of This Database Date Update contents 2015/12/21 Rice Expression Database English archi...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RED | LSDB Archive ... ...ve site is opened. 2000/10/1 Rice Expression Database ( http://red.dna.affrc.go.jp/RED/ ) is opened. About Thi

  2. Update History of This Database - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RPD Update History of This Database Date Update contents 2016/02/02 Rice Proteome Database English archi...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - RPD | LSDB Archive ... ...ve site is opened. 2003/01/07 Rice Proteome Database ( http://gene64.dna.affrc.go.jp/RPD/ ) is opened. About Thi

  3. The PDBbind database: methodologies and updates.

    Science.gov (United States)

    Wang, Renxiao; Fang, Xueliang; Lu, Yipin; Yang, Chao-Yie; Wang, Shaomeng

    2005-06-16

    We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein-ligand complexes that meet our definition. Experimentally determined binding affinities (K(d), K(i), and IC(50)) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a "refined set", which is of particular value as a standard data set for docking and scoring studies. All of the final data, including binding affinity data, reference citations, and processed structural files, have been incorporated into the PDBbind database accessible on-line at http:// www.pdbbind.org/.

  4. Update History of This Database - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us D-HaploDB Update History of This Database Date Update contents 2016/12/13 Description of the.../orca.gen.kyushu-u.ac.jp/) is released. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - D-HaploDB | LSDB Archive ... ... original site is updated. 2011/09/22 D-HaploDB English archive site is opened. 2005/07/20 D-HaploDB (http:/

  5. Update History of This Database - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DGBY Update History of This Database Date Update contents 2014/10/20 The URL of the portal s...aro.affrc.go.jp/yakudachi/yeast/index.html ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - DGBY | LSDB Archive ... ... Expression of attribution in License is updated. 2012/03/08 DGBY English archive site is opened. 2006/10/02

  6. Update History of This Database - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us JSNP Update History of This Database Date Update contents 2016/12/06 Description of the orig...ption Download License Update History of This Database Site Policy | Contact Us Update History of This Database - JSNP | LSDB Archive ... ...inal site (http://snp.ims.u-tokyo.ac.jp/index.html) is updated. 2016/02/01 JSNP English archive site is open...ed. 2000/07/07 JSNP (http://snp.ims.u-tokyo.ac.jp/index.html) is opened. About This Database Database Descri

  7. Update History of This Database - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us KAIKOcDNA Update History of This Database Date Update contents 2014/10/20 The URL of the dat... database ( http://sgp.dna.affrc.go.jp/EST/ ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - KAIKOcDNA | LSDB Archive ... ...abase maintenance site is changed. 2014/10/08 KAIKOcDNA English archive site is opened. 2004/04/12 KAIKOcDNA

  8. Update History of This Database - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PLACE Update History of This Database Date Update contents 2016/08/22 The contact address is...s Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - PLACE | LSDB Archive ... ... changed. 2014/10/20 The URLs of the database maintenance site and the portal site are changed. 2014/07/17 PLACE English archi

  9. Update History of This Database - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us RMG Update History of This Database Date Update contents 2016/08/22 The contact address is c...dna.affrc.go.jp/ ) is opened. About This Database Database Description Download License Update Hi...story of This Database Site Policy | Contact Us Update History of This Database - RMG | LSDB Archive ... ... URL of the portal site is changed. 2013/08/07 RMG archive site is opened. 2002/09/25 RMG ( http://rmg.rice.

  10. Update History of This Database - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us GETDB Update History of This Database Date Update contents 2014/05/09 URL of the portal site...GETDB/getdb.html ) is released. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - GETDB | LSDB Archive ... ... is changed. 2010/03/29 GETDB English archive site is opened. 2003/8/1 GETDB( http://kyotofly.kit.jp/stocks/

  11. Update History of This Database - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us AcEST Update History of This Database Date Update contents 2013/01/10 Errors found on AcEST ...s Database Database Description Download License Update History of This Data...base Site Policy | Contact Us Update History of This Database - AcEST | LSDB Archive ... ...Conting data have been correceted. For details, please refer to the following page. Data correction 2010/03/29 AcEST English archi

  12. Update History of This Database - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us KOME Update History of This Database Date Update contents 2014/10/22 The URL of the whole da...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - KOME | LSDB Archive ... ... portal site are changed. 2013/12/17 The URL of the portal site is changed. 2013/07/30 KOME English archive ...site is opened. 2003/07/18 KOME ( http://cdna01.dna.affrc.go.jp/cDNA/ ) is opened. About Thi

  13. Update History of This Database - ConfC | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us ConfC Update History of This Database Date Update contents 2016/09/20 ConfC English archive ...tion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - ConfC | LSDB Archive ... ...site is opened. 2005/05/01 ConfC (http://mbs.cbrc.jp/ConfC/) is opened. About This Database Database Descrip

  14. Update History of This Database - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us fRNAdb Update History of This Database Date Update contents 2016/03/29 fRNAdb English archiv...on Download License Update History of This Database Site Policy | Contact Us Update History of This Database - fRNAdb | LSDB Archive ... ...e site is opened. 2006/12 fRNAdb ( http://www.ncrna.org/ ) is opened. About This Database Database Descripti

  15. Update History of This Database - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us TogoTV Update History of This Database Date Update contents 2017/05/12 TogoTV English archiv...ription Download License Update History of This Database Site Policy | Contact Us Update History of This Database - TogoTV | LSDB Archive ... ...e site is opened. 2007/07/20 TogoTV ( http://togotv.dbcls.jp/ ) is opened. About This Database Database Desc

  16. Update History of This Database - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us TP Atlas Update History of This Database Date Update contents 2013/12/16 The email address i...s ( http://www.tanpaku.org/tpatlas/ ) is opened. About This Database Database Description Download License Update History of Thi...s Database Site Policy | Contact Us Update History of This Database - TP Atlas | LSDB Archive ... ...n the contact information is corrected. 2013/11/19 TP Atlas English archive site is opened. 2008/4/1 TP Atla

  17. Update History of This Database - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Q-TARO Update History of This Database Date Update contents 2014/10/20 The URL of the portal...ption Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Q-TARO | LSDB Archive ... ... site is changed. 2013/12/17 The URL of the portal site is changed. 2013/12/13 Q-TARO English archive site i...s opened. 2009/11/15 Q-TARO ( http://qtaro.abr.affrc.go.jp/ ) is opened. About This Database Database Descri

  18. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

    Directory of Open Access Journals (Sweden)

    Guillermo Barturen

    2013-01-01

    Full Text Available Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.

  19. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

    OpenAIRE

    Fernández-Suárez, Xosé M.; Rigden, Daniel J.; Galperin, Michael Y.

    2013-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, D...

  20. Update History of This Database - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us GenLibi Update History of This Database Date Update contents 2014/03/25 GenLibi English archi...base Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - GenLibi | LSDB Archive ... ...ve site is opened. 2007/03/01 GenLibi ( http://gene.biosciencedbc.jp/ ) is opened. About This Database Data

  1. Update History of This Database - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us dbQSNP Update History of This Database Date Update contents 2017/02/16 dbQSNP English archiv...e Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - dbQSNP | LSDB Archive ... ...e site is opened. 2002/10/23 dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/) is opened. About This Database Databas

  2. Update History of This Database - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DB-SPIRE Update History of This Database Date Update contents 2017/02/16 DB-SPIRE English archi...ase Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - DB-SPIRE | LSDB Archive ... ...ve site is opened. 2005/04/01 DB-SPIRE (http://mbs.cbrc.jp/DB-SPIRE) is opened. About This Database Datab

  3. Update of the Diatom EST Database: a new tool for digital transcriptomics

    Science.gov (United States)

    Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

    2009-01-01

    The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

  4. The Papillomavirus Episteme: a major update to the papillomavirus sequence database

    Science.gov (United States)

    Van Doorslaer, Koenraad; Li, Zhiwen; Xirasagar, Sandhya; Maes, Piet; Kaminsky, David; Liou, David; Sun, Qiang; Kaur, Ramandeep; Huyen, Yentram; McBride, Alison A.

    2017-01-01

    The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/. PMID:28053164

  5. Update History of This Database - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us FANTOM5 Update History of This Database Date Update contents 2017/03/14 FANTOM5 English archi...escription Download License Update History of This Database Site Policy | Contact Us Update History of This Database - FANTOM5 | LSDB Archive ... ...ve site is opened. 2016/12/20 Archive V2 is released. The following data are added. 「 (reprocessed)Heliscop... CAGE TSS aggregation 」 「 CAGE peaks 」 2015/12/07 FANTOM5 archive site is opened. (Archive V1) 2014/03/27 FA

  6. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser.

    Science.gov (United States)

    Walsh, Thomas P; Webber, Caleb; Searle, Stephen; Sturrock, Shane S; Barton, Geoffrey J

    2008-07-01

    SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance. This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks. Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases. A web server developed to run SCANPS searches is now available at http://www.compbio.dundee.ac.uk/www-scanps. The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains. The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly. For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.

  7. Update History of This Database - Nikkaji-InChI Mapping Table | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Nikkaji-InChI Mapping Table Update History of This Database Date Update contents 2016/08/26 ...InChI Mapping Table English archive site is opened. About This Database Database Description Download License Update Histor...y of This Database Site Policy | Contact Us Update History of This Database - Nikkaji-InChI Mapping Table | LSDB Archive ...

  8. ODB: a database for operon organizations, 2011 update

    OpenAIRE

    Okuda, Shujiro; Yoshizawa, Akiyasu C

    2011-01-01

    ODB (Operon DataBase) aims to collect data of all known and conserved operons in completely sequenced genomes. Three newly updated features of this database have been added as follows: (i) Data from included operons were updated. The genome-wide analysis of transcription and transcriptional units has become popular recently and ODB successfully integrates these high-throughput operon data, including genome-wide transcriptional units of five prokaryotes and two eukaryotes. The current version ...

  9. Update History of This Database - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Budding yeast cDNA sequencing project Update History of This Database Date Update contents 2...cription Download License Update History of This Database Site Policy | Contact Us Update Histor

  10. Updating and maintaining the accident database.

    CSIR Research Space (South Africa)

    Jaku, EP

    2001-03-01

    Full Text Available A database was developed in 1990 to store and allow analysis of information on rockfall and rockburst fatal accidents that have occurred in the South African gold mining industry. The information populating the database is extracted from the inquiry...

  11. The Danish (Q)SAR Database Update Project

    DEFF Research Database (Denmark)

    Nikolov, Nikolai Georgiev; Dybdahl, Marianne; Abildgaard Rosenberg, Sine

    2013-01-01

    The Danish (Q)SAR Database is a collection of predictions from quantitative structure–activity relationship ((Q)SAR) models for over 70 environmental and human health-related endpoints (covering biodegradation, metabolism, allergy, irritation, endocrine disruption, teratogenicity, mutagenicity......, carcinogenicity and others), each of them available for 185,000 organic substances. The database has been available online since 2005 (http://qsar.food.dtu.dk). A major update project for the Danish (Q)SAR database is under way, with a new online release planned in the beginning of 2015. The updated version...

  12. The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

    Science.gov (United States)

    Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

    2014-01-01

    The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

  13. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    Science.gov (United States)

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  14. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    Science.gov (United States)

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-04

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  15. Updated site compilation of the Latin American Pollen Database

    NARCIS (Netherlands)

    Flantua, S.G.A.; Hooghiemstra, H.; Grimm, E.C.; Behling, H.; Bush, M.B; González-Arrango, C.; Gosling, W.D.; Ledru, M.-P.; Lozano-Garciá, S.; Maldonado, A.; Prieto, A.R.; Rull, V.; van Boxel, J.H.

    2015-01-01

    The updated inventory of the Latin American Pollen Database (LAPD) offers a wide range of new insights. This paper presents a systematic compilation of palynological research in Latin America. A comprehensive inventory of publications in peer-reviewed and grey literature shows a major expansion of

  16. 77 FR 71089 - Pilot Loading of Aeronautical Database Updates

    Science.gov (United States)

    2012-11-29

    ... Association (AOPA), stated that a definition for databases approved for pilot-performed updates would, in... navigation and communication. AOPA suggested that the FAA should write the rule to accommodate later... date would negatively impact system performance. Several commenters, including AOPA and NetJets, were...

  17. PGSB PlantsDB: updates to the database framework for comparative plant genome research.

    Science.gov (United States)

    Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C; Martis, Mihaela M; Seidel, Michael; Kugler, Karl G; Gundlach, Heidrun; Mayer, Klaus F X

    2016-01-04

    PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/). © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. ODB: a database for operon organizations, 2011 update.

    Science.gov (United States)

    Okuda, Shujiro; Yoshizawa, Akiyasu C

    2011-01-01

    ODB (Operon DataBase) aims to collect data of all known and conserved operons in completely sequenced genomes. Three newly updated features of this database have been added as follows: (i) Data from included operons were updated. The genome-wide analysis of transcription and transcriptional units has become popular recently and ODB successfully integrates these high-throughput operon data, including genome-wide transcriptional units of five prokaryotes and two eukaryotes. The current version of our database contains information from about 10,000 known operons in more than 50 genomes, and more than 400,000 conserved operons obtained from more than 1000 bacterial genomes. (ii) ODB proposes the idea of reference operons as a new operon prediction tool. A reference operon, a set of possible orthologous genes that organize operons, is defined by clustering all known operons. A large number of known operons, including the recently added genome-wide analysis of operons, allowed us to define more reliable reference operons. (iii) ODB also provides new graphical interfaces. One is for comparative analyses of operon structures in multiple genomes. The other is for visualization of possible operons in multiple genomes obtained from the reference operons. The 2011 updated version of ODB is now available at http://operondb.jp/.

  19. Updated Palaeotsunami Database for Aotearoa/New Zealand

    Science.gov (United States)

    Gadsby, M. R.; Goff, J. R.; King, D. N.; Robbins, J.; Duesing, U.; Franz, T.; Borrero, J. C.; Watkins, A.

    2016-12-01

    The updated configuration, design, and implementation of a national palaeotsunami (pre-historic tsunami) database for Aotearoa/New Zealand (A/NZ) is near completion. This tool enables correlation of events along different stretches of the NZ coastline, provides information on frequency and extent of local, regional and distant-source tsunamis, and delivers detailed information on the science and proxies used to identify the deposits. In A/NZ a plethora of data, scientific research and experience surrounds palaeotsunami deposits, but much of this information has been difficult to locate, has variable reporting standards, and lacked quality assurance. The original database was created by Professor James Goff while working at the National Institute of Water & Atmospheric Research in A/NZ, but has subsequently been updated during his tenure at the University of New South Wales. The updating and establishment of the national database was funded by the Ministry of Civil Defence and Emergency Management (MCDEM), led by Environment Canterbury Regional Council, and supported by all 16 regions of A/NZ's local government. Creation of a single database has consolidated a wide range of published and unpublished research contributions from many science providers on palaeotsunamis in A/NZ. The information is now easily accessible and quality assured and allows examination of frequency, extent and correlation of events. This provides authoritative scientific support for coastal-marine planning and risk management. The database will complement the GNS New Zealand Historical Database, and contributes to a heightened public awareness of tsunami by being a "one-stop-shop" for information on past tsunami impacts. There is scope for this to become an international database, enabling the pacific-wide correlation of large events, as well as identifying smaller regional ones. The Australian research community has already expressed an interest, and the database is also compatible with a

  20. Update of the androgen receptor gene mutations database.

    Science.gov (United States)

    Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

    1999-01-01

    The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). Copyright 1999 Wiley-Liss, Inc.

  1. The proteome browser web portal.

    Science.gov (United States)

    Goode, Robert J A; Yu, Simon; Kannan, Anitha; Christiansen, Jeffrey H; Beitz, Anthony; Hancock, William S; Nice, Edouard; Smith, A Ian

    2013-01-04

    In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), aimed at identifying and characterizing the proteome of the human body. To support complete coverage, one arm of the project will take a gene- or chromosomal-centric strategy (C-HPP) aimed at identifying at least one protein product from each protein-coding gene. Despite multiple large international biological databases housing genomic and protein data, there is currently no single system that integrates updated pertinent information from each of these data repositories and assembles the information into a searchable format suitable for the type of global proteomics effort proposed by the C-HPP. We have undertaken the goal of producing a data integration and analysis software system and browser for the C-HPP effort and of making data collections from this resource discoverable through metadata repositories, such as Australian National Data Service's Research Data Australia. Here we present our vision and progress toward the goal of developing a comprehensive data integration and analysis software tool that provides a snapshot of currently available proteomic related knowledge around each gene product, which will ultimately assist in analyzing biological function and the study of human physiology in health and disease.

  2. The BioGRID interaction database: 2017 update.

    Science.gov (United States)

    Chatr-Aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

    2017-01-04

    The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

    Directory of Open Access Journals (Sweden)

    Fabrice Lopez

    Full Text Available BACKGROUND: As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. METHODOLOGY: We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484. This approach led to the definition of 18,250 transcriptional signatures (TS that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%. We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/. User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs or associated with a set of functional terms. CONCLUSIONS/SIGNIFICANCE: As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.

  4. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

    Science.gov (United States)

    Lopez, Fabrice; Textoris, Julien; Bergon, Aurélie; Didier, Gilles; Remy, Elisabeth; Granjeaud, Samuel; Imbert, Jean; Nguyen, Catherine; Puthier, Denis

    2008-01-01

    As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms. As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.

  5. National Solar Radiation Database 1991-2005 Update: User's Manual

    Energy Technology Data Exchange (ETDEWEB)

    Wilcox, S.

    2007-04-01

    This manual describes how to obtain and interpret the data products from the updated 1991-2005 National Solar Radiation Database (NSRDB). This is an update of the original 1961-1990 NSRDB released in 1992.

  6. The BioGRID interaction database: 2015 update.

    Science.gov (United States)

    Chatr-Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Oughtred, Rose; Boucher, Lorrie; Heinicke, Sven; Chen, Daici; Stark, Chris; Breitkreutz, Ashton; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Nixon, Julie; Ramage, Lindsay; Winter, Andrew; Sellam, Adnane; Chang, Christie; Hirschman, Jodi; Theesfeld, Chandra; Rust, Jennifer; Livstone, Michael S; Dolinski, Kara; Tyers, Mike

    2015-01-01

    The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749,912 interactions as drawn from 43,149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. MODOMICS: a database of RNA modification pathways. 2017 update.

    Science.gov (United States)

    Boccaletto, Pietro; Machnicka, Magdalena A; Purta, Elzbieta; Piatkowski, Pawel; Baginski, Blazej; Wirecki, Tomasz K; de Crécy-Lagard, Valérie; Ross, Robert; Limbach, Patrick A; Kotter, Annika; Helm, Mark; Bujnicki, Janusz M

    2018-01-04

    MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Key Techniques for Dynamic Updating of National Fundamental Geographic Information Database

    Directory of Open Access Journals (Sweden)

    WANG Donghua

    2015-07-01

    Full Text Available One of the most important missions of fundamental surveying and mapping work is to keep the fundamental geographic information fresh. In this respect, National Administration of Surveying, Mapping and Geoinformation has launched the project of dynamic updating of national fundamental geographic information database since 2012, which aims to update 1:50 000, 1:250 000 and 1:1 000 000 national fundamental geographic information database continuously and quickly, by updating and publishing once a year. This paper introduces the general technical thinking of dynamic updating, states main technical methods, such as dynamic updating of fundamental database, linkage updating of derived databases, and multi-tense database management and service and so on, and finally introduces main technical characteristics and engineering applications.

  9. Update History of This Database - BodyParts3D | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us BodyParts... (Release 2.0) is updated. 2010/03/29 BodyParts3D English archive site is opened. 2009/02/09 3D data (Releas... Policy | Contact Us Update History of This Database - BodyParts3D | LSDB Archive ...

  10. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

    Science.gov (United States)

    Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R; Tan, Ge; Baranasic, Damir; Arenillas, David J; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W; Parcy, François; Mathelier, Anthony

    2017-11-13

    JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Trajectory Browser Website

    Science.gov (United States)

    Foster, Cyrus; Jaroux, Belgacem A.

    2012-01-01

    The Trajectory Browser is a web-based tool developed at the NASA Ames Research Center to be used for the preliminary assessment of trajectories to small-bodies and planets and for providing relevant launch date, time-of-flight and V requirements. The site hosts a database of transfer trajectories from Earth to asteroids and planets for various types of missions such as rendezvous, sample return or flybys. A search engine allows the user to find trajectories meeting desired constraints on the launch window, mission duration and delta V capability, while a trajectory viewer tool allows the visualization of the heliocentric trajectory and the detailed mission itinerary. The anticipated user base of this tool consists primarily of scientists and engineers designing interplanetary missions in the context of pre-phase A studies, particularly for performing accessibility surveys to large populations of small-bodies. The educational potential of the website is also recognized for academia and the public with regards to trajectory design, a field that has generally been poorly understood by the public. The website is currently hosted on NASA-internal URL http://trajbrowser.arc.nasa.gov/ with plans for a public release as soon as development is complete.

  12. National Solar Radiation Database 1991-2010 Update: User's Manual

    Energy Technology Data Exchange (ETDEWEB)

    Wilcox, S. M.

    2012-08-01

    This user's manual provides information on the updated 1991-2010 National Solar Radiation Database. Included are data format descriptions, data sources, production processes, and information about data uncertainty.

  13. An Incremental Updating Method for Land Cover Database Using Refined 2-dimensional Intersection Type

    Directory of Open Access Journals (Sweden)

    ZHOU Xiaoguang

    2017-01-01

    Full Text Available In order to incremental updating the land cover database using the change-only information from imagery change detection methods, an vector change-only information model is designed to represent the spatial and attribute information after change, and an automatic incremental updating method for land cover database based on refined 2-dimensional intersection type is presented. As the differentiation and identification of 2-dimensional intersection type between new updates and existing objects is one of the first steps in the automatic incremental updating process for a land cover database, the 14 refined 2-dimensional intersection types are distinguished by the E-WID topological hierarchical model. Then according to the 14 refined 2-dimensional intersection types, 9 automatic updating rules for land cover database are presented. An automatic incremental updating for land cover database prototype system is developed. The effectiveness of the models and rules was verified using real data. The results of this study represent a new avenue for automatic spatial data handling in incremental updating processes.

  14. A zooming Web browser

    Energy Technology Data Exchange (ETDEWEB)

    Bederson, B.B.; Hollan, J.D.; Stewart, J.; Rogers, D.; Vick, D. [New Mexico Univ., Albuquerque, NM (United States). Dept. of Computer Science; Ring, L.; Grose, E.; Forsythe, C. [Sandia National Labs., Albuquerque, NM (United States)

    1996-12-31

    We are developing a prototype zooming World-Wide Web browser within Pad++, a multiscale graphical environment. Instead of having a single page visible at a time, multiple pages and the links between them are depicted on a large zoomable information surface. Pages are scaled so that the page in focus is clearly readable with connected pages shown at smaller scales to provide context. We quantitatively compared performance with the Pad++ Web browser and Netscape in several different scenarios. We examined how quickly users could answer questions about a specific Web site designed for this test. Initially we found that subjects answered questions slightly slower with Pad++ than with Netscape. After analyzing the results of this study, we implemented several changes to the Pad++ Web browser, and repeated one Pad++ condition. After improvements were made to the Pad++ browser, subjects using Pad++ answered questions 23% faster than those using Netscape.

  15. An application of TOPSIS for ranking internet web browsers

    Directory of Open Access Journals (Sweden)

    Shahram Rostampour

    2012-07-01

    Full Text Available Web browser is one of the most important internet facilities for surfing the internet. A good web browser must incorporate literally tens of features such as integrated search engine, automatic updates, etc. Each year, ten web browsers are formally introduced as top best reviewers by some organizations. In this paper, we propose the implementation of TOPSIS technique to rank ten web browsers. The proposed model of this paper uses five criteria including speed, features, security, technical support and supported configurations. In terms of speed, Safari is the best web reviewer followed by Google Chrome and Internet Explorer while Opera is the best web reviewer when we look into 20 different features. We have also ranked these web browsers using all five categories together and the results indicate that Opera, Internet explorer, Firefox and Google Chrome are the best web browsers to be chosen.

  16. The GEM fault database: an update on design and approach

    Science.gov (United States)

    Gould, M.; Grant, L.; Donnellan, A.; McLeod, D.

    2003-04-01

    We are developing a fault database for California, USA that includes geological and paleoseismic data. This abstract describes our approach to designing the database. The fault database is part of a larger database system that must manage a variety of types of earthquake science data and information. One of the most critical aspects of our proposed system is that it must support interoperability for a variety of application programs, tools, and simulation packages, as well as heterogeneous data. Our system must also be designed to handle real and simulated data. For hypothesis testing and predictive simulation, it is important to separate nonprimary parameters from primary observations, and to know the source of input data. Our goal is to design and develop a database that includes primary geologic and paleoseismic fault parameters, as well as separate nonprimary fault parameters, with all data referenced to the original source. The fault database should accommodate primary observational parameters such as fault location and geometry, kinematic indicators, slip rate, rupture history and recurrence observations, and measurements of displacement. Nonprimary parameters include fault names, strand names, segments, characteristic recurrence interval, and magnitude. Our database will include simulated faults, mapped faults, and hypothesized faults for testing through our simulations. The separation of primary and nonprimary data will allow assimilation of data into models with minimal bias. An XML scheme will be utilized to describe parameters of faults and input data. The fault database will eventually be supported by a state-of-the-art commercially-available general-purpose database management system (DBMS). Initially, our database system will be developed on a public domain DBMS. We have developed extended entity relationships, which will be mapped to a relational database and will initially be implemented in MySQL.

  17. Spatial coincidence modelling, automated database updating and data consistency in vector GIS

    NARCIS (Netherlands)

    Kufoniyi, O.

    1995-01-01

    This thesis presents formal approaches for automated database updating and consistency control in vector- structured spatial databases. To serve as a framework, a conceptual data model is formalized for the representation of geo-data from multiple map layers in which a map layer denotes a

  18. Reasons of the Incremental Information in the Updating Spatial Database

    OpenAIRE

    Zhu, Huaji; Wu, Huarui; Sun, Xiang

    2010-01-01

    International audience; In order to quickly extract and distribute the incremental information of spatial database, this work analyses the reasons of incremental information of spatial database with the instance of residential feature. Firstly, a new concept of increment is proposed based on the spatio-temporal change type and data delta. The change type describes the semantics of increment information and data delta describes the content of increment information. Based on this concept, the t...

  19. Natural Language Access to Databases: Interpreting Update Requests

    Science.gov (United States)

    1981-09-30

    opaque context, therefore, we must consider the sense of the expression, in addition to its referent ( Frege , 1952). In a database system, this sense is...Database Systems" TR 11-79, Center for Research in Cjtnputing Technology, Harvard University, 1979. Frege , Gottlob: "On Sense and Reference": trans...Max Black, in Translations from the Philosophical V _ 22 Writinge of Gottlob Frege , P. Geach and M1. Black, eds., Bltackwell, Oxford, 1952 Hammer

  20. Rasmuson Library DVD Browser: Fun with Screen Scraping and Drupal

    Directory of Open Access Journals (Sweden)

    Mark Morlino

    2008-12-01

    Full Text Available The DVD Browser is a simple application that lets library patrons browse movie covers, titles, and reviews. It works by screen scraping the the Rasmuson Library catalog for DVD movies and dumps the data into a Drupal MySQL database. This paper describes the process of setting up the DVD Browser.

  1. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services a...

  2. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology[1]. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary service...

  3. HERVd: the Human Endogenous RetroViruses Database: update.

    Science.gov (United States)

    Paces, Jan; Pavlícek, Adam; Zika, Radek; Kapitonov, Vladimir V; Jurka, Jerzy; Paces, Václav

    2004-01-01

    An elaboration of HERVd (http://herv.img.cas.cz) is being carried out in two directions. One of them is the integration and better classification of families that diverge considerably from typical retroviral genomes. This leads to a more precise identification of members with individual families. The second improvement is better accessibility of the database and connection with human genome annotation.

  4. Decoding Technology: Web Browsers

    Science.gov (United States)

    Walker, Tim; Donohue, Chip

    2007-01-01

    More than ever, early childhood administrators are relying on the Internet for information. A key to becoming an exceptional Web "surfer" is getting to know the ins and outs of the Web browser being used. There are several options available, and almost all can be downloaded for free. However, many of the functions and features they offer are very…

  5. Web Browser Programming

    OpenAIRE

    Luján Mora, Sergio

    2006-01-01

    Presentaciones del curso "Web Browser Programming" impartido en la Université M'Hamed Bougara (Bourmerdes, Argelia) en junio de 2006. Proyecto financiado por la Unión Europea: TEMPUS JEP-32102-2004, Licence Professionnelle Technologies des Applications Web (Professional License for Web Application Technologies).

  6. Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update

    DEFF Research Database (Denmark)

    Gregersen, Pernille Axel

    2016-01-01

    , we review the molecular basis of MFDM in the 69 individuals described to date, and report mutations in 38 new individuals, bringing the total number of reported individuals to 107 individuals from 94 kindreds. Pathogenic EFTUD2 variants comprise 76 distinct mutations and 7 microdeletions. Among point...... mutations, missense substitutions are infrequent (14/76; 18%) relative to stopgain (29/76; 38%), and splicing (33/76; 43%) mutations. Where known, mutation origin was de novo in 48/64 individuals (75%), dominantly-inherited in 12/64 (19%), and due to proven germline mosaicism in 4/64 (6%). Highly penetrant......-reported anomalies, include vestibular and ossicular malformations, reduced mouth opening, atrophy of cerebral white matter, structural brain malformations, and epibulbar dermoid. All reported EFTUD2 mutations can be found in the EFTUD2 mutation database (http://databases.lovd.nl/shared/genes/EFTUD2). This article...

  7. An update of the DEF database of protein fold class predictions

    DEFF Research Database (Denmark)

    Reczko, Martin; Karras, Dimitris; Bohr, Henrik

    1997-01-01

    An update is given on the Database of Expected Fold classes (DEF) that contains a collection of fold-class predictions made from protein sequences and a mail server that provides new predictions for new sequences. To any given sequence one of 49 fold-classes is chosen to classify the structure...... related to the sequence with high accuracy. The updated predictions system is developed using data from the new version of the 3D-ALI database of aligned protein structures and thus is giving more reliable and more detailed predictions than the previous DEF system....

  8. The BioGRID Interaction Database: 2011 update.

    Science.gov (United States)

    Stark, Chris; Breitkreutz, Bobby-Joe; Chatr-Aryamontri, Andrew; Boucher, Lorrie; Oughtred, Rose; Livstone, Michael S; Nixon, Julie; Van Auken, Kimberly; Wang, Xiaodong; Shi, Xiaoqi; Reguly, Teresa; Rust, Jennifer M; Winter, Andrew; Dolinski, Kara; Tyers, Mike

    2011-01-01

    The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347,966 interactions (170,162 genetic, 177,804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48,831 human protein interactions that have been curated from 10,247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions.

  9. An Updating System for the Gridded Population Database of China Based on Remote Sensing, GIS and Spatial Database Technologies

    Directory of Open Access Journals (Sweden)

    Xiaohuan Yang

    2009-02-01

    Full Text Available The spatial distribution of population is closely related to land use and land cover (LULC patterns on both regional and global scales. Population can be redistributed onto geo-referenced square grids according to this relation. In the past decades, various approaches to monitoring LULC using remote sensing and Geographic Information Systems (GIS have been developed, which makes it possible for efficient updating of geo-referenced population data. A Spatial Population Updating System (SPUS is developed for updating the gridded population database of China based on remote sensing, GIS and spatial database technologies, with a spatial resolution of 1 km by 1 km. The SPUS can process standard Moderate Resolution Imaging Spectroradiometer (MODIS L1B data integrated with a Pattern Decomposition Method (PDM and an LULC-Conversion Model to obtain patterns of land use and land cover, and provide input parameters for a Population Spatialization Model (PSM. The PSM embedded in SPUS is used for generating 1 km by 1 km gridded population data in each population distribution region based on natural and socio-economic variables. Validation results from finer township-level census data of Yishui County suggest that the gridded population database produced by the SPUS is reliable.

  10. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  11. The BioGRID interaction database: 2013 update.

    Science.gov (United States)

    Chatr-Aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heinicke, Sven; Boucher, Lorrie; Winter, Andrew; Stark, Chris; Nixon, Julie; Ramage, Lindsay; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Breitkreutz, Ashton; Sellam, Adnane; Chen, Daici; Chang, Christie; Rust, Jennifer; Livstone, Michael; Oughtred, Rose; Dolinski, Kara; Tyers, Mike

    2013-01-01

    The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin.

  12. Updated folate data in the Dutch Food Composition Database and implications for intake estimates

    Directory of Open Access Journals (Sweden)

    Susanne Westenbrink

    2012-04-01

    Full Text Available Background and objective: Nutrient values are influenced by the analytical method used. Food folate measured by high performance liquid chromatography (HPLC or by microbiological assay (MA yield different results, with in general higher results from MA than from HPLC. This leads to the question of how to deal with different analytical methods in compiling standardised and internationally comparable food composition databases? A recent inventory on folate in European food composition databases indicated that currently MA is more widely used than HPCL. Since older Dutch values are produced by HPLC and newer values by MA, analytical methods and procedures for compiling folate data in the Dutch Food Composition Database (NEVO were reconsidered and folate values were updated. This article describes the impact of this revision of folate values in the NEVO database as well as the expected impact on the folate intake assessment in the Dutch National Food Consumption Survey (DNFCS. Design: The folate values were revised by replacing HPLC with MA values from recent Dutch analyses. Previously MA folate values taken from foreign food composition tables had been recalculated to the HPLC level, assuming a 27% lower value from HPLC analyses. These recalculated values were replaced by the original MA values. Dutch HPLC and MA values were compared to each other. Folate intake was assessed for a subgroup within the DNFCS to estimate the impact of the update. Results: In the updated NEVO database nearly all folate values were produced by MA or derived from MA values which resulted in an average increase of 24%. The median habitual folate intake in young children was increased by 11–15% using the updated folate values. Conclusion: The current approach for folate in NEVO resulted in more transparency in data production and documentation and higher comparability among European databases. Results of food consumption surveys are expected to show higher folate intakes

  13. Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

    Science.gov (United States)

    Giardine, Belinda; Borg, Joseph; Viennas, Emmanouil; Pavlidis, Cristiana; Moradkhani, Kamran; Joly, Philippe; Bartsakoulia, Marina; Riemer, Cathy; Miller, Webb; Tzimas, Giannis; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

    2014-01-01

    HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for α-, and β-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.

  14. MoonProt 2.0: an expansion and update of the moonlighting proteins database.

    Science.gov (United States)

    Chen, Chang; Zabad, Shadi; Liu, Haipeng; Wang, Wangfei; Jeffery, Constance

    2018-01-04

    MoonProt 2.0 (http://moonlightingproteins.org) is an updated, comprehensive and open-access database storing expert-curated annotations for moonlighting proteins. Moonlighting proteins contain two or more physiologically relevant distinct functions performed by a single polypeptide chain. Here, we describe developments in the MoonProt website and database since our previous report in the Database Issue of Nucleic Acids Research. For this V 2.0 release, we expanded the number of proteins annotated to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release. The new entries include more examples from humans and several model organisms, more proteins involved in disease, and proteins with different combinations of functions. The updated web interface includes a search function using BLAST to enable users to search the database for proteins that share amino acid sequence similarity with a protein of interest. The updated website also includes additional background information about moonlighting proteins and an expanded list of links to published articles about moonlighting proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. An update of a national database of low-level radioactive waste in Canada

    Energy Technology Data Exchange (ETDEWEB)

    De, P.L.; Barker, R.C. [Atomic Energy Canada Ltd. Research, Ottawa, Ontario (Canada). Low-Level Radioactive Waste Management Office

    1993-03-01

    This paper gives an overview and update of a national database of low-level radioactive waste in Canada. To provide a relevant perspective, Canadian data are compared with US data on annual waste arisings and with disposal initiatives of the US compacts and states. Presented also is an assessment of the data and its implications for disposal solutions in Canada.

  16. An updated active structure database of Taiwan for seismic hazard assessments

    Science.gov (United States)

    Shyu, J. B. H.; Chuang, Y. R.; Chen, Y. L.; Lee, Y.; Cheng, T. C. T.

    2014-12-01

    In order to build a complete seismogenic source model to assess future seismic hazards in Taiwan, we have constructed an updated active structure database for the island. We reviewed existing active structure databases, and obtained new information for structures that have not been thoroughly analyzed before. For example, the Central Geological Survey of Taiwan has published a comprehensive database of active faults in Taiwan, including all of the historically ruptured faults. Many other active structures, such as blind faults or folds that can be identified from geomorphic or structural analysis, have also been mapped and reported in several previous investigations. We have combined information from these existing databases to build an updated and digitized three-dimensional active structure map for Taiwan. Furthermore, for detailed information of individual structure such as long-term slip rates and potential recurrence intervals, we have collected the data from existing publications, as well as calculated from results of our own field surveys and investigations. We hope this updated database would become a significant constraint for the calculations of seismic hazard assessments in Taiwan, and would provide important information for engineers and hazard mitigation agencies.

  17. Integration of Narrative Processing, Data Fusion, and Database Updating Techniques in an Automated System.

    Science.gov (United States)

    1981-10-29

    are implemented, respectively, in the files "W-Update," "W-combine" and RW-Copy," listed in the appendix. The appendix begins with a typescript of an...the typescript ) and the copying process (steps 45 and 46) are shown as human actions in the typescript , but can be performed easily by a "master...for Natural Language, M. Marcus, MIT Press, 1980. I 29 APPENDIX: DATABASE UPDATING EXPERIMENT 30 CONTENTS Typescript of an experiment in Rosie

  18. BrowserAudit: Automated testing of browser security features

    OpenAIRE

    Hothersall-Thomas, C; Maffeis, S; Novakovic, C

    2015-01-01

    The security of the client side of a web application relies on browser features such as cookies, the same-origin policy and HTTPS. As the client side grows increasingly powerful and sophisticated, browser vendors have stepped up their offering of security mechanisms which can be leveraged to protect it. These are often introduced experimentally and informally and, as adoption increases, gradually become standardised (e.g., CSP, CORS and HSTS). Considering the diverse landscape of browser vend...

  19. Second Generation MOSAIC:A Novel Mechanism Based on Reference Database for Map Updating

    Science.gov (United States)

    Hu, G.; Bignone, F.

    2011-08-01

    A totally new automatic workflow mechanism, named Second generation Mosaic module, based on the well-known Pixel Factory system, will be introduced here, which enables existing digital orthoimages and mosaics to be quickly updated. The process extracts all required parameters from the reference database to be able to perform automatic bundle adjustment and radiometric adaptation.In this paper, two examples for both satellite data and aerial data processed based on this mechanism will be presented here and discussed. Finally, the cost reduction will also be analysed according to the real mapping updating project.In a final statement, this paper will present an integrated solution named second generation mosaic module based on the well-known Pixel Factory system which is completely dedicated to fast processing of photogrammetric products Thanks to this integrated hardware and software solution, it is even possible to manage large data volume quickly in order to have precise map updating information as soon as possible after acquisition.

  20. A NEW PROCEDURE FOR FORESTRY DATABASE UPDATING WITH GIS AND REMOTE SENSING

    Directory of Open Access Journals (Sweden)

    Luis M. T. de Carvalho

    2003-07-01

    Full Text Available The aim of this study was to develop an automated, simple and flexibleprocedure for updating raster-based forestry database. Four modules compose the procedure:(1 location of changed sites, (2 quantification of changed area, (3 identification of the newland cover, and (4 database updating. Firstly, a difference image is decomposed with wavelettransforms in order to extract changed sites. Secondly, segmentation is performed on thedifference image. Thirdly, each changed pixel or each segmented region is assigned to theland cover class with the highest probability of membership. Then, the output is used toupdate the GIS layer where changes took place. This procedure was less sensitive togeometric and radiometric misregistration, and less dependent on ground truth, whencompared with post classification comparison and direct multidate classification.

  1. PGSB PlantsDB: updates to the database framework for comparative plant genome research

    OpenAIRE

    Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai C; Martis, Mihaela-Maria; Seidel, Michael; Karl G Kugler; Gundlach, Heidrun; Mayer, Klaus F.X.

    2016-01-01

    PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyw...

  2. M4FT-16LL080302052-Update to Thermodynamic Database Development and Sorption Database Integration

    Energy Technology Data Exchange (ETDEWEB)

    Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Glenn T. Seaborg Inst.. Physical and Life Sciences; Wolery, T. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Akima Infrastructure Services, LLC; Atkins-Duffin, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Global Security

    2016-08-16

    This progress report (Level 4 Milestone Number M4FT-16LL080302052) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Argillite Disposal R&D Work Package Number FT-16LL08030205. The focus of this research is the thermodynamic modeling of Engineered Barrier System (EBS) materials and properties and development of thermodynamic databases and models to evaluate the stability of EBS materials and their interactions with fluids at various physico-chemical conditions relevant to subsurface repository environments. The development and implementation of equilibrium thermodynamic models are intended to describe chemical and physical processes such as solubility, sorption, and diffusion.

  3. An efficient algorithm for updating regular expression indexes in RDF databases.

    Science.gov (United States)

    Lee, Jinsoo; Kasperovics, Romans; Han, Wook-Shin; Lee, Jeong-Hoon; Kim, Min Soo; Cho, Hune

    2015-01-01

    The Resource Description Framework (RDF) is widely used for sharing biomedical data, such as gene ontology or the online protein database UniProt. SPARQL is a native query language for RDF, featuring regular expressions in queries for which exact values are either irrelevant or unknown. The use of regular expression indexes in SPARQL query processing improves the performance of queries containing regular expressions by up to two orders of magnitude. In this study, we address the update operation for regular expression indexes in RDF databases. We identify major performance problems of straightforward index update algorithms and propose a new algorithm that utilises unique properties of regular expression indexes to increase performance. Our contributions can be summarised as follows: (1) we propose an efficient update algorithm for regular expression indexes in RDF databases, (2) we build a prototype system for the proposed algorithm in C++ and (3) we conduct extensive experiments demonstrating the improvement of our algorithm over the straightforward approaches by an order of magnitude.

  4. Update of a thermodynamic database for radionuclides to assist solubility limits calculation for performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Duro, L.; Grive, M.; Cera, E.; Domenech, C.; Bruno, J. (Enviros Spain S.L., Barcelona (ES))

    2006-12-15

    This report presents and documents the thermodynamic database used in the assessment of the radionuclide solubility limits within the SR-Can Exercise. It is a supporting report to the solubility assessment. Thermodynamic data are reviewed for 20 radioelements from Groups A and B, lanthanides and actinides. The development of this database is partially based on the one prepared by PSI and NAGRA. Several changes, updates and checks for internal consistency and completeness to the reference NAGRA-PSI 01/01 database have been conducted when needed. These modifications are mainly related to the information from the various experimental programmes and scientific literature available until the end of 2003. Some of the discussions also refer to a previous database selection conducted by Enviros Spain on behalf of ANDRA, where the reader can find additional information. When possible, in order to optimize the robustness of the database, the description of the solubility of the different radionuclides calculated by using the reported thermodynamic database is tested in front of experimental data available in the open scientific literature. When necessary, different procedures to estimate gaps in the database have been followed, especially accounting for temperature corrections. All the methodologies followed are discussed in the main text

  5. Designing, Implementing, and Evaluating Secure Web Browsers

    Science.gov (United States)

    Grier, Christopher L.

    2009-01-01

    Web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems using browser-based attacks. Efforts that retrofit existing browsers have had limited success since modern browsers are not designed to withstand attack. To enable more secure web browsing, we design and implement new web browsers from the ground…

  6. Web Browser Trends and Technologies.

    Science.gov (United States)

    Goodwin-Jones, Bob

    2000-01-01

    Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

  7. Geothopica and the interactive analysis and visualization of the updated Italian National Geothermal Database

    Science.gov (United States)

    Trumpy, Eugenio; Manzella, Adele

    2017-02-01

    The Italian National Geothermal Database (BDNG), is the largest collection of Italian Geothermal data and was set up in the 1980s. It has since been updated both in terms of content and management tools: information on deep wells and thermal springs (with temperature > 30 °C) are currently organized and stored in a PostgreSQL relational database management system, which guarantees high performance, data security and easy access through different client applications. The BDNG is the core of the Geothopica web site, whose webGIS tool allows different types of user to access geothermal data, to visualize multiple types of datasets, and to perform integrated analyses. The webGIS tool has been recently improved by two specially designed, programmed and implemented visualization tools to display data on well lithology and underground temperatures. This paper describes the contents of the database and its software and data update, as well as the webGIS tool including the new tools for data lithology and temperature visualization. The geoinformation organized in the database and accessible through Geothopica is of use not only for geothermal purposes, but also for any kind of georesource and CO2 storage project requiring the organization of, and access to, deep underground data. Geothopica also supports project developers, researchers, and decision makers in the assessment, management and sustainable deployment of georesources.

  8. Absorption Cross-Sections in HITRAN2016: Major Database Update for Atmospheric, Industrial, and Climate Applications

    Science.gov (United States)

    Kochanov, Roman V.; Gordon, Iouli E.; Rothman, Laurence S.; Shine, Keith; Sharpe, Steven W.; Johnson, Timothy J.; Harrison, Jeremy J.; Bernath, Peter F.; Wallington, Timothy; Birk, Manfred; Wagner, Georg; Hill, Christian

    2017-06-01

    In this talk, an overview is given for the recent absorption cross-section update in the new HITRAN2016 spectroscopic database release. The updated cross-sections include data for around 330 molecules for applications in atmospheric remote sensing, industrial pollution tracking, climate change monitoring, remote sensing, spectral calibration, and more. These cross-sections come from high-resolution laboratory observations, predominantly using FT-IR technique. The update largely relies on spectra from the PNNL quantitative spectroscopic database and the Hodnebrog et al. (Rev Geophys 2013) compilation, but also on other recently published data for many applications such as biomass burning detection, remote sensing in the UTLS, environment monitoring, etc. (references will be given in the talk). The described data are available via the HITRANonline website and HITRAN Application Programing Interface (HAPI). This work is supported by NASA AURA (NNX14AI55G) and NASA PDART (NNX16AG51G) grants. Hill C. et al. JQSRT 2016;177:4-14. Kochanov RV et al.JQSRT 2016;177:15-30.

  9. rVarBase: an updated database for regulatory features of human variants.

    Science.gov (United States)

    Guo, Liyuan; Du, Yang; Qu, Susu; Wang, Jing

    2016-01-04

    We present here the rVarBase database (http://rv.psych.ac.cn), an updated version of the rSNPBase database, to provide reliable and detailed regulatory annotations for known and novel human variants. This update expands the database to include additional types of human variants, such as copy number variations (CNVs) and novel variants, and include additional types of regulatory features. Now rVarBase annotates variants in three dimensions: chromatin states of the surrounding regions, overlapped regulatory elements and variants' potential target genes. Two new types of regulatory elements (lncRNAs and miRNA target sites) have been introduced to provide additional annotation. Detailed information about variants' overlapping transcription factor binding sites (TFBSs) (often less than 15 bp) within experimentally supported TF-binding regions (∼ 150 bp) is provided, along with the binding motifs of matched TF families. Additional types of extended variants and variant-associated phenotypes were also added. In addition to the enrichment in data content, an element-centric search module was added, and the web interface was refined. In summary, rVarBase hosts more types of human variants and includes more types of up-to-date regulatory information to facilitate in-depth functional research and to provide practical clues for experimental design. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Comprehensive Thematic T-Matrix Reference Database: A 2015-2017 Update

    Science.gov (United States)

    Mishchenko, Michael I.; Zakharova, Nadezhda; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

    2017-01-01

    The T-matrix method pioneered by Peter C. Waterman is one of the most versatile and efficient numerically exact computer solvers of the time-harmonic macroscopic Maxwell equations. It is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, periodic structures (including metamaterials), and particles in the vicinity of plane or rough interfaces separating media with different refractive indices. This paper is the eighth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated in 2004 and lists relevant publications that have appeared since 2015. It also references a small number of earlier publications overlooked previously.

  11. Updating methodological and source database of binominal denominations of introduced cultivars with elements of extrapolation

    Directory of Open Access Journals (Sweden)

    Н. В. Лещук

    2013-02-01

    Full Text Available The article discloses the meaning of botanical semantics, highlights practical appliance of binary scientific botanic nomenclature during plant varieties identification. It is the binary nomenclature of introduced cultivars that requires a scientific approach to structuring and developing the methodological and source learning database of botanical names in Ukrainian and Latin. According to the results of analytic monitoring, research aspects of differentiation of systematic units are shown, as well as certain rules and recommendations concerning theoretically sustained names of botanical taxa in Ukrainian and Latin. The scientific search for harmonization will enable to improve the practical appliance of methodological and linguistic and orthographic requirements and rules of spelling for botanical taxa names during the registration of rights on them. Spelling harmonization by Linnaeus semantic (in Latin will facilitate a uniform approach to updating methodological and source studying database of binary names of the introduced cultivars of botanical taxa.

  12. An Update of the Bodeker Scientific Vertically Resolved, Global, Gap-Free Ozone Database

    Science.gov (United States)

    Kremser, S.; Bodeker, G. E.; Lewis, J.; Hassler, B.

    2016-12-01

    High vertical resolution ozone measurements from multiple satellite-based instruments have been merged with measurements from the global ozonesonde network to calculate monthly mean ozone values in 5º latitude zones. Ozone number densities and ozone mixing ratios are provided on 70 altitude levels (1 to 70 km) and on 70 pressure levels spaced approximately 1 km apart (878.4 hPa to 0.046 hPa). These data are sparse and do not cover the entire globe or altitude range. To provide a gap-free database, a least squares regression model is fitted to these data and then evaluated globally. By applying a single fit at each level, and using the approach of allowing the regression fits to change only slightly from one level to the next, the regression is less sensitive to measurement anomalies at individual stations or to individual satellite-based instruments. Particular attention is paid to ensuring that the low ozone abundances in the polar regions are captured. This presentation reports on updates to an earlier version of the vertically resolved ozone database, including the incorporation of new ozone measurements and new techniques for combining the data. Compared to previous versions of the database, particular attention is paid to avoiding spatial and temporal sampling biases and tracing uncertainties through to the final product. This updated database, developed within the New Zealand Deep South National Science Challenge, is suitable for assessing ozone fields from chemistry-climate model simulations or for providing the ozone boundary conditions for global climate model simulations that do not treat stratospheric chemistry interactively.

  13. SECOND GENERATION MOSAIC:A NOVEL MECHANISM BASED ON REFERENCE DATABASE FOR MAP UPDATING

    Directory of Open Access Journals (Sweden)

    G. Hu

    2012-08-01

    Full Text Available A totally new automatic workflow mechanism, named Second generation Mosaic module, based on the well-known Pixel Factory system, will be introduced here, which enables existing digital orthoimages and mosaics to be quickly updated. The process extracts all required parameters from the reference database to be able to perform automatic bundle adjustment and radiometric adaptation.In this paper, two examples for both satellite data and aerial data processed based on this mechanism will be presented here and discussed. Finally, the cost reduction will also be analysed according to the real mapping updating project.In a final statement, this paper will present an integrated solution named second generation mosaic module based on the well-known Pixel Factory system which is completely dedicated to fast processing of photogrammetric products Thanks to this integrated hardware and software solution, it is even possible to manage large data volume quickly in order to have precise map updating information as soon as possible after acquisition.

  14. Research of Cadastral Data Modelling and Database Updating Based on Spatio-temporal Process

    Directory of Open Access Journals (Sweden)

    ZHANG Feng

    2016-02-01

    Full Text Available The core of modern cadastre management is to renew the cadastre database and keep its currentness,topology consistency and integrity.This paper analyzed the changes and their linkage of various cadastral objects in the update process.Combined object-oriented modeling technique with spatio-temporal objects' evolution express,the paper proposed a cadastral data updating model based on the spatio-temporal process according to people's thought.Change rules based on the spatio-temporal topological relations of evolution cadastral spatio-temporal objects are drafted and further more cascade updating and history back trace of cadastral features,land use and buildings are realized.This model implemented in cadastral management system-ReGIS.Achieved cascade changes are triggered by the direct driving force or perceived external events.The system records spatio-temporal objects' evolution process to facilitate the reconstruction of history,change tracking,analysis and forecasting future changes.

  15. A Web-Based Geospatial Metadata Browser

    Science.gov (United States)

    Arko, R. A.; Chayes, D. N.

    2002-12-01

    We are developing a simple Web-based browser for the search and display of earth science metadata. Our design goals are: 1. to permit both map-based (geographical) and forms-based (textual) searching; 2. to integrate a wide variety of data types in a hierarchical fashion; 3. to conform to the FGDC metadata standard; 4. to take advantage of existing open source software wherever possible; 5. to be platform-independent, browser-independent, and "robust" (i.e. avoid application layers which are resource-intensive or behave unpredictably, such as Java applets); and 6. to present metadata in a dynamic fashion via live database connections. Our implementation is based on the MapServer GIS platform (developed at the University of Minnesota with NSF and NASA funding), PostgreSQL relational database management system, and PostGIS geographic database extensions (developed by Refractions Research Inc and available under GNU Public License). All of these packages are well-documented open source software and have been proven in commercial-grade applications. We combine geographical searching (click-and-drag on maps, in both global and polar projections) and textual searching (drop-down menus organized by FGDC category) for a range of geophysical, chemical, and biological data types. A corresponding framework for collecting and ingesting earth science metadata is reported elsewhere at this meeting (Chayes & Arko, "Real-time Metadata Capture Implementations").

  16. Web-browser encryption of personal health information.

    Science.gov (United States)

    Morse, Richard E; Nadkarni, Prakash; Schoenfeld, David A; Finkelstein, Dianne M

    2011-11-10

    Electronic health records provide access to an unprecedented amount of clinical data for research that can accelerate the development of effective medical practices. However it is important to protect patient confidentiality, as many medical conditions are stigmatized and disclosure could result in personal and/or financial loss. We describe a system for remote data entry that allows the data that would identify the patient to be encrypted in the web browser of the person entering the data. These data cannot be decrypted on the server by the staff at the data center but can be decrypted by the person entering the data or their delegate. We developed this system to solve a problem that arose in the context of clinical research, but it is applicable in a range of situations where sensitive information is stored and updated in a database and it is necessary to ensure that it cannot be viewed by any except those intentionally given access. By developing this system, we are able to centralize the collection of some patient data while minimizing the risk that protected health information be made available to study personnel who are not authorized to use it.

  17. The 2011 Bioinformatics Links Directory update: more resources, tools and databases and features to empower the bioinformatics community.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David S; Yamada, Joseph T; Ouellette, B F Francis

    2011-07-01

    The Bioinformatics Links Directory continues its collaboration with Nucleic Acids Research to collaboratively publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2011 Web Server issue of Nucleic Acids Research adds an additional 78 web server tools and 14 updates to the directory at http://bioinformatics.ca/links_directory/.

  18. EVALUATING EFFECTIVENESS OF MOBILE BROWSER SECURITY WARNINGS

    Directory of Open Access Journals (Sweden)

    Ronak Shah

    2016-09-01

    Full Text Available This work precisely evaluates whether browser security warnings are as ineffective as proposed by popular sentiments and past writings. This research used different kinds of Android mobile browsers as well as desktop browsers to evaluate security warnings. Security experts and developers should give emphasis on making a user aware of security warnings and should not neglect aim of communicating this to users. Security experts and system architects should emphasis the goal of communicating security information to end users. In most of the browsers, security warnings are not emphasized, and browsers simply do not show warnings, or there are a number of ways to hide those warnings of malicious sites. This work precisely finds that how inconsistent browsers really are in prompting security warnings. In particular, majority of the modern mobile web browsers are vulnerable to these security threats. We find inconsistency in SSL warnings among web browsers. Based on this work, we make recommendations for warning designers and researchers.

  19. Extending a browser C++ simulator

    OpenAIRE

    Segarra Roca, Albert

    2017-01-01

    Getting started in computer programming involves using a number of tools such as editors, compilers, debuggers, and terminals. Learning how to use them can be challenging for programming begginers, and installing them may be demanding for certain organizations such as high schools. C– is a project that aims to bridge this gap by providing an educational C++ development environment that runs in a web browser. The goal of this thesis is to extend and improve the current implement...

  20. Updates on the web-based VIOLIN vaccine database and analysis system.

    Science.gov (United States)

    He, Yongqun; Racz, Rebecca; Sayers, Samantha; Lin, Yu; Todd, Thomas; Hur, Junguk; Li, Xinna; Patel, Mukti; Zhao, Boyang; Chung, Monica; Ostrow, Joseph; Sylora, Andrew; Dungarani, Priya; Ulysse, Guerlain; Kochhar, Kanika; Vidri, Boris; Strait, Kelsey; Jourdian, George W; Xiang, Zuoshuang

    2014-01-01

    The integrative Vaccine Investigation and Online Information Network (VIOLIN) vaccine research database and analysis system (http://www.violinet.org) curates, stores, analyses and integrates various vaccine-associated research data. Since its first publication in NAR in 2008, significant updates have been made. Starting from 211 vaccines annotated at the end of 2007, VIOLIN now includes over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases (e.g. cancers and allergies). Under the umbrella of VIOLIN, >10 relatively independent programs are developed. For example, Protegen stores over 800 protective antigens experimentally proven valid for vaccine development. VirmugenDB annotated over 200 'virmugens', a term coined by us to represent those virulence factor genes that can be mutated to generate successful live attenuated vaccines. Specific patterns were identified from the genes collected in Protegen and VirmugenDB. VIOLIN also includes Vaxign, the first web-based vaccine candidate prediction program based on reverse vaccinology. VIOLIN collects and analyzes different vaccine components including vaccine adjuvants (Vaxjo) and DNA vaccine plasmids (DNAVaxDB). VIOLIN includes licensed human vaccines (Huvax) and veterinary vaccines (Vevax). The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines.

  1. Rice SNP-seek database update: new SNPs, indels, and queries.

    Science.gov (United States)

    Mansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L; Alexandrov, Nickolai

    2017-01-04

    We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Update of KDBI: Kinetic Data of Bio-molecular Interaction database.

    Science.gov (United States)

    Kumar, Pankaj; Han, B C; Shi, Z; Jia, J; Wang, Y P; Zhang, Y T; Liang, L; Liu, Q F; Ji, Z L; Chen, Y Z

    2009-01-01

    Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation of biological systems. Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein-protein, protein-nucleic acid, protein-ligand, nucleic acid-ligand binding or reaction events described in the literature. To accommodate increasing demand for studying and simulating biological systems, numerous improvements and updates have been made to KDBI, including new ways to access data by pathway and molecule names, data file in System Biology Markup Language format, more efficient search engine, access to published parameter sets of simulation models of 63 pathways, and 2.3-fold increase of data (19,263 entries of 10,532 distinctive biomolecular binding and 11,954 interaction events, involving 2635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and 45 multi-step processes). KDBI is publically available at http://bidd.nus.edu.sg/group/kdbi/kdbi.asp.

  3. H-DBAS: human-transcriptome database for alternative splicing: update 2010.

    Science.gov (United States)

    Takeda, Jun-ichi; Suzuki, Yutaka; Sakate, Ryuichi; Sato, Yoshiharu; Gojobori, Takashi; Imanishi, Tadashi; Sugano, Sumio

    2010-01-01

    H-DBAS (http://h-invitational.jp/h-dbas/) is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. We generated a total of 148,376,598 RNA-Seq tags from RNAs extracted from cytoplasmic, nuclear and polysome fractions. Analysis of the RNA-Seq tags allowed us to identify 90,900 exons that are very likely to be used for protein synthesis. On the other hand, 254 AS junctions of human RefSeq transcripts are unique to nuclear RNA and may not have any translational consequences. We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. With the unique experimental data closely connected with intensively curated cDNA information, H-DBAS provides a unique platform for the analysis of complex AS.

  4. Quantifying the web browser ecosystem.

    Science.gov (United States)

    Ferdman, Sela; Minkov, Einat; Bekkerman, Ron; Gefen, David

    2017-01-01

    Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to "sneak in" through third party installations or to get "kicked out" by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market.

  5. Botnet in the Browser: Understanding Threats Caused by Malicious Browser Extensions

    OpenAIRE

    Perrotta, Raffaello; Hao, Feng

    2017-01-01

    Browser extensions have been established as a common feature present in modern browsers. However, some extension systems risk exposing APIs which are too permissive and cohesive with the browser's internal structure, thus leaving a hole for malicious developers to exploit security critical functionality within the browser itself. In this paper, we raise the awareness of the threats caused by browser extensions by presenting a botnet framework based on malicious extensions installed in the use...

  6. Xenopus genomic data and browser resources.

    Science.gov (United States)

    Vize, Peter D; Zorn, Aaron M

    2017-06-15

    The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Mouse Resource Browser-a database of mouse databases

    NARCIS (Netherlands)

    Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M.; Schofield, Paul N.; Kollias, George; Aidinis, Vassilis

    2010-01-01

    The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the

  8. The Swedish Family-Cancer Database: Update, Application to Colorectal Cancer and Clinical Relevance

    Directory of Open Access Journals (Sweden)

    Hemminki Kari

    2005-01-01

    Full Text Available Abstract The Swedish Family-Cancer Database has been used for almost 10 years in the study of familial risks at all common sites. In the present paper we describe some main features of version VI of this Database, assembled in 2004. This update included all Swedes born in 1932 and later (offspring with their biological parents, a total of 10.5 million individuals. Cancer cases were retrieved from the Swedish Cancer Registry from 1958-2002, including over 1.2 million first and multiple primary cancers and in situ tumours. Compared to previous versions, only 6.0% of deceased offspring with a cancer diagnosis lack any parental information. We show one application of the Database in the study of familial risks in colorectal adenocarcinoma, with defined age-group and anatomic site specific analyses. Familial standardized incidence ratios (SIRs were determined for offspring when parents or sibling were diagnosed with colon or rectal cancer. As a novel finding it was shown that risks for siblings were higher than those for offspring of affected parents. The excess risk was limited to colon cancer and particularly to right-sided colon cancer. The SIRs for colon cancer in age matched populations were 2.58 when parents were probands and 3.81 when siblings were probands; for right-sided colon cancer the SIRs were 3.66 and 7.53, respectively. Thus the familial excess (SIR-1.00 was more than two fold higher for right-sided colon cancer. Colon and rectal cancers appeared to be distinguished between high-penetrant and recessive conditions that only affect the colon, whereas low-penetrant familial effects are shared by the two sites. Epidemiological studies can be used to generate clinical estimates for familial risk, conditioned on numbers of affected family members and their ages of onset. Useful risk estimates have been developed for familial breast and prostate cancers. Reliable risk estimates for other cancers should also be seriously considered for

  9. 76 FR 64859 - Pilot Loading of Navigation and Terrain Awareness Database Updates

    Science.gov (United States)

    2011-10-19

    ... that mechanics and repair stations perform updates for modern Nav-Systems. Absent the safety concerns... determined that the ease of successfully updating modern Nav- Systems remains the same regardless of the... pedestal-mounted navigational equipment. Large transport category airplanes generally operated under Part...

  10. Memoirs of a Browser: A Cross-browser Detection Model for Privacy-breaching Extensions

    NARCIS (Netherlands)

    Giuffrida, C.; Ortolani, S.; Crispo, B.

    2012-01-01

    Web browsers are undoubtedly one of the most popular user applications. This is even more evident in recent times, with Google introducing a platform where the browser is the only application provided to the user. With their modular and extensible architecture, modern browsers are also an appealing

  11. The Navigational Power of Web Browsers

    NARCIS (Netherlands)

    Bielecki, M.; Hidders, J.; Paredaens, J.; Spielmann, M.; Tyszkiewicz, J.; Van den Bussche, J.; http://link.springer.com/article/10.1007/s00224-010-9294-3

    2010-01-01

    We investigate the computational capabilities of Web browsers, when equipped with a standard finite automaton. We observe that Web browsers are Turingcomplete. We introduce the notion of a navigational problem, and investigate the complexity of solving Web queries and navigational problems by Web

  12. Web browser accessibility using open source software

    NARCIS (Netherlands)

    Z. Obrenovic; J.R. van Ossenbruggen (Jacco)

    2007-01-01

    htmlabstractA Web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional

  13. Distributed Computing on an Ensemble of Browsers

    NARCIS (Netherlands)

    Cushing, R.; Herawan, G.; Putra, H.; Belloum, A.; Bubak, M.; de Laat, C.

    2013-01-01

    In this article, the authors propose a new approach to distributed computing with Web browsers and introduce the WeevilScout prototype framework. The proliferation of Web browsers and the performance gains being achieved by current JavaScript virtual machines raises the question whether Internet

  14. Line-mode browser development days

    CERN Multimedia

    Anna Pantelia

    2013-01-01

    Twelve talented web developers have travelled to CERN from all over the world to recreate a piece of web history: the line-mode browser. See the line-mode browser simulator that they created here. Read more about the birth of the web here.

  15. Exploring the enjoyment of playing browser games.

    Science.gov (United States)

    Klimmt, Christoph; Schmid, Hannah; Orthmann, Julia

    2009-04-01

    Browser games--mostly persistent game worlds that can be used without client software and monetary cost with a Web browser--belong to the understudied digital game types, although they attract large player communities and motivate sustained play. The present work reports findings from an online survey of 8,203 players of a German strategy browser game ("Travian"). Results suggest that multiplayer browser games are enjoyed primarily because of the social relationships involved in game play and the specific time and flexibility characteristics ("easy-in, easy-out"). Competition, in contrast, seems to be less important for browser gamers than for users of other game types. Findings are discussed in terms of video game enjoyment and game addiction.

  16. The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches.

    Science.gov (United States)

    Khan, Ishita K; Wei, Qing; Chapman, Samuel; Kc, Dukka B; Kihara, Daisuke

    2015-01-01

    Functional annotation of novel proteins is one of the central problems in bioinformatics. With the ever-increasing development of genome sequencing technologies, more and more sequence information is becoming available to analyze and annotate. To achieve fast and automatic function annotation, many computational (automated) function prediction (AFP) methods have been developed. To objectively evaluate the performance of such methods on a large scale, community-wide assessment experiments have been conducted. The second round of the Critical Assessment of Function Annotation (CAFA) experiment was held in 2013-2014. Evaluation of participating groups was reported in a special interest group meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in Boston in 2014. Our group participated in both CAFA1 and CAFA2 using multiple, in-house AFP methods. Here, we report benchmark results of our methods obtained in the course of preparation for CAFA2 prior to submitting function predictions for CAFA2 targets. For CAFA2, we updated the annotation databases used by our methods, protein function prediction (PFP) and extended similarity group (ESG), and benchmarked their function prediction performances using the original (older) and updated databases. Performance evaluation for PFP with different settings and ESG are discussed. We also developed two ensemble methods that combine function predictions from six independent, sequence-based AFP methods. We further analyzed the performances of our prediction methods by enriching the predictions with prior distribution of gene ontology (GO) terms. Examples of predictions by the ensemble methods are discussed. Updating the annotation database was successful, improving the Fmax prediction accuracy score for both PFP and ESG. Adding the prior distribution of GO terms did not make much improvement. Both of the ensemble methods we developed improved the average Fmax score over all individual component methods except for

  17. MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data.

    Science.gov (United States)

    Pabinger, Stephan; Snajder, Rene; Hardiman, Timo; Willi, Michaela; Dander, Andreas; Trajanoski, Zlatko

    2014-01-01

    The MEtabolic MOdel research and development System (MEMOSys) is a versatile database for the management, storage and development of genome-scale models (GEMs). Since its initial release, the database has undergone major improvements, and the new version introduces several new features. First, the novel concept of derived models allows users to create model hierarchies that automatically propagate modifications along their order. Second, all stored components can now be easily enhanced with additional annotations that can be directly extracted from a supplied Systems Biology Markup Language (SBML) file. Third, the web application has been substantially revised and now features new query mechanisms, an easy search system for reactions and new link-out services to publicly available databases. Fourth, the updated database now contains 20 publicly available models, which can be easily exported into standardized formats for further analysis. Fifth, MEMOSys 2.0 is now also available as a fully configured virtual image and can be found online at http://www.icbi.at/memosys and http://memoys.i-med.ac.at. Database URL: http://memosys.i-med.ac.at.

  18. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

    Science.gov (United States)

    Kibbe, Warren A; Arze, Cesar; Felix, Victor; Mitraka, Elvira; Bolton, Evan; Fu, Gang; Mungall, Christopher J; Binder, Janos X; Malone, James; Vasant, Drashtti; Parkinson, Helen; Schriml, Lynn M

    2015-01-01

    The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. DMPD: Signalling adaptors used by Toll-like receptors: an update. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available ) Open .csml file with CIOPlayer Open .csml file with CIOPlayer - ※CIO Playerのご利用上の注意 Open .csml file with CIO Open .csml file with CIO - ※CIOのご利用上の注意 ... ...18706831 Signalling adaptors used by Toll-like receptors: an update. Kenny EF, O'Ne...ill LA. Cytokine. 2008 Sep;43(3):342-9. Epub 2008 Aug 15. (.png) (.svg) (.html) (.csml) Show Signalling adaptors use...d by Toll-like receptors: an update. PubmedID 18706831 Title Signalling adaptors used by Toll-like r

  20. 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.

  1. The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

    Science.gov (United States)

    Fernández, Xosé M

    2018-01-01

    Abstract The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. PMID:29316735

  2. RESIS-II: An Updated Version of the Original Reservoir Sedimentation Survey Information System (RESIS) Database

    Science.gov (United States)

    Ackerman, Katherine V.; Mixon, David M.; Sundquist, Eric T.; Stallard, Robert F.; Schwarz, Gregory E.; Stewart, David W.

    2009-01-01

    The Reservoir Sedimentation Survey Information System (RESIS) database, originally compiled by the Soil Conservation Service (now the Natural Resources Conservation Service) in collaboration with the Texas Agricultural Experiment Station, is the most comprehensive compilation of data from reservoir sedimentation surveys throughout the conterminous United States (U.S.). The database is a cumulative historical archive that includes data from as early as 1755 and as late as 1993. The 1,823 reservoirs included in the database range in size from farm ponds to the largest U.S. reservoirs (such as Lake Mead). Results from 6,617 bathymetric surveys are available in the database. This Data Series provides an improved version of the original RESIS database, termed RESIS-II, and a report describing RESIS-II. The RESIS-II relational database is stored in Microsoft Access and includes more precise location coordinates for most of the reservoirs than the original database but excludes information on reservoir ownership. RESIS-II is anticipated to be a template for further improvements in the database.

  3. FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

    Science.gov (United States)

    Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E.

    2017-01-01

    The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches. PMID:27924039

  4. Comparing records to understand past rapid climate change: An INTIMATE database update

    Science.gov (United States)

    Kearney, Rebecca; Bronk Ramsey, Christopher; Staff, Richard A.; Albert, Paul G.

    2017-04-01

    Integrating multi-proxy records from ice, terrestrial and marine records enhances the understanding of the temporal and spatial variation of past rapid climatic changes globally. By handling these records on their own individual timescales and linking them through known chronological relationships (e.g. tephra, 10Be and 14C), regional comparisons can be made for these past climatic events. Furthermore, the use of time-transfer functions enables the chronological uncertainties between different archives to be quantified. The chronological database devised by the working group 1 (WG1) of INTIMATE, exclusively uses this methodology to provide a means to visualise and compare palaeoclimate records. Development of this database is ongoing, with numerous additional records being added to the database with a particular focus on European archives spanning the Late Glacial period. Here we present a new phase of data collection. Through selected cases study sites across Europe, we aim to illustrate the database as a novel tool in understanding spatial and temporal variations in rapid climatic change. Preliminary results allow questions such as time transgression and regional expressions of rapid climate change to be investigated. The development of this database will continue through additional input of raw climate proxy data, linking to other relevant databases (e.g. Fossil Pollen Database) and providing output data that can be analysed in the statistical programming language of R. A major goal of this work to is not only provide a detailed database, but allow researchers to integrate their own climate proxy data with that on the database.

  5. Browser Based Platform in Maintaining Clinical Activities - Use of The iPads in Head and Neck Clinics

    Science.gov (United States)

    Yang, W. Y.; Moore, J.; Quon, H.; Evans, K.; Sharabi, A.; Herman, J.; Hacker-Prietz, A.; McNutt, T.

    2014-03-01

    Purpose: Incompatibility between documentation and clinical workflow causes physician resistance in organized data collection, which in turn complicates the use of data in patient care improvement. To resolve the gap, we developed an iPad compatible in situ browser-based platform that integrates clinical activity with data collection and analysis presentation. The ability to perform in-clinic activities and monitor decision making using the iPad was evaluated. Methods: A browser-based platform that can exchange and present analysed data from the MOSAIQ database was developed in situ, the iPads were distributed in head and neck clinics to present the browser for clinical activities, data collection and assessment monitoring. Performance of the iPads for in-clinic activities was observed. Results: All in-clinic documentation activities can be performed without workstation computers. Accessing patient record and previous assessments was significantly faster without having to open the MOSAIQ application. Patient assessments can be completed with the physician facing the patient. Graphical presentation of toxicity progression and patient radiation plans to the patient can be performed in single interface without patient leaving the seating area. Updates in patient treatment status and medical history were presented in real time without having to move paper charts around. Conclusions: The iPad can be used in clinical activities independent of computer workstations. Improvements in clinical workflow can be critical in reducing physician resistance in data maintenance. Using the iPad in providing real-time quality monitoring is intuitive to both providers and patients.

  6. Browsers for Distributed Systems: Universal Paradigm or Siren's Song?

    National Research Council Canada - National Science Library

    Seacord, Robett

    1998-01-01

    Web based browsers are quickly becoming ubiquitous in the workplace. Software development managers are quick to incorporate browsers into a broad range of software development projects, often inappropriately...

  7. PHI-base update: additions to the pathogen–host interaction database

    Science.gov (United States)

    Winnenburg, Rainer; Urban, Martin; Beacham, Andrew; Baldwin, Thomas K.; Holland, Sabrina; Lindeberg, Magdalen; Hansen, Hilde; Rawlings, Christopher; Hammond-Kosack, Kim E.; Köhler, Jacob

    2008-01-01

    The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/. PMID:17942425

  8. WebPlus: lxplus in your browser

    CERN Multimedia

    CERN. Geneva

    2017-01-01

    This talk will cover the possibility of offering a lxplus like service directly on the browser. How we could rely on containers and schedulers to maintain long lived sessions, and how to offer integration with common CERN services.

  9. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  10. The updated Swedish family-cancer database used to assess familial risks of prostate cancer during rapidly increasing incidence

    Directory of Open Access Journals (Sweden)

    Hemminki Kari

    2006-12-01

    Full Text Available Abstract The Swedish Family-Cancer Database has been used for some 10 years in the study of familial risks at all common sites. In the present paper we describe some of the main features of version VII of this Database, assembled in year 2006. This update included all residents in Sweden born or immigrated in 1932 and later (offspring with their biological parents, a total of 11.5 million individuals. Cancer cases were retrieved from the Swedish Cancer Registry from years 1958 to 2004, including over 1.2 million first and multiple primary cancers and in situ tumours. We show one application of the Database in the study of familial risks in prostate cancer, with special reference to the modification of familial risk at the time of about 50% increase in incidence due to prostate specific antigen (PSA screening. The familial risks for prostate cancer were 1.92 for sons of affected fathers, 3.03 for brothers and 5.44 for men with an affected father and an affected brother. Familial risk for prostate cancer according to the time since the first family member was diagnosed showed significant increases for two family members being diagnosed in the same year compared to 5+ years apart. Increased surveillance and the availability of PSA screening are the likely reasons for the overestimated familial relative risk shortly after the first diagnosis. This lead time bias should be considered in clinical counselling.

  11. Phospho.ELM: a database of phosphorylation sites--update 2011

    DEFF Research Database (Denmark)

    Dinkel, Holger; Chica, Claudia; Via, Allegra

    2011-01-01

    The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises ...

  12. Effective Generation and Update of a Building Map Database Through Automatic Building Change Detection from LiDAR Point Cloud Data

    Directory of Open Access Journals (Sweden)

    Mohammad Awrangjeb

    2015-10-01

    Full Text Available Periodic building change detection is important for many applications, including disaster management. Building map databases need to be updated based on detected changes so as to ensure their currency and usefulness. This paper first presents a graphical user interface (GUI developed to support the creation of a building database from building footprints automatically extracted from LiDAR (light detection and ranging point cloud data. An automatic building change detection technique by which buildings are automatically extracted from newly-available LiDAR point cloud data and compared to those within an existing building database is then presented. Buildings identified as totally new or demolished are directly added to the change detection output. However, for part-building demolition or extension, a connected component analysis algorithm is applied, and for each connected building component, the area, width and height are estimated in order to ascertain if it can be considered as a demolished or new building-part. Using the developed GUI, a user can quickly examine each suggested change and indicate his/her decision to update the database, with a minimum number of mouse clicks. In experimental tests, the proposed change detection technique was found to produce almost no omission errors, and when compared to the number of reference building corners, it reduced the human interaction to 14% for initial building map generation and to 3% for map updating. Thus, the proposed approach can be exploited for enhanced automated building information updating within a topographic database.

  13. [Development of a Web-based laboratory data browser integrated with heterogeneous clinical information].

    Science.gov (United States)

    Fujikawa, Jun

    2009-02-01

    To demonstrate the feasibility of a Web-based laboratory data browser integrated with heterogeneous clinical information in a hospital setting. A Java-based web application was developed in-house, using free open-source software. The server side manages queries to heterogeneous hospital databases containing patient data. Order entry information including laboratory test results, drug prescriptions, injection orders, physiological test orders and, imaging test orders, was retrieved from a replication database, and integrated with nursing data from a nursing system database. The result was visualized in a time-series table format, and accessed by web browsers on computers connected to the hospital intranet. The laboratory data browser system achieved practical response times over huge databases (> 90 million records). The medical personnel accepted the system well, and applied the system to various clinical situations. Integrating heterogeneous data from hospital databases in a Web-based laboratory data browser is a practical approach. Presenting relevant medical information simultaneously added value to the laboratory data, and may promote better medical management.

  14. ABrowse - a customizable next-generation genome browser framework

    Directory of Open Access Journals (Sweden)

    Kong Lei

    2012-01-01

    Full Text Available Abstract Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for

  15. Updates on Resources, Software Tools, and Databases for Plant Proteomics in 2016-2017.

    Science.gov (United States)

    Misra, Biswapriya B

    2018-02-08

    Proteomics data processing, annotation, and analysis can often lead to major hurdles in large-scale high throughput bottom-up proteomics experiments. Given the recent rise in protein-based big datasets being generated, efforts in in silico tool development occurrences have had an unprecedented increase; so much so, that it has become increasingly difficult to keep track of all the advances in a particular academic year. However, these tools benefit the proteomics community in circumventing critical issues in data analysis and visualization, as these continually developing one-source and community-developed tools hold potential in future research efforts. This review will aim to introduce and summarize more than 50 software tools, databases, and resources developed and published during 2016-2017 under the following categories: tools for data re-processing and analysis, statistical analysis tools, peptide identification tools, databases and spectral libraries, and data visualization and interpretation tools. Intended for a well-informed proteomics community, finally, efforts in data archiving and validation datasets for the community will be discussed as well. Additionally, the author delineates the current and most commonly used proteomics tools in order to introduce novice users to this -omics discovery platform. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  16. FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update.

    Science.gov (United States)

    Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E

    2017-01-04

    The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

    Science.gov (United States)

    Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

    2017-05-03

    The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Analysis of 17 STR data on 5362 southern Portuguese individuals-an update on reference database.

    Science.gov (United States)

    Cabezas Silva, Raquel; Ribeiro, Teresa; Lucas, Isabel; Porto, Maria João; Costa Santos, Jorge; Dario, Paulo

    2016-03-01

    The main objective of this work consisted of the updating of allele frequencies and other relevant forensic parameters for the 17 autosomal STR loci provided by the combination of the two types of kits used routinely in our laboratory casework: AmpF/STR Identifiler(®) and the Powerplex(®) 16 Systems. This aim was of significant importance, given that the last study on these kits within the southern Portuguese population dates back to 2006, and, as a consequence, it was necessary to correct the deviation caused by population evolution over the last ten years so that they might be better applied to our forensic casework. For this reason genetic data from 5362 unrelated Caucasian Portuguese individuals from the south of Portugal who were involved in paternity testing casework from 2005 to 2014 was used. Of all the markers, TPOX proved to be the least polymorphic, and Penta E the most. Secondly, this up-to-date southern Portuguese population was compared not only with the northern and central Portuguese populations, but also with that of southern Portugal in 2006, along with populations from Spain, Italy, Greece, Romania, Morocco, Angola and Korea in order to infer information about the relatedness of these respective populations, and the variation of the southern Portuguese population over time. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs.

    Science.gov (United States)

    Ning, Shangwei; Yue, Ming; Wang, Peng; Liu, Yue; Zhi, Hui; Zhang, Yan; Zhang, Jizhou; Gao, Yue; Guo, Maoni; Zhou, Dianshuang; Li, Xin; Li, Xia

    2017-01-04

    We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. NA-SWS-2.1: An Updated Uniform Database of Teleseismic Shear-wave Splitting Measurements for North America

    Science.gov (United States)

    Refayee, H. A.; Liu, K.; Ray, M. A.; Purevsuren, U.; Gao, S. S.

    2011-12-01

    This updated version of shear wave splitting database for North America contains about 17000 pairs of XKS (including SKS, SKKS, and PKS) splitting parameters. The data used to generate the database were recorded by about 1800 digital broadband seismic stations over the period of 1980-2010. Those represent all the available data from both permanent and portable seismic networks at the IRIS Data Management Center. The data set was produced by following the same automated batch processing and the manual screening and ranking techniques used to create the first version of the uniform shear-wave splitting database for North America, NA-SWS1.1 (Liu, 2009, G-cubed). About 50% of the measurements were from USArray TA stations located west of 94 degree west. Approximately 12000 of the measurements were from the SKS phase, 3000 the SKKS, and 2000 the PKS phase. This study revealed several new first-order features, and enhanced some features that were previously observed in the first version of the database and/or by previous studies. These include the circular pattern of fast polarization directions in the Great Basin and in the vicinity of the San Andreas Fault in southern California. Outside the area with the circular pattern, the fast directions are dominantly parallel to the Absolute Plate Motion (APM) direction of the North American Plate, suggesting an asthenospheric origin of most of the observed anisotropy. However, inconsistency between the fast direction and the APM directions exists in a number of regions such as the southwestern US, the Black Hills region, the Snake River valley/Yellowstone area, Colorado Plateau, and the vicinity of the Rio Grande rift. Such variations reflect either lithospheric contribution to the observed anisotropy or local change in asthenospheric flow direction. Systematic spatial variation in splitting times is also evident, mostly due to the strength and depth of the mantle flow field. In particular, the average splitting time is about 1

  1. The Society of Thoracic Surgeons Congenital Heart Surgery Database: 2017 Update on Outcomes and Quality.

    Science.gov (United States)

    Jacobs, Jeffrey P; Mayer, John E; Mavroudis, Constantine; O'Brien, Sean M; Austin, Erle H; Pasquali, Sara K; Hill, Kevin D; Overman, David M; St Louis, James D; Karamlou, Tara; Pizarro, Christian; Hirsch-Romano, Jennifer C; McDonald, Donna; Han, Jane M; Becker, Susan; Tchervenkov, Christo I; Lacour-Gayet, Francois; Backer, Carl L; Fraser, Charles D; Tweddell, James S; Elliott, Martin J; Walters, Hal; Jonas, Richard A; Prager, Richard L; Shahian, David M; Jacobs, Marshall L

    2017-03-01

    The Society of Thoracic Surgeons Congenital Heart Surgery Database is the largest congenital and pediatric cardiac surgical clinical data registry in the world. It is the platform for all activities of The Society of Thoracic Surgeons related to the analysis of outcomes and the improvement of quality in this subspecialty. This report summarizes current aggregate national outcomes in congenital and pediatric cardiac surgery and reviews related activities in the areas of quality measurement, performance improvement, and transparency. The reported data about aggregate national outcomes are exemplified by an analysis of 10 benchmark operations performed from January 2012 to December 2015. This analysis documents the overall aggregate operative mortality (interquartile range among all participating programs) for the following procedural groups: off-bypass coarctation repair, 1.3% (0.0% to 1.8%); ventricular septal defect repair, 0.6% (0.0% to 0.9%); tetralogy of Fallot repair, 1.1% (0.0% to 1.4%); complete atrioventricular canal repair, 3.0% (0.0% to 4.7%); arterial switch operation, 2.7% (0.0% to 4.1%); arterial switch operation and ventricular septal defect repair, 5.3% (0.0% to 6.7%); Glenn/hemi-Fontan, 2.5% (0.0% to 4.5%); Fontan operation, 1.2% (0.0% to 1.2%); truncus arteriosus repair, 9.4% (0.0% to 16.7%); and Norwood procedure, 15.7% (8.9% to 25.0%). Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  2. Plugin free remote visualization in the browser

    Science.gov (United States)

    Tamm, Georg; Slusallek, Philipp

    2015-01-01

    Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

  3. A Lead Provided by Bookmarks - Intelligent Browsers

    Directory of Open Access Journals (Sweden)

    Dan Balanescu

    2015-05-01

    Full Text Available Browsers are applications that allow Internet access. A defining characteristic is their unidirectionality: Navigator-> Internet. The purpose of this article is to support the idea of Intelligent Browsers that is defined by bidirectional: Navigator-> Internet and Internet-> Navigator. The fundamental idea is that the Internet contains huge resources of knowledge, but they are “passive”. The purpose of this article is to propose the “activation” of this knowledge so that they, through “Intelligent Browsers”, to become from Sitting Ducks to Active Mentors. Following this idea, the present article proposes changes to Bookmarks function, from the current status of Favorites to Recommendations. The article presents an analysis of the utility of this function (by presenting a research of web browsing behaviors and in particular finds that the significance of this utility has decreased lately (to the point of becoming almost useless, as will be shown, in terms data-information-knowledge. Finally, it presents the idea of a project which aims to be an applied approach that anticipates the findings of this study and the concept of Intelligent Browsers (or Active Browsers required in the context of the Big Data concept.

  4. PubChem BioAssay: 2017 update

    Science.gov (United States)

    Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

    2017-01-01

    PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

  5. Enabling interspecies epigenomic comparison with CEpBrowser

    OpenAIRE

    Cao, Xiaoyi; Zhong, Sheng

    2013-01-01

    Summary: We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. Availability: CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/. Contact: Supplementary inf...

  6. Online Marketing Strategy for a browser games portal

    OpenAIRE

    Vinaixa Campos, Joan

    2008-01-01

    The Browser games industry: Introduction and description of browser games and browser games portals. Description of the main characteristics that define the browser games industry and its competitive environment. Analysis of all the factors that need to be considered in order to make a successful market entry. Online marketing techniques: Introduction and description to the main online marketing techniques that exist to market a product or service in internet: Search Engine Marketing...

  7. A Comparative Performance Analysis of Popular Internet Browsers ...

    African Journals Online (AJOL)

    ... and take advantage of the World Wide Web (www). The window to the World Wide Web is a web browser, hence the development of various web browsers in the market today. A comparative study of four web browsers namely Internet Explorer, Mozilla Firefox, Opera and Netscape was carried out. A web portal developed ...

  8. 78 FR 30226 - Accessibility Requirements for Internet Browsers

    Science.gov (United States)

    2013-05-22

    ...] Accessibility Requirements for Internet Browsers AGENCY: Federal Communications Commission. ACTION: Final rule... and Video Accessibility Act of 2010 (CVAA). Section 718 of the Act requires Internet browsers built..., the Commission also affirms that section 716 of the Act requires certain Internet browsers used for...

  9. Zbrowse: an interactive GWAS results browser

    Directory of Open Access Journals (Sweden)

    Greg R. Ziegler

    2015-05-01

    Full Text Available The growing number of genotyped populations, the advent of high-throughput phenotyping techniques and the development of GWAS analysis software has rapidly accelerated the number of GWAS experimental results. Candidate gene discovery from these results files is often tedious, involving many manual steps searching for genes in windows around a significant SNP. This problem rapidly becomes more complex when an analyst wishes to compare multiple GWAS studies for pleiotropic or environment specific effects. To this end, we have developed a fast and intuitive interactive browser for the viewing of GWAS results with a focus on an ability to compare results across multiple traits or experiments. The software can easily be run on a desktop computer with software that bioinformaticians are likely already familiar with. Additionally, the software can be hosted or embedded on a server for easy access by anyone with a modern web browser.

  10. GTB - an online genome tolerance browser.

    Science.gov (United States)

    Shihab, Hashem A; Rogers, Mark F; Ferlaino, Michael; Campbell, Colin; Gaunt, Tom R

    2017-01-06

    Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and prioritize SNVs across the human genome for further investigation. However, no tool exists to visualize the predicted tolerance of the genome to mutation, or the similarities between these methods. We present the Genome Tolerance Browser (GTB, http://gtb.biocompute.org.uk ): an online genome browser for visualizing the predicted tolerance of the genome to mutation. The server summarizes several in silico prediction algorithms and conservation scores: including 13 genome-wide prediction algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specific algorithms. The GTB enables users to visualize the similarities and differences between several prediction algorithms and to upload their own data as additional tracks; thereby facilitating the rapid identification of potential regions of interest.

  11. UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

    Science.gov (United States)

    Robasky, Kimberly; Bulyk, Martha L

    2011-01-01

    The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

  12. Aladin Lite: Lightweight sky atlas for browsers

    Science.gov (United States)

    Boch, Thomas

    2014-02-01

    Aladin Lite is a lightweight version of the Aladin tool, running in the browser and geared towards simple visualization of a sky region. It allows visualization of image surveys (JPEG multi-resolution HEALPix all-sky surveys) and permits superimposing tabular (VOTable) and footprints (STC-S) data. Aladin Lite is powered by HTML5 canvas technology and is easily embeddable on any web page and can also be controlled through a Javacript API.

  13. The GLOBE 3D Genome Browser

    OpenAIRE

    Knoch, Tobias; Eussen, Bert; Moorhouse, Michael

    2007-01-01

    textabstractThe combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various forms of reoccurring sequence features and clone sets etc. Currently, one possibility to represent this information in a visual form - and thus to reveal its scientific meaning - is to use genome browsers su...

  14. Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009

    OpenAIRE

    Wakaguri, Hiroyuki; Suzuki, Yutaka; Katayama, Toshiaki; Kawashima, Shuichi; Kibukawa, Eri; Hiranuka, Kazushi; Sasaki, Masahide; Sugano, Sumio; Watanabe, Junichi

    2008-01-01

    Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this update, the database has been expanded to contain the shogun sequencing for the entire sequences of 14 818 non-redundant full-length cDNA clones from six apicomplexa parasites and 6.8 million of transcription start sites (TSS), both of which had been produced by novel protocols using the oligo-ca...

  15. Change Detection and Land Use / Land Cover Database Updating Using Image Segmentation, GIS Analysis and Visual Interpretation

    Science.gov (United States)

    Mas, J.-F.; González, R.

    2015-08-01

    This article presents a hybrid method that combines image segmentation, GIS analysis, and visual interpretation in order to detect discrepancies between an existing land use/cover map and satellite images, and assess land use/cover changes. It was applied to the elaboration of a multidate land use/cover database of the State of Michoacán, Mexico using SPOT and Landsat imagery. The method was first applied to improve the resolution of an existing 1:250,000 land use/cover map produced through the visual interpretation of 2007 SPOT images. A segmentation of the 2007 SPOT images was carried out to create spectrally homogeneous objects with a minimum area of two hectares. Through an overlay operation with the outdated map, each segment receives the "majority" category from the map. Furthermore, spectral indices of the SPOT image were calculated for each band and each segment; therefore, each segment was characterized from the images (spectral indices) and the map (class label). In order to detect uncertain areas which present discrepancy between spectral response and class label, a multivariate trimming, which consists in truncating a distribution from its least likely values, was applied. The segments that behave like outliers were detected and labeled as "uncertain" and a probable alternative category was determined by means of a digital classification using a decision tree classification algorithm. Then, the segments were visually inspected in the SPOT image and high resolution imagery to assign a final category. The same procedure was applied to update the map to 2014 using Landsat imagery. As a final step, an accuracy assessment was carried out using verification sites selected from a stratified random sampling and visually interpreted using high resolution imagery and ground truth.

  16. QMachine: commodity supercomputing in web browsers.

    Science.gov (United States)

    Wilkinson, Sean R; Almeida, Jonas S

    2014-06-09

    Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

  17. QMachine: commodity supercomputing in web browsers

    Science.gov (United States)

    2014-01-01

    Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

  18. Update History of This Database - The Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us The Rice Growth Monitoring for The Phenotypic Functional Analysis Update History of This Dat...ged. 2014/02/10 The Rice Growth Monitoring for the Phenotypic Functional Analysis English archive site is op...ened. 2003/10/01 The Rice Growth Monitoring System for the Phenotypic Functional ...Rice Growth Monitoring for The Phenotypic Functional Analysis | LSDB Archive ...

  19. Taking advantage of HTML5 browsers to realize the concepts of session state and workflow sharing in web-tool applications

    Science.gov (United States)

    Suftin, I.; Read, J. S.; Walker, J.

    2013-12-01

    Scientists prefer not having to be tied down to a specific machine or operating system in order to analyze local and remote data sets or publish work. Increasingly, analysis has been migrating to decentralized web services and data sets, using web clients to provide the analysis interface. While simplifying workflow access, analysis, and publishing of data, the move does bring with it its own unique set of issues. Web clients used for analysis typically offer workflows geared towards a single user, with steps and results that are often difficult to recreate and share with others. Furthermore, workflow results often may not be easily used as input for further analysis. Older browsers further complicate things by having no way to maintain larger chunks of information, often offloading the job of storage to the back-end server or trying to squeeze it into a cookie. It has been difficult to provide a concept of "session storage" or "workflow sharing" without a complex orchestration of the back-end for storage depending on either a centralized file system or database. With the advent of HTML5, browsers gained the ability to store more information through the use of the Web Storage API (a browser-cookie holds a maximum of 4 kilobytes). Web Storage gives us the ability to store megabytes of arbitrary data in-browser either with an expiration date or just for a session. This allows scientists to create, update, persist and share their workflow without depending on the backend to store session information, providing the flexibility for new web-based workflows to emerge. In the DSASWeb portal ( http://cida.usgs.gov/DSASweb/ ), using these techniques, the representation of every step in the analyst's workflow is stored as plain-text serialized JSON, which we can generate as a text file and provide to the analyst as an upload. This file may then be shared with others and loaded back into the application, restoring the application to the state it was in when the session file

  20. French MeSH Browser: a cross-language tool to access MEDLINE/PubMed.

    Science.gov (United States)

    Thirion, Benoit; Pereira, Susanne; Névéol, Aurélie; Dahamna, Badisse; Darmoni, Stéfan

    2007-10-11

    When searching the medical literature, health professionals and lay people strongly prefer to use their native language. Therefore, Medical Subject Headings (MeSH) translations would be helpful to those who are not fluent in English to access scientific papers indexed in the MEDLINE bibliographic database. Furthermore, medical terminologies such as MeSH are challenging in any language. In this context, a French MeSH Browser was developed.

  1. Reactive non-interference for a browser model

    OpenAIRE

    Bielova N.; Devriese D.; Massacci F.; Piessens F.

    2011-01-01

    We investigate non-interference (secure information flow) policies for web browsers, replacing or complementing the Same Origin Policy. First, we adapt a recently proposed dynamic information flow enforcement mechanism to support asynchronous I/O. We prove detailed security and precision results for this enforcement mechanism, and implement it for the Featherweight Firefox browser model. Second, we investigate three useful web browser security policies that can be enforced ...

  2. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

    Science.gov (United States)

    Guo, Liyuan; Wang, Jing

    2017-11-11

    Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Snowstorm Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Snowstorm Database is a collection of over 500 snowstorms dating back to 1900 and updated operationally. Only storms having large areas of heavy snowfall (10-20...

  4. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    Science.gov (United States)

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

  5. Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

    Science.gov (United States)

    Kono, Nobuaki; Arakawa, Kazuharu; Ogawa, Ryu; Kido, Nobuhiro; Oshita, Kazuki; Ikegami, Keita; Tamaki, Satoshi; Tomita, Masaru

    2009-11-11

    Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/).

  6. Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

    Directory of Open Access Journals (Sweden)

    Nobuaki Kono

    Full Text Available BACKGROUND: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. METHODOLOGY/PRINCIPAL FINDINGS: We have identified five central requirements for a pathway browser: (1 availability of large integrated maps showing genes, enzymes, and metabolites; (2 comprehensive search features and data access; (3 data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4 easy exchange of pathway data; and (5 intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. CONCLUSIONS/SIGNIFICANCE: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/.

  7. Jet browser model accelerated by GPUs

    Directory of Open Access Journals (Sweden)

    Forster Richárd

    2016-12-01

    Full Text Available In the last centuries the experimental particle physics began to develop thank to growing capacity of computers among others. It is allowed to know the structure of the matter to level of quark gluon. Plasma in the strong interaction. Experimental evidences supported the theory to measure the predicted results. Since its inception the researchers are interested in the track reconstruction. We studied the jet browser model, which was developed for 4π calorimeter. This method works on the measurement data set, which contain the components of interaction points in the detector space and it allows to examine the trajectory reconstruction of the final state particles. We keep the total energy in constant values and it satisfies the Gauss law. Using GPUs the evaluation of the model can be drastically accelerated, as we were able to achieve up to 223 fold speedup compared to a CPU based parallel implementation.

  8. Interactive metagenomic visualization in a Web browser.

    Science.gov (United States)

    Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

    2011-09-30

    A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  9. Interactive metagenomic visualization in a Web browser

    Directory of Open Access Journals (Sweden)

    Phillippy Adam M

    2011-09-01

    Full Text Available Abstract Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  10. Verification and Updating of the Database of Topographic Objects with Geometric Information About Buildings by Means of Airborne Laser Scanning Data

    Directory of Open Access Journals (Sweden)

    Mendela-Anzlik Małgorzata

    2017-06-01

    Full Text Available Airborne laser scanning data (ALS are used mainly for creation of precise digital elevation models. However, it appears that the informative potential stored in ALS data can be also used for updating spatial databases, including the Database of Topographic Objects (BDOT10k. Typically, geometric representations of buildings in the BDOT10k are equal to their entities in the Land and Property Register (EGiB. In this study ALS is considered as supporting data source. The thresholding method of original ALS data with the use of the alpha shape algorithm, proposed in this paper, allows for extraction of points that represent horizontal cross section of building walls, leading to creation of vector, geometric models of buildings that can be then used for updating the BDOT10k. This method gives also the possibility of an easy verification of up-to-dateness of both the BDOT10k and the district EGiB databases within geometric information about buildings. For verification of the proposed methodology there have been used the classified ALS data acquired with a density of 4 points/m2. The accuracy assessment of the identified building outlines has been carried out by their comparison to the corresponding EGiB objects. The RMSE values for 78 buildings are from a few to tens of centimeters and the average value is about 0,5 m. At the same time for several objects there have been revealed huge geometric discrepancies. Further analyses have shown that these discrepancies could be resulted from incorrect representations of buildings in the EGiB database.

  11. [The design and realization of Web-view PACS browser].

    Science.gov (United States)

    Yu, Pei-liang; Ye, Zhi-qian

    2006-05-01

    This article analyses the system structure and realization model of Web-view PACS browser in combination with the characteristic of PACS, and presents the realizing process of the web-view PACS browser using JSP mode and B/S model.

  12. MLitB: Machine Learning in the Browser

    NARCIS (Netherlands)

    Meeds, E.; Hendriks, R.; Al Faraby, S.; Bruntink, M.; Welling, M.

    2015-01-01

    With few exceptions, the field of Machine Learning (ML) research has largely ignored the browser as a computational engine. Beyond an educational resource for ML, the browser has vast potential to not only improve the state-of-the-art in ML research, but also, inexpensively and on a massive scale,

  13. Dietary overlap between Boer goats and indigenous browsers in a ...

    African Journals Online (AJOL)

    The winter diet of free ranging Boer goats in Valley Bushveld, KwaZulu-Natal, was determined by direct observations and compared with the diet of indigenous browsers (kudu, eland, giraffe, black rhinoceros) in order to determine which browsers are most compatible with goats for ensuring more efficient use of savanna ...

  14. Ajax and Firefox: New Web Applications and Browsers

    Science.gov (United States)

    Godwin-Jones, Bob

    2005-01-01

    Alternative browsers are gaining significant market share, and both Apple and Microsoft are releasing OS upgrades which portend some interesting changes in Web development. Of particular interest for language learning professionals may be new developments in the area of Web browser based applications, particularly using an approach dubbed "Ajax."…

  15. A Comparative Performance Analysis of Popular Internet Browsers ...

    African Journals Online (AJOL)

    The lack of awareness of available web browser and their characteristics, discourages many Nigerians from having ... Internet access and awareness are currently available in most part of Nigeria. Though bandwidth is restricted ..... memory, speed and brand, results will be obtained for the criteria of comparison of browsers.

  16. Selfrando: Securing the Tor Browser against De-anonymization Exploits

    Directory of Open Access Journals (Sweden)

    Conti Mauro

    2016-10-01

    Full Text Available Tor is a well-known anonymous communication system used by millions of users, including journalists and civil rights activists all over the world. The Tor Browser gives non-technical users an easy way to access the Tor Network. However, many government organizations are actively trying to compromise Tor not only in regions with repressive regimes but also in the free world, as the recent FBI incidents clearly demonstrate. Exploiting software vulnerabilities in general, and browser vulnerabilities in particular, constitutes a clear and present threat to the Tor software. The Tor Browser shares a large part of its attack surface with the Firefox browser. Therefore, Firefox vulnerabilities (even patched ones are highly valuable to attackers trying to monitor users of the Tor Browser.

  17. World Ocean Database 2013 Updates 01/02/2017 through 05/08/2017 (NCEI Accession 0164297)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The World Ocean Database (WOD) is the World’s largest publicly available uniform format quality controlled ocean profile dataset. Ocean profile data are sets of...

  18. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

    Science.gov (United States)

    Bryne, Jan Christian; Valen, Eivind; Tang, Man-Hung Eric; Marstrand, Troels; Winther, Ole; da Piedade, Isabelle; Krogh, Anders; Lenhard, Boris; Sandelin, Albin

    2008-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database-the JASPAR CORE sub-database-has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net.

  19. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    OpenAIRE

    Bryne, Jan Christian; Valen, Eivind; Tang, Man-Hung Eric; Marstrand, Troels; Winther, Ole; da Piedade, Isabelle; Krogh, Anders; Lenhard, Boris; Sandelin, Albin

    2007-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database—the JASPAR CORE sub-database—has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generat...

  20. Third millenium ideal gas and condensed phase thermochemical database for combustion (with update from active thermochemical tables).

    Energy Technology Data Exchange (ETDEWEB)

    Burcat, A.; Ruscic, B.; Chemistry; Technion - Israel Inst. of Tech.

    2005-07-29

    The thermochemical database of species involved in combustion processes is and has been available for free use for over 25 years. It was first published in print in 1984, approximately 8 years after it was first assembled, and contained 215 species at the time. This is the 7th printed edition and most likely will be the last one in print in the present format, which involves substantial manual labor. The database currently contains more than 1300 species, specifically organic molecules and radicals, but also inorganic species connected to combustion and air pollution. Since 1991 this database is freely available on the internet, at the Technion-IIT ftp server, and it is continuously expanded and corrected. The database is mirrored daily at an official mirror site, and at random at about a dozen unofficial mirror and 'finger' sites. The present edition contains numerous corrections and many recalculations of data of provisory type by the G3//B3LYP method, a high-accuracy composite ab initio calculation. About 300 species are newly calculated and are not yet published elsewhere. In anticipation of the full coupling, which is under development, the database started incorporating the available (as yet unpublished) values from Active Thermochemical Tables. The electronic version now also contains an XML file of the main database to allow transfer to other formats and ease finding specific information of interest. The database is used by scientists, educators, engineers and students at all levels, dealing primarily with combustion and air pollution, jet engines, rocket propulsion, fireworks, but also by researchers involved in upper atmosphere kinetics, astrophysics, abrasion metallurgy, etc. This introductory article contains explanations of the database and the means to use it, its sources, ways of calculation, and assessments of the accuracy of data.

  1. Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.

    Science.gov (United States)

    Wakaguri, Hiroyuki; Suzuki, Yutaka; Katayama, Toshiaki; Kawashima, Shuichi; Kibukawa, Eri; Hiranuka, Kazushi; Sasaki, Masahide; Sugano, Sumio; Watanabe, Junichi

    2009-01-01

    Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources. In this update, the database has been expanded to contain the shogun sequencing for the entire sequences of 14,818 non-redundant full-length cDNA clones from six apicomplexa parasites and 6.8 million of transcription start sites (TSS), both of which had been produced by novel protocols using the oligo-capping method and the Illumina GA sequencer. The former should be the ultimate data for exact annotation of the expressed genes, while the latter should be useful for ultra-deep expression analysis. Furthermore, we have launched Full-Arthropods, a full-length cDNA database for arthropods of medical importance. Full-Arthropods contains 50 343 one-pass sequences, 10 399 shotgun complete sequences and 22.4 million TSS tags in anopheles mosquitoes that transmit malaria, tsetse flies that transmit trypanosomiasis and dust mites that cause allergic dermatitis and bronchial asthma. By providing the largest integrated full-length cDNA data resources in the apicomplexa parasites as well as their vectors, Full-Malaria/Parasites and Full-Arthropods should help combat parasitic diseases. Full-Malaria/Parasites and Full-Arthropods are accessible from http://fullmal.hgc.jp/.

  2. BrainBrowser: distributed, web-based neurological data visualization.

    Science.gov (United States)

    Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

    2014-01-01

    Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

  3. BrainBrowser: distributed, web-based neurological data visualization

    Directory of Open Access Journals (Sweden)

    Tarek eSherif

    2015-01-01

    Full Text Available Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern Web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

  4. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P

    1995-01-01

    chemoluminescence (ECL) detection. Identified proteins are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Ultimately, the aim of the comprehensive database is to gather...

  5. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    DEFF Research Database (Denmark)

    Bryne, J.C.; Valen, E.; Tang, M.H.E.

    2008-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR...

  6. Measured energy savings and economics of retrofitting existing single- family homes: An update of the BECA-B database

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, S.D.; Goldman, C.A.; Harris, J.P.

    1991-02-01

    These appendices are the companion volume to report number LBL--28147 Vol.1, with the same title. The summary data tables include physical characteristics, energy consumption, savings, and the retrofit measures installed and their costs for each retrofit project. Each existing single family residential building'' retrofit project in the BECA-B database is described. 99 refs. (BM)

  7. Information-Flow-Based Access Control for Web Browsers

    Science.gov (United States)

    Yoshihama, Sachiko; Tateishi, Takaaki; Tabuchi, Naoshi; Matsumoto, Tsutomu

    The emergence of Web 2.0 technologies such as Ajax and Mashup has revealed the weakness of the same-origin policy[1], the current de facto standard for the Web browser security model. We propose a new browser security model to allow fine-grained access control in the client-side Web applications for secure mashup and user-generated contents. We propose a browser security model that is based on information-flow-based access control (IBAC) to overcome the dynamic nature of the client-side Web applications and to accurately determine the privilege of scripts in the event-driven programming model.

  8. Spoken Language Processing in the Clarissa Procedure Browser

    Science.gov (United States)

    Rayner, M.; Hockey, B. A.; Renders, J.-M.; Chatzichrisafis, N.; Farrell, K.

    2005-01-01

    Clarissa, an experimental voice enabled procedure browser that has recently been deployed on the International Space Station, is as far as we know the first spoken dialog system in space. We describe the objectives of the Clarissa project and the system's architecture. In particular, we focus on three key problems: grammar-based speech recognition using the Regulus toolkit; methods for open mic speech recognition; and robust side-effect free dialogue management for handling undos, corrections and confirmations. We first describe the grammar-based recogniser we have build using Regulus, and report experiments where we compare it against a class N-gram recogniser trained off the same 3297 utterance dataset. We obtained a 15% relative improvement in WER and a 37% improvement in semantic error rate. The grammar-based recogniser moreover outperforms the class N-gram version for utterances of all lengths from 1 to 9 words inclusive. The central problem in building an open-mic speech recognition system is being able to distinguish between commands directed at the system, and other material (cross-talk), which should be rejected. Most spoken dialogue systems make the accept/reject decision by applying a threshold to the recognition confidence score. NASA shows how a simple and general method, based on standard approaches to document classification using Support Vector Machines, can give substantially better performance, and report experiments showing a relative reduction in the task-level error rate by about 25% compared to the baseline confidence threshold method. Finally, we describe a general side-effect free dialogue management architecture that we have implemented in Clarissa, which extends the "update semantics'' framework by including task as well as dialogue information in the information state. We show that this enables elegant treatments of several dialogue management problems, including corrections, confirmations, querying of the environment, and regression

  9. CompaGB: An open framework for genome browsers comparison

    Directory of Open Access Journals (Sweden)

    Chiapello Hélène

    2011-05-01

    Full Text Available Abstract Background Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. Findings To assist in this task, we propose a community-based framework based on two cornerstones: (i the implementation of industry promoted software qualification method (QSOS adapted for genome browser evaluations, and (ii a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile with features of interest to a community-based framework: easy management of evolving data, user comments... Conclusions The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1 choose a genome browser that would better fit their particular project, (2 visualize features comparatively with easily accessible formats, such as tables or radar plots and (3 perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology

  10. CompaGB: An open framework for genome browsers comparison.

    Science.gov (United States)

    Lacroix, Thomas; Loux, Valentin; Gendrault, Annie; Gibrat, Jean-François; Chiapello, Hélène

    2011-05-04

    Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming. To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments... The framework is available at http://genome.jouy.inra.fr/CompaGB. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome

  11. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions

    KAUST Repository

    Schmeier, Sebastian

    2016-10-17

    Transcription factors (TFs) play a pivotal role in transcriptional regulation, making them crucial for cell survival and important biological functions. For the regulation of transcription, interactions of different regulatory proteins known as transcription co-factors (TcoFs) and TFs are essential in forming necessary protein complexes. Although TcoFs themselves do not bind DNA directly, their influence on transcriptional regulation and initiation, although indirect, has been shown to be significant, with the functionality of TFs strongly influenced by the presence of TcoFs. In the TcoF-DB v2 database, we collect information on TcoFs. In this article, we describe updates and improvements implemented in TcoF-DB v2. TcoF-DB v2 provides several new features that enables exploration of the roles of TcoFs. The content of the database has significantly expanded, and is enriched with information from Gene Ontology, biological pathways, diseases and molecular signatures. TcoF-DB v2 now includes many more TFs; has substantially increased the number of human TcoFs to 958, and now includes information on mouse (418 new TcoFs). TcoF-DB v2 enables the exploration of information on TcoFs and allows investigations into their influence on transcriptional regulation in humans and mice. TcoF-DB v2 can be accessed at http://tcofdb.org/.

  12. Update on emergence of HIV-1 resistance to antiretroviral drug classes in an Italian national database: 2007-2009.

    Science.gov (United States)

    Di Giambenedetto, S; Prosperi, M; Fanti, I; Bruzzone, B; Paolucci, S; Penco, G; Meini, G; Di Biagio, A; Paolini, E; Micheli, V; Meraviglia, P; Castelli, P; Corsi, P; Gonnelli, A; Fabbiani, M; Zazzi, M; De Luca, A

    2011-09-01

    We analysed trends of human immunodeficiency virus type 1 (HIV-1) drug resistance during 2007-2009 in the Italian national HIV drug resistance database 'ARCA'. Prevalence of resistance in each year was examined on the basis of the presence of major International AIDS Society-2009 mutations. Predictors of resistance were analysed by multivariable logistic regression. Nine hundred and sixty-six patients were selected. Resistance to nucleoside reverse transcriptase inhibitors and protease inhibitors showed a significant decline with respect to previous surveys. Resistance to any class of drug and three drug classes remained stable. Independent predictors of three-class resistance were the number of treatment regimens experienced, prior suboptimal nucleoside reverse transcriptase inhibitor therapy and the current use of ritonavir-boosted protease inhibitors. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

  13. Intended Use of a Building in Terms of Updating the Cadastral Database and Harmonizing the Data with other Public Records

    Science.gov (United States)

    Buśko, Małgorzata

    2017-06-01

    According to the original wording of the Regulation on the register of land and buildings of 2001, in the real estate cadastre there was one attribute associated with the use of a building structure - its intended use, which was applicable until the amendment to the Regulation was introduced in 2013. Then, additional attributes were added, i.e. the type of the building according to the Classification of Fixed Assets (KST), the class of the building according to the Polish Classification of Types of Constructions (PKOB) and, at the same time, the main functional use and other functions of the building remained in the Regulation as well. The record data on buildings are captured for the real estate cadastre from other data sets, for example those maintained by architectural and construction authorities. At the same time, the data contained in the cadastre, after they have been entered or changed in the database, are transferred to other registers, such as tax records, or land and mortgage court registers. This study is the result of the analysis of the laws applicable to the specific units and registers. A list of discrepancies in the attributes occurring in the different registers was prepared. The practical part of the study paid particular attention to the legal bases and procedures for entering the function of a building in the real estate cadastre, which is extremely significant, as it is the attribute determining the property tax basis.

  14. Intended Use of a Building in Terms of Updating the Cadastral Database and Harmonizing the Data with other Public Records

    Directory of Open Access Journals (Sweden)

    Buśko Małgorzata

    2017-06-01

    Full Text Available According to the original wording of the Regulation on the register of land and buildings of 2001, in the real estate cadastre there was one attribute associated with the use of a building structure - its intended use, which was applicable until the amendment to the Regulation was introduced in 2013. Then, additional attributes were added, i.e. the type of the building according to the Classification of Fixed Assets (KST, the class of the building according to the Polish Classification of Types of Constructions (PKOB and, at the same time, the main functional use and other functions of the building remained in the Regulation as well. The record data on buildings are captured for the real estate cadastre from other data sets, for example those maintained by architectural and construction authorities. At the same time, the data contained in the cadastre, after they have been entered or changed in the database, are transferred to other registers, such as tax records, or land and mortgage court registers. This study is the result of the analysis of the laws applicable to the specific units and registers. A list of discrepancies in the attributes occurring in the different registers was prepared. The practical part of the study paid particular attention to the legal bases and procedures for entering the function of a building in the real estate cadastre, which is extremely significant, as it is the attribute determining the property tax basis.

  15. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  16. Database Description - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name PSCDB Alternative n...rial Science and Technology (AIST) Takayuki Amemiya E-mail: Database classification Structure Databases - Protein structure Database...554-D558. External Links: Original website information Database maintenance site Graduate School of Informat...available URL of Web services - Need for user registration Not available About This Database Database Descri...ption Download License Update History of This Database Site Policy | Contact Us Database Description - PSCDB | LSDB Archive ...

  17. Comparative assembly hubs: Web-accessible browsers for comparative genomics

    Science.gov (United States)

    Nguyen, Ngan; Hickey, Glenn; Raney, Brian J.; Armstrong, Joel; Clawson, Hiram; Zweig, Ann; Karolchik, Donna; Kent, William James; Haussler, David; Paten, Benedict

    2014-01-01

    Motivation: Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers. Results: We introduce a pipeline to easily generate collections of Web-accessible UCSC Genome Browsers interrelated by an alignment. It is intended to democratize our comparative genomic browser resources, serving the broad and growing community of evolutionary genomicists and facilitating easy public sharing via the Internet. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications. To demonstrate this work, we create a comparative assembly hub containing 57 Escherichia coli and 9 Shigella genomes and show examples that highlight their unique biology. Availability and implementation: The source code is available as open source at: https://github.com/glennhickey/progressiveCactus The E.coli and Shigella genome hub is now a public hub listed on the UCSC browser public hubs Web page. Contact: benedict@soe.ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25138168

  18. Adverse outcomes associated with nerve stimulator-guided and ultrasound-guided peripheral nerve blocks by supervised trainees: update of a single-site database.

    Science.gov (United States)

    Orebaugh, Steven L; Kentor, Michael L; Williams, Brian A

    2012-01-01

    We previously published a retrospective review of complications related to peripheral nerve blocks performed by supervised trainees, from our quality assurance and billing data, guided by either ultrasound, with nerve stimulator confirmation, or landmark-based nerve stimulator techniques. This report updates our results, for the period from May 2008 through December 2011, representing ongoing transition to near-complete combined ultrasound/nerve stimulator guidance in a block-oriented, outpatient orthopedic anesthesia practice. We queried our deidentified departmental quality improvement electronic database for adverse outcomes associated with peripheral nerve blocks. Billing records were also deidentified and used to provide the denominator of total number of blocks using each technique of neurolocation. The types of blocks considered in this analysis were interscalene, axillary, femoral, sciatic, and popliteal-sciatic blocks. Nerve block complications based on each type of guidance were then compared for the entire recent 30-month time period, as well as for the 6-year period of this report. There were 9062 blocks performed by ultrasound/nerve stimulator, and 5436 by nerve stimulator alone over the entire 72-month period. Nerve injuries lasting longer than 1 year were rare, but similar in frequency with both nerve guidance techniques. The incidence of local anesthetic systemic toxicity was found to be higher with landmark-nerve stimulator technique than with use of ultrasound-guided nerve blocks (6/5436 vs 0/9069, P = 0.0061). We report a large series of combined ultrasound/nerve stimulator nerve blocks by supervised trainees without major local anesthetic systemic toxicity. While lacking the compelling evidence of randomized controlled trials, this observational database nonetheless allows increased confidence in the safety of using combined ultrasound/nerve stimulator in the setting of anesthesiologists-in-training.

  19. Teleradiology system accessible through a common web browser.

    Science.gov (United States)

    Luccichenti, Giacomo; Ngo Dinh, Nhan; Cademartiri, Filippo; Evangelisti, Giulio; Paolillo, Andrea; Bastianello, Stefano

    2004-01-01

    To describe a teleradiology system accessible via a PC and a common web browser. A dedicated system is connected to several radiological imagers (DR, US, CT, MR) with DICOM standard and TCP/IP protocol. The images are visualised in a common web browser on a remote PC by connecting to the dedicated web-site. Compressed images are visualised on a web page. Special toolbars allow specific operations to be performed on the images (brightness-contrast, zoom, distance measurement and ROI defining) and the communication with the radiological centre. The graphic interface is user-friendly and does not require any special knowledge, except for basic PC and internet surfing. Image compression can be set to preserve image quality, and image transfer is fast. The system presented overcomes the limitations of conventional teleradiology systems since it requires no special network or dedicated software, allowing for visualisation of a radiological examination on a PC and a common web browser.

  20. Savant Genome Browser 2: visualization and analysis for population-scale genomics.

    Science.gov (United States)

    Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

    2012-07-01

    High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

  1. Update of the pompe disease mutation database with 60 novel GAA sequence variants and additional studies on the functional effect of 34 previously reported variants.

    Science.gov (United States)

    Kroos, Marian; Hoogeveen-Westerveld, Marianne; Michelakakis, Helen; Pomponio, Robert; Van der Ploeg, Ans; Halley, Dicky; Reuser, Arnold

    2012-08-01

    Pompe disease is an autosomal recessive lysosomal glycogen storage disorder, characterized by progressive muscle weakness. Deficiency of acid α-glucosidase (EC; 3.2.1.20/3) can be caused by numerous pathogenic variants in the GAA gene. The Pompe Disease Mutation Database at http://www.pompecenter.nl aims to list all variants and their effect. This update reports on 94 variants. We examined 35 novel and 34 known mutations by site-directed mutagenesis and transient expression in COS-7 cells or HEK293T cells. Each of these mutations was given a severity rating using a previously published system, based on the level of acid α-glucosidase activity in medium and transfected cells and on the quantity and quality of the different molecular mass species in the posttranslational modification and transport of acid α-glucosidase. This approach enabled to classify 55 missense mutations as pathogenic and 13 as likely nonpathogenic. Based on their nature and the use of in silico analysis (Alamut® software), 12 of the additional 25 novel mutations were predicted to be pathogenic including 4 splicing mutations, 6 mutations leading to frameshift, and 2 point mutations causing stop codons. Seven of the additional mutations were considered nonpathogenic (4 silent and 3 occurring in intron regions), and 6 are still under investigation. © 2012 Wiley Periodicals, Inc.

  2. Database Description - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us GRIPDB Database Description General information of database Database name GRIPDB Alternative... databases - Protein sequence motifs and active sites Organism Taxonomy Name: Homo Sapiens Taxonomy ID: 9606 Database descript...ailable Web services Not available URL of Web services - Need for user registration Available About This Database Database Descript...ion Download License Update History of This Database Site Policy | Contact Us Database Description - GRIPDB | LSDB Archive ...

  3. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption

    Directory of Open Access Journals (Sweden)

    Hu Quanjun

    2012-11-01

    Full Text Available Abstract Background The yak (Bos grunniens is a long-haired bovine that lives at high altitudes and is an important source of milk, meat, fiber and fuel. The recent sequencing, assembly and annotation of its genome are expected to further our understanding of the means by which it has adapted to life at high altitudes and its ecologically important traits. Description The Yak Genome Database (YGD is an internet-based resource that provides access to genomic sequence data and predicted functional information concerning the genes and proteins of Bos grunniens. The curated data stored in the YGD includes genome sequences, predicted genes and associated annotations, non-coding RNA sequences, transposable elements, single nucleotide variants, and three-way whole-genome alignments between human, cattle and yak. YGD offers useful searching and data mining tools, including the ability to search for genes by name or using function keywords as well as GBrowse genome browsers and/or BLAST servers, which can be used to visualize genome regions and identify similar sequences. Sequence data from the YGD can also be downloaded to perform local searches. Conclusions A new yak genome database (YGD has been developed to facilitate studies on high-altitude adaption and bovine genomics. The database will be continuously updated to incorporate new information such as transcriptome data and population resequencing data. The YGD can be accessed at http://me.lzu.edu.cn/yak.

  4. Vulnerability Assessment of Open Source Wireshark and Chrome Browser

    Science.gov (United States)

    2013-08-01

    UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

  5. The Project Browser : Supporting information access for a project team

    NARCIS (Netherlands)

    Cremers, A.H.M.; Kuijper, I.; Groenewegen, P.L.M.; Post, W.M.

    2007-01-01

    The objective of our study was to design and evaluate a user interface concept for a so-called Project Browser, following a user-centered design method. Previous work has suggested that users prefer to access project-related information instrumental to the task they have to carry out. First, a

  6. Quality Search Content: A Reality With Next Generation Browsers

    Digital Repository Service at National Institute of Oceanography (India)

    Lakshminarayana, S.

    moderate user is browsing through at the most 30 to 40 links out of the total delivery set from a search engine. Next Generation browsers are to reach the user with intelligence to address issues related the content filtering, address blocking, user...

  7. Faecal nitrogen of browser and mixed feeder game species during ...

    African Journals Online (AJOL)

    A practical measure of assessing periods of potential nutritional stress of game species is needed in the management of these species in the Acacia karroo Riparian Thicket of the central Free State. The objectives of the study were to determine Nf concentration of four game species (browsers and mixed feeders) during ...

  8. A Comparative Performance Analysis of Popular Internet Browsers ...

    African Journals Online (AJOL)

    enable users make informed decisions about the use, installation and recommendation of the major web browsers considered in work. The tool was designed and implemented using industry standard technologies such as: 1. JavaScript Scripting Language. 2. Hypertext Markup language (HTML). 3. Document Object Model ...

  9. An investigation of retail outcomes comparing two types of browsers

    National Research Council Canada - National Science Library

    Reynolds, Kristy E; Jones, Michael A; Musgrove, Carolyn Findley; Gillison, Stephanie T

    ... ) that allow retailers to gain a better understanding of consumers' browsing behavior also provides evidence as to the importance of browsing in the retailing industry. Previous research indicates that browsers, consumers who are engaged in browsing activity, are beneficial to retailers as they demonstrate higher levels of product involveme...

  10. SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

    Directory of Open Access Journals (Sweden)

    Kim Seungill

    2008-12-01

    Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

  11. The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser

    Directory of Open Access Journals (Sweden)

    Gasparre Giuseppe

    2011-10-01

    Full Text Available Abstract Background Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear mitochondrial Sequences, whose mode and time of insertion, as well as their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence of NumtS. Some NumtS are involved in recombination events leading to fragment duplication. Moreover, NumtS are polymorphic, a feature that renders them candidates as population markers. Finally, they are a cause of contamination during human mtDNA sequencing, leading to the generation of false heteroplasmies. Results Here we present RHNumtS.2, the most exhaustive human NumtSome catalogue annotating 585 NumtS, 97% of which were here validated in a European individual and in HapMap samples. The NumtS complete dataset and related features have been made available at the UCSC Genome Browser. The produced sequences have been submitted to INSDC databases. The implementation of the RHNumtS.2 tracks within the UCSC Genome Browser has been carried out with the aim to facilitate browsing of the NumtS tracks to be exploited in a wide range of research applications. Conclusions We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support several research applications, such as studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC Genome Browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks.

  12. Database Reports Over the Internet

    Science.gov (United States)

    Smith, Dean Lance

    2002-01-01

    Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

  13. RPAN: rice pan-genome browser for ∼3000 rice genomes.

    Science.gov (United States)

    Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

    2017-01-25

    A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Database Description - Society Catalog | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Society Catalog Database Description General information of database Database name Society C...81-3-5214-8470 Email: Database classification Catalog Database description Society Catalog provides informat...out This Database Database Description Download License Update History of This Da...tabase Site Policy | Contact Us Database Description - Society Catalog | LSDB Archive ...

  15. Database Description - ConfC | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name ConfC Alternative name Database...amotsu Noguchi Tel: 042-495-8736 E-mail: Database classification Structure Database...s - Protein structure Structure Databases - Small molecules Structure Databases - Nucleic acid structure Database... services - Need for user registration - About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Database Description - ConfC | LSDB Archive ...

  16. Fiberweb: Diffusion Visualization and Processing in the Browser.

    Science.gov (United States)

    Ledoux, Louis-Philippe; Morency, Felix C; Cousineau, Martin; Houde, Jean-Christophe; Whittingstall, Kevin; Descoteaux, Maxime

    2017-01-01

    Data visualization is one of the most important tool to explore the brain as we know it. In this work, we introduce a novel browser-based solution for medical imaging data visualization and interaction with diffusion-weighted magnetic resonance imaging (dMRI) and tractography data: Fiberweb. It uses a recent technology, WebGL, that has yet to be fully explored for medical imaging purposes. There are currently very few software tools that allow medical imaging data visualization in the browser, and none of these tools support efficient data interaction and processing, such as streamlines selection and real-time deterministic and probabilistic tractography (RTT). With Fiberweb allowing these types of interaction, it is no longer the case. We show results of the visualization of medical imaging data, and demonstrate that our new RTT probabilistic algorithm can compare to a state of the art offline algorithm. Overall, Fiberweb pushes the boundary of interaction combined with scientific visualization, which opens great perspectives for quality control and neurosurgical navigation on browser-based mobile and static devices.

  17. Using a Web Browser for Environmental and Climate Change Studies

    Science.gov (United States)

    Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

    2005-01-01

    A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth's radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth's Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

  18. Download - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RED | LSDB Archive ...

  19. License - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ut notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - SAHG | LSDB Archive ...

  20. Download - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...cess [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - PSCDB | LSDB Archive ...

  1. Download - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - FANTOM5 | LSDB Archive ...

  2. Download - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...is Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - ASTRA | LSDB Archive ...

  3. Download - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - GRIPDB | LSDB Archive ...

  4. Download - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...out This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - TMFunction | LSDB Archive ...

  5. Download - RGP caps | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RGP caps | LSDB Archive ...

  6. Development of a browser application to foster research on linking climate and health datasets: Challenges and opportunities.

    Science.gov (United States)

    Hajat, Shakoor; Whitmore, Ceri; Sarran, Christophe; Haines, Andy; Golding, Brian; Gordon-Brown, Harriet; Kessel, Anthony; Fleming, Lora E

    2017-01-01

    Improved data linkages between diverse environment and health datasets have the potential to provide new insights into the health impacts of environmental exposures, including complex climate change processes. Initiatives that link and explore big data in the environment and health arenas are now being established. To encourage advances in this nascent field, this article documents the development of a web browser application to facilitate such future research, the challenges encountered to date, and how they were addressed. A 'storyboard approach' was used to aid the initial design and development of the application. The application followed a 3-tier architecture: a spatial database server for storing and querying data, server-side code for processing and running models, and client-side browser code for user interaction and for displaying data and results. The browser was validated by reproducing previously published results from a regression analysis of time-series datasets of daily mortality, air pollution and temperature in London. Data visualisation and analysis options of the application are presented. The main factors that shaped the development of the browser were: accessibility, open-source software, flexibility, efficiency, user-friendliness, licensing restrictions and data confidentiality, visualisation limitations, cost-effectiveness, and sustainability. Creating dedicated data and analysis resources, such as the one described here, will become an increasingly vital step in improving understanding of the complex interconnections between the environment and human health and wellbeing, whilst still ensuring appropriate confidentiality safeguards. The issues raised in this paper can inform the future development of similar tools by other researchers working in this field. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Database Description - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name SAHG Alternative nam...h: Contact address Chie Motono Tel : +81-3-3599-8067 E-mail : Database classification Structure Databases - ...e databases - Protein properties Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database description... Links: Original website information Database maintenance site The Molecular Profiling Research Center for D...stration Not available About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - SAHG | LSDB Archive ...

  8. Database Description - RGP gmap98 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RGP gmap98 Database Description General information of database Database name RGP gmap98 Alt...nomy ID: 4530 Database description According to the publication of our high-densi... available About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - RGP gmap98 | LSDB Archive ...

  9. Database Description - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us GenLibi Database Description General information of database Database name GenLibi Alternati...sculus Taxonomy ID: 10090 Taxonomy Name: Rattus norvegicus Taxonomy ID: 10116 Database description GenLibi (...bout This Database Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - GenLibi | LSDB Archive ...

  10. Callisto Crater Database

    Data.gov (United States)

    National Aeronautics and Space Administration — This web page leads to a database of images and information about the 150 major impact craters on Callisto and is updated semi-regularly based on continuing analysis...

  11. Figure summarizer browser extensions for PubMed Central.

    Science.gov (United States)

    Agarwal, Shashank; Yu, Hong

    2011-06-15

    Figures in biomedical articles present visual evidence for research facts and help readers understand the article better. However, when figures are taken out of context, it is difficult to understand their content. We developed a summarization algorithm to summarize the content of figures and used it in our figure search engine (http://figuresearch.askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images. The extensions can be downloaded from http://figuresearch.askhermes.org/articlesearch/extensions.php.

  12. Open source MySQL Browser for Open Innovation

    Directory of Open Access Journals (Sweden)

    Radu Bucea-Manea-Tonis

    2014-07-01

    Full Text Available Abstract. Our purpose is to cross-compile MySQL driver source code for Linux on Windows architecture using a tool chain in order to build a neutral valid graphic interface on 32 bits. Once achieving this goal we could say that every possible Open source application can be built and run on Windows with maximum efficiency concerning costs and resource. This browser is an example of open innovation because its source code is free for anybody willing to develop new software apps for business and uses only Open source tools.

  13. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture...

  14. PopGeV: a web-based large-scale population genome browser.

    Science.gov (United States)

    Shi, Xinyi; Peng, Jing; Yu, Xiaohan; Zhang, Xiaohong; Li, Dongye; Liu, Baohui; Kong, Fanjiang; Yuan, Xiaohui

    2015-09-15

    The development of high-throughput sequencing technology has made it possible for more and more researchers to use population sequencing data to mine genes associated with specific traits. However, the massive amounts of sequencing data have also brought new challenges to the researchers. The question of how to browse population genomic data in an easy and intuitive manner must be addressed. Web-based genome browsers allow user to conveniently view the results of genomic analyses, but heavy usage can reduce the response speed of the webpage, which limits its usefulness in the display of large-scale genome data. IndexedDB technology is a good solution to this problem; it supports web browsers and so creates local databases. In this way, data can be read from the local storage, achieving a smooth display of population genomic data. PopGeV has the following characteristics. First, it uses a new encoding method for compression of population SNP and INDEL data. IndexedDB technology is used to download the results to local storage so that users can browse the results smoothly even when the network traffic is heavy. Second, PopGeV identify similar genomic regions between two individuals based on SNP data. Population diversity indexes are calculated when comparing two populations. Third, user defined annotation information can be integrated for user-friendly mining of gene functions. Simulation shows that PopGeV can smoothly display analysis results of population genome containing over 500 individuals with 2 millions SNP data. PopGeV is available at www.soyomics.com/popgev/ yuanxh@iga.ac.cn. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Aladin Lite: Embed your Sky in the Browser

    Science.gov (United States)

    Boch, T.; Fernique, P.

    2014-05-01

    I will introduce and describe Aladin Lite1, a lightweight interactive sky viewer running natively in the browser. The past five years have seen the emergence of powerful and complex web applications, thanks to major improvements in JavaScript engines and the advent of HTML5. At the same time, browser plugins Java applets, Flash, Silverlight) that were commonly used to run rich Internet applications are declining and are not well suited for mobile devices. The Aladin team took this opportunity to develop Aladin Lite, a lightweight version of Aladin geared towards simple visualization of a sky region. Relying on the widely supported HTML5 canvas element, it provides an intuitive user interface running on desktops and tablets. This first version allows one to interactively visualize multi-resolution HEALPix image and superimpose tabular data and footprints. Aladin Lite is easily embeddable on any web page and may be of interest for data providers which will be able to use it as an interactive previewer for their own image surveys, previously pre-processed as explained in details in the poster "Create & publish your Hierarchical Progressive Survey". I will present the main features of Aladin Lite as well as the JavaScript API which gives the building blocks to create rich interactions between a web page and Aladin Lite.

  16. Introduction to the fathead minnow genome browser and ...

    Science.gov (United States)

    Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism. The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporti

  17. ASCIIGenome: a command line genome browser for console terminals.

    Science.gov (United States)

    Beraldi, Dario

    2017-05-15

    Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io . Dario.beraldi@cruk.cam.ac.uk. Supplementary data are available at Bioinformatics online.

  18. MLitB: machine learning in the browser

    Directory of Open Access Journals (Sweden)

    Edward Meeds

    2015-07-01

    Full Text Available With few exceptions, the field of Machine Learning (ML research has largely ignored the browser as a computational engine. Beyond an educational resource for ML, the browser has vast potential to not only improve the state-of-the-art in ML research, but also, inexpensively and on a massive scale, to bring sophisticated ML learning and prediction to the public at large. This paper introduces MLitB, a prototype ML framework written entirely in Javascript, capable of performing large-scale distributed computing with heterogeneous classes of devices. The development of MLitB has been driven by several underlying objectives whose aim is to make ML learning and usage ubiquitous (by using ubiquitous compute devices, cheap and effortlessly distributed, and collaborative. This is achieved by allowing every internet capable device to run training algorithms and predictive models with no software installation and by saving models in universally readable formats. Our prototype library is capable of training deep neural networks with synchronized, distributed stochastic gradient descent. MLitB offers several important opportunities for novel ML research, including: development of distributed learning algorithms, advancement of web GPU algorithms, novel field and mobile applications, privacy preserving computing, and green grid-computing. MLitB is available as open source software.

  19. JavaScript Access to DICOM Network and Objects in Web Browser

    National Research Council Canada - National Science Library

    Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

    2017-01-01

    .... Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies...

  20. DIGITAL FLOOD INSURANCE RATE MAP DATABASE, DODGE COUNTY, WISCONSIN, USA - MIP Dodge Portion Upper Rock River Watershed RiskMap DFIRM Update

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk information and supporting data used to develop the risk data. The primary risk;...

  1. DIGITAL FLOOD INSURANCE RATE MAP DATABASE, COLUMBIA COUNTY, WISCONSIN, USA - MIP Columbia Portion Baraboo River Watershed RiskMap DFIRM Update

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk information and supporting data used to develop the risk data. The primary risk;...

  2. OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

    Science.gov (United States)

    Ravagli, Carlo; Pognan, Francois; Marc, Philippe

    2017-01-01

    The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting. The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com This software is designed to run on a Java EE application server and store data in a relational database. philippe.marc@novartis.com. © The Author 2016. Published by Oxford University Press.

  3. Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser.

    Science.gov (United States)

    Byrne, Kevin P; Wolfe, Kenneth H

    2006-01-01

    The Yeast Gene Order Browser (YGOB) is an online tool designed to facilitate the comparative genomic visualization and appraisal of synteny within and between the genomes of seven hemiascomycete yeast species. Three of these genomes are polyploid, and hence contain intra-genomic syntenic regions, the correct assembly of which is a particular success of YGOB. Designed to accurately assemble, display and score gene order relationships, YGOB is both an interactive tool for browsing genomic data, and a software engine now being used for evolutionary analyses on a whole-genome scale. Underlying the online interface is the YGOB database, which consists of homology assignments across the species, extensively curated based on sequence similarity and novelly, an appraisal of genomic context (synteny) in multiple genomes. Currently the YGOB database incorporates genome data from Saccharomyces cerevisiae, Candida glabrata, Saccharomyces castellii, Ashbya gossypii, Kluyveromyces lactis, Kluyveromyces waltii and Saccharomyces kluyveri, but the system is scaleable to accommodate additional genomes. This paper discusses the usage and utility of version 1.0 of YGOB, which is publicly available at http://wolfe.gen.tcd.ie/ygob.

  4. Structure, design and statistical programme library of the meteorological database of Potsdam-Institut fuer Klimaforschung; Struktur, Aufbau und statistische Programmbibliothek der meteorologischen Datenbank am Potsdam-Institut fuer Klimaforschung

    Energy Technology Data Exchange (ETDEWEB)

    Oesterle, H.; Glauer, J. [Potsdam-Institut fuer Klimafolgenforschung (PIK), Potsdam (Germany); Denhard, M. [Frankfurt Univ. (Germany). Inst. fuer Meteorologie und Geophysik

    1999-01-01

    The relational database management system (ORACLE) using different client interfaces (browser, SQL, precompiler) is the most important basis for data organization and storage. The creation of a data bank system at PIK includes: Acquisition of meteorological data series for the projects executed at PIK; development of a database structure on the basis of daily values; control, analysis and classification of data into given storage formats; development and application of statistical software. There are currently 20 different types of data sets with daily, monthly and annual data which are functionally interconnected and updated. All data sets are continuously updated. (orig.) [Deutsch] Wesentliche Grundlage der Datenorganisation und -speicherung bildet das relationale Datenbanksystem ORACLE mit den dazugehoerigen Werkzeugen (Browser, SQL- und Precompiler). Die Entwicklung des Datenbanksystems am PIK umfasst folgende Etappen: - Erwerb von meteorologischen Datensaetzen fuer die am Institut laufenden Forschungsvorhaben; - Entwicklung einer Speicherstruktur auf der Basis von Tageswerten; - Kontrolle, Analyse und Einordnung der Daten in die vorgegebenen Speicherformate; - Entwicklung der zur Datennutzung notwendigen statistischen Programmbibliothek. Zur Zeit gibt es 20 verschiedene Typen von Datensaetzen. Sie enthalten taegliche, monatliche und jaehrliche Daten und sind funktional miteinander verbunden. Alle Datensaetze werden kontinuierlich erweitert. (orig.)

  5. Database Description - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Dicty_cDB Database Description General information of database Database name Dicty_cDB Alter...ssification Genomics Databases (non-vertebrate) - Unicellular eukaryotes genome databases Database descripti...user registration - About This Database Database Description Download License Upd...ate History of This Database Site Policy | Contact Us Database Description - Dicty_cDB | LSDB Archive ...

  6. Database Description - NBDC NikkajiRDF | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us NBDC NikkajiRDF Database Description General information of database Database name NBDC Nikk...ddress Email: Database classification Chemical Database Database description NBDC NikkajiRDF is RDF data of ...Need for user registration Not available About This Database Database Description... Download License Update History of This Database Site Policy | Contact Us Database Description - NBDC NikkajiRDF | LSDB Archive ...

  7. Context Aware Concurrent Execution Framework for Web Browsers

    DEFF Research Database (Denmark)

    Saeed, Aamir; Erbad, Aiman; Olsen, Rasmus Løvenstein

    2016-01-01

    Computing hungry multimedia web applications need to efficiently utilize all the resources of a device. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multicore hardware. HTML5 web workers are implemented by major browser...... vendors to facilitate concurrent execution in web clients and enhance the quality of ambitious web applications. The concurrent execution in web workers allows parallel processing using available cores at the expense of communication overhead and extra computation. The benefits of concurrent execution can...... be maximized by balancing load across workers/CPU cores. This work presents load-balancing algorithms between web workers using parameters such as scheduler throughput, computation priority and game entities locality. An award-winning web-based multimedia game (raptjs.com) is used to evaluate the performance...

  8. Context Aware Concurrent Execution Framework for Web Browser

    DEFF Research Database (Denmark)

    Saeed, Aamir; Erbad, Aiman Mahmood; Olsen, Rasmus Løvenstein

    Computing hungry multimedia web applications need to efficiently utilize the device resources. HTML5 web workers is a non-sharing concurrency platform that enables multimedia web application to utilize the available multi-core hardware. HTML5 web workers are implemented by major browser vendors...... to facilitate concurrent execution in web clients and enhance the quality of ambitious web applications. The concurrent execution in web workers allows parallel processing using available cores at the expense of communication overhead and extra computation. The benefits of concurrent execution can be maximized...... by balancing load across workers/CPU cores. This work presents load-balancing algorithms between web workers using parameters such as scheduler throughput, computation priority and game entity locality. An award-winning web-based multimedia game (raptjs.com) is used to test the performance of the load balance...

  9. Browser-based Analysis of Web Framework Applications

    Directory of Open Access Journals (Sweden)

    Benjamin Kersten

    2010-09-01

    Full Text Available Although web applications evolved to mature solutions providing sophisticated user experience, they also became complex for the same reason. Complexity primarily affects the server-side generation of dynamic pages as they are aggregated from multiple sources and as there are lots of possible processing paths depending on parameters. Browser-based tests are an adequate instrument to detect errors within generated web pages considering the server-side process and path complexity a black box. However, these tests do not detect the cause of an error which has to be located manually instead. This paper proposes to generate metadata on the paths and parts involved during server-side processing to facilitate backtracking origins of detected errors at development time. While there are several possible points of interest to observe for backtracking, this paper focuses user interface components of web frameworks.

  10. Web Pages Content Analysis Using Browser-Based Volunteer Computing

    Directory of Open Access Journals (Sweden)

    Wojciech Turek

    2013-01-01

    Full Text Available Existing solutions to the problem of finding valuable information on the Websuffers from several limitations like simplified query languages, out-of-date in-formation or arbitrary results sorting. In this paper a different approach to thisproblem is described. It is based on the idea of distributed processing of Webpages content. To provide sufficient performance, the idea of browser-basedvolunteer computing is utilized, which requires the implementation of text pro-cessing algorithms in JavaScript. In this paper the architecture of Web pagescontent analysis system is presented, details concerning the implementation ofthe system and the text processing algorithms are described and test resultsare provided.

  11. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    Science.gov (United States)

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

    2016-01-04

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. The NASA Ames PAH IR Spectroscopic Database: Computational Version 3.00 with Updated Content and the Introduction of Multiple Scaling Factors

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Ricca, A.; Boersma, C.; Allamandola, L. J.

    2018-02-01

    Version 3.00 of the library of computed spectra in the NASA Ames PAH IR Spectroscopic Database (PAHdb) is described. Version 3.00 introduces the use of multiple scale factors, instead of the single scaling factor used previously, to align the theoretical harmonic frequencies with the experimental fundamentals. The use of multiple scale factors permits the use of a variety of basis sets; this allows new PAH species to be included in the database, such as those containing oxygen, and yields an improved treatment of strained species and those containing nitrogen. In addition, the computed spectra of 2439 new PAH species have been added. The impact of these changes on the analysis of an astronomical spectrum through database-fitting is considered and compared with a fit using Version 2.00 of the library of computed spectra. Finally, astronomical constraints are defined for the PAH spectral libraries in PAHdb.

  13. National Utility Rate Database: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Ong, S.; McKeel, R.

    2012-08-01

    When modeling solar energy technologies and other distributed energy systems, using high-quality expansive electricity rates is essential. The National Renewable Energy Laboratory (NREL) developed a utility rate platform for entering, storing, updating, and accessing a large collection of utility rates from around the United States. This utility rate platform lives on the Open Energy Information (OpenEI) website, OpenEI.org, allowing the data to be programmatically accessed from a web browser, using an application programming interface (API). The semantic-based utility rate platform currently has record of 1,885 utility rates and covers over 85% of the electricity consumption in the United States.

  14. Integrating heterogeneous open-source software into web browsers using AMICO:WEB

    NARCIS (Netherlands)

    Z. Obrenovic; J.R. van Ossenbruggen (Jacco)

    2007-01-01

    textabstractA web browser provides a uniform user interface to different types of information. Making this interface universally accessible and more interactive is a long term goal still far from being achieved. Universally accessible browsers require novel interaction modalities and additional

  15. Lexicon Sextant: Modeling a Mnemonic System for Customizable Browser Information Organization and Management

    Science.gov (United States)

    Shen, Siu-Tsen

    2016-01-01

    This paper presents an ongoing study of the development of a customizable web browser information organization and management system, which the author has named Lexicon Sextant (LS). LS is a user friendly, graphical web based add-on to the latest generation of web browsers, such as Google Chrome, making it easier and more intuitive to store and…

  16. HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

    Science.gov (United States)

    Machovec, George S., Ed.

    1995-01-01

    Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

  17. Nomenclature and databases for the surgical treatment of congenital cardiac disease - an updated primer and an analysis of opportunities for improvement

    NARCIS (Netherlands)

    Jacobs, Jeffrey Phillip; Jacobs, Marshall Lewis; Mavroudis, Constantine; Backer, Carl Lewis; Lacour-Gayet, Francois G.; Tchervenkov, Christo I.; Franklin, Rodney C. G.; Beland, Marie J.; Jenkins, Kathy J.; Walters, Hal; Bacha, Emile A.; Maruszewski, Bohdan; Kurosawa, Hiromi; Clarke, David Robinson; Gaynor, J. William; Spray, Thomas L.; Stellin, Giovanni; Ebels, Tjark; Krogmann, Otto N.; Aiello, Vera D.; Colan, Steven D.; Weinberg, Paul; Giroud, Jorge M.; Everett, Allen; Wernovsky, Gil; Elliott, Martin J.; Edwards, Fred H.

    2008-01-01

    This review discusses the historical aspects, current state of the art, and potential future advances in the areas of nomenclature and databases for the analysis Of Outcomes of treatments for patients with congenitally malformed hearts. We will consider the current state of analysis of outcomes, lay

  18. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection

    National Research Council Canada - National Science Library

    Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

    2015-01-01

    The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously...

  19. D3GB: An Interactive Genome Browser for R, Python, and WordPress.

    Science.gov (United States)

    Barrios, David; Prieto, Carlos

    2017-05-01

    Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

  20. Download - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Database Description Download License Update History of This Database Site Policy | Contact Us Download - SAHG | LSDB Archive ...

  1. Download - DMPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...atabase Database Description Download License Update History of This Database Site Policy | Contact Us Download - DMPD | LSDB Archive ...

  2. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available pliance with the terms and conditions of the license described below. The license s...List Contact us Trypanosomes Database License License to Use This Database Last updated : 2014/02/04 You may use this database in com

  3. Nomenclature and databases for the surgical treatment of congenital cardiac disease--an updated primer and an analysis of opportunities for improvement.

    Science.gov (United States)

    Jacobs, Jeffrey Phillip; Jacobs, Marshall Lewis; Mavroudis, Constantine; Backer, Carl Lewis; Lacour-Gayet, Francois G; Tchervenkov, Christo I; Franklin, Rodney C G; Béland, Marie J; Jenkins, Kathy J; Walters, Hal; Bacha, Emile A; Maruszewski, Bohdan; Kurosawa, Hiromi; Clarke, David Robinson; Gaynor, J William; Spray, Thomas L; Stellin, Giovanni; Ebels, Tjark; Krogmann, Otto N; Aiello, Vera D; Colan, Steven D; Weinberg, Paul; Giroud, Jorge M; Everett, Allen; Wernovsky, Gil; Elliott, Martin J; Edwards, Fred H

    2008-12-01

    This review discusses the historical aspects, current state of the art, and potential future advances in the areas of nomenclature and databases for the analysis of outcomes of treatments for patients with congenitally malformed hearts. We will consider the current state of analysis of outcomes, lay out some principles which might make it possible to achieve life-long monitoring and follow-up using our databases, and describe the next steps those involved in the care of these patients need to take in order to achieve these objectives. In order to perform meaningful multi-institutional analyses, we suggest that any database must incorporate the following six essential elements: use of a common language and nomenclature, use of an established uniform core dataset for collection of information, incorporation of a mechanism of evaluating case complexity, availability of a mechanism to assure and verify the completeness and accuracy of the data collected, collaboration between medical and surgical subspecialties, and standardised protocols for life-long follow-up. During the 1990s, both The European Association for Cardio-Thoracic Surgery and The Society of Thoracic Surgeons created databases to assess the outcomes of congenital cardiac surgery. Beginning in 1998, these two organizations collaborated to create the International Congenital Heart Surgery Nomenclature and Database Project. By 2000, a common nomenclature, along with a common core minimal dataset, were adopted by The European Association for Cardio-Thoracic Surgery and The Society of Thoracic Surgeons, and published in the Annals of Thoracic Surgery. In 2000, The International Nomenclature Committee for Pediatric and Congenital Heart Disease was established. This committee eventually evolved into the International Society for Nomenclature of Paediatric and Congenital Heart Disease. The working component of this international nomenclature society has been The International Working Group for Mapping and Coding

  4. Database Description - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Taxonomy Icon Database Description General information of database Database name Taxonomy Ic...-8666 Japan Tel : +81-3-5214-8491 Fax : +81-3-5214-8470 E-mail : Database classification Images Database descript... URL of Web services - Need for user registration Not available About This Database Database Description Dow...nload License Update History of This Database Site Policy | Contact Us Database Description - Taxonomy Icon | LSDB Archive ...

  5. Database Description - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us KAIKOcDNA Database Description General information of database Database name KAIKOcDNA Alter...ssification Nucleotide Sequence Databases Organism Taxonomy Name: Bombyx mori Taxonomy ID: 7091 Database descript...is Database Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - KAIKOcDNA | LSDB Archive ... ...available URL of Web services - Need for user registration Not available About Th

  6. Dietary shifts: do grazers become browsers in the Thicket Biome?

    Directory of Open Access Journals (Sweden)

    M. Landman

    2001-07-01

    Full Text Available The diet of buffalo (Syncerus coffer and Burchell's zebra (Equus burchelli was investigated in the Addo Elephant National Park to test the hypothesis that the shortage of grass associated with thicket vegetation results in grazers increasing the proportion of dicotyledonous plant species in their diet. Diet composition, estimated from faecal analysis, indicated that 19 and 21 plant species were identified in the faeces of zebra and buffalo, respectively. Buffalo proved to have a higher percentage dicotyledonous (28.1 vs. 8.5 and lower percentage monocotyledonous (71.9 vs. 91.5 species in their diet than zebra. The grass Eragrostis curvula was found to be the dominant food item for both buffalo (18 of diet and zebra (39 of diet during the period of study. The present study indicated that a great proportion of the buffalo diet does in fact consist of grass, thereby refuting the perception that the Addo buffalo are primarily browsers. Both buffalo and zebra are specialised grazers and unsuited to a diet of browse. The probability of dietary shift by these grazers in the grass limited thicket vegetation is therefore challenged.

  7. Savant: genome browser for high-throughput sequencing data.

    Science.gov (United States)

    Fiume, Marc; Williams, Vanessa; Brook, Andrew; Brudno, Michael

    2010-08-15

    The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictions and understand the functional effects, especially in the context of other datasets. We introduce Savant, the Sequence Annotation, Visualization and ANalysis Tool, a desktop visualization and analysis browser for genomic data. Savant was developed for visualizing and analyzing HTS data, with special care taken to enable dynamic visualization in the presence of gigabases of genomic reads and references the size of the human genome. Savant supports the visualization of genome-based sequence, point, interval and continuous datasets, and multiple visualization modes that enable easy identification of genomic variants (including single nucleotide polymorphisms, structural and copy number variants), and functional genomic information (e.g. peaks in ChIP-seq data) in the context of genomic annotations. Savant is freely available at http://compbio.cs.toronto.edu/savant.

  8. Download - GenLibi | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - GenLibi | LSDB Archive ...

  9. License - Q-TARO | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...thout notice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - Q-TARO | LSDB Archive ...

  10. Mapping Information - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Search Image Search Home About Archive Update History Data List Contact us fRNAdb Mapping Information...Database Database Description Download License Update History of This Database Site Policy | Contact Us Mapping

  11. Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...out This Database Database Description Download License Update History of This Database Site Policy | Contac

  12. [Update the wood dust exposure values included in the job-exposure matrix MatEmESp by making use of the WOODEX database].

    Science.gov (United States)

    Ramoneda Paniagua, Alex; van der Haar, Rudolf

    2016-01-01

    To revise and complete information on prevalence and intensity of wood dust exposure among Spanish workers in the MatEmESp job-exposure matrix, based on data from the WOODEX database. Exposure groups by economic activity in WOODEX were linked to the occupations in MatEmESp. The WOODEX data were then used to calculate new values of exposure prevalence and intensity for the occupations included in MatEmESp. A total of 18 occupations in MatEmESp were linked to exposure groups in the WOODEX database. This allowed estimation of new exposure intensity values for these 18 occupations and calculation of new exposure prevalence values for 16 of them. In addition, a new at-risk occupation, previously not in MatEmESp, was identified. The occupations with the highest prevalence values are sawmill operators (CNO-94 code 8141) and operators of machinery for making wood products (CNO-94 code 8340). The new calculations indicate that 10.5% of at-risk workers in MatEmESp are exposed to concentrations above 5 mg/m3. The WOODEX data provided more detailed information about exposure profiles to wood dust and are mainly based on Spanish data. In contrast, 95% of the data on wood dust exposure inMatEmESp is based on extrapolations from other countries or on expert considerations. Copyright belongs to the Societat Catalana de Salut Laboral.

  13. HOME USERS SECURITY AND THE WEB BROWSER INBUILT SETTINGS, FRAMEWORK TO SETUP IT AUTOMATICALLY

    OpenAIRE

    Mohammed Serrhini; Abdelazziz Ait Moussa

    2013-01-01

    We are living in the electronic age where electronic transactions such as e-mail, e-banking, e-commerce and e-learning becoming more and more prominent. To access online for this services, the web browser is todayâs almost unique software used. These daysâ hackers know that browsers are installed into all computers and can be used to compromise a machine by distributing malware via malicious or hacked websites. Also these sites use JavaScript to manipulate browsers and can drive user system t...

  14. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Stærfeldt, Hans Henrik; Rotenberg, Eva

    2009-01-01

    , standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. [Supplemental material including interactive...... atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/]....... readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot, allowing for example visualization of gene expression and regulation data. Further...

  15. Nuclear Science References Database

    Science.gov (United States)

    Pritychenko, B.; Běták, E.; Singh, B.; Totans, J.

    2014-06-01

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center http://www.nndc.bnl.gov/nsr.

  16. A Web services-based distributed system with browser-client architecture to promote tele-audiology assessment.

    Science.gov (United States)

    Yao, Jianchu; Givens, Gregg D; Wan, Yongbo

    2009-10-01

    The purpose of this research was to extend applications of the Internet and other telecommunication means to the assessment of hearing. The newly developed distributed system consists primarily of an application server and its database, and Web services under browser-server architecture to support remote hearing assessment. A pilot study was conducted: three independent audiologists assessed hearing of 25 subjects using testing approaches with different data communication configurations. Analysis of the results demonstrated the feasibility of replacing conventional "face-to-face" tests with the remote hearing tests using the distributed system. Because of its distributed architecture, the present system supports a new service model and separates technical maintenance and clinical services. Consequently, the system shows great potential to benefit the clinical hearing care profession. Future research is planned to apply this system to medical facilities and for distance applications.

  17. Multiple browsers structure tree recruitment in logged temperate forests

    Science.gov (United States)

    Faison, Edward K.; DeStefano, Stephen; Foster, David R.; Rapp, Joshua M.; Compton, Justin A.

    2016-01-01

    Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus), and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus) in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores–no-ungulates (full exclosure), deer (partial exclosure), and deer + moose (control) was established. After 6–7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3–6 fold, and species richness by 1.7 species (19%). In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%). Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps), suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were

  18. Autoplot: a Browser for Science Data on the Web

    Science.gov (United States)

    Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.

    2008-12-01

    Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.

  19. Multiple Browsers Structure Tree Recruitment in Logged Temperate Forests.

    Directory of Open Access Journals (Sweden)

    Edward K Faison

    Full Text Available Historical extirpations have resulted in depauperate large herbivore assemblages in many northern forests. In eastern North America, most forests are inhabited by a single wild ungulate species, white-tailed deer (Odocoileus virginianus, and relationships between deer densities and impacts on forest regeneration are correspondingly well documented. Recent recolonizations by moose (Alces americanus in northeastern regions complicate established deer density thresholds and predictions of browsing impacts on forest dynamics because size and foraging differences between the two animals suggest a lack of functional redundancy. We asked to what extent low densities of deer + moose would structure forest communities differently from that of low densities of deer in recently logged patch cuts of Massachusetts, USA. In each site, a randomized block with three treatment levels of large herbivores-no-ungulates (full exclosure, deer (partial exclosure, and deer + moose (control was established. After 6-7 years, deer + moose reduced stem densities and basal area by 2-3-fold, Prunus pensylvanica and Quercus spp. recruitment by 3-6 fold, and species richness by 1.7 species (19%. In contrast, in the partial exclosures, deer had non-significant effects on stem density, basal area, and species composition, but significantly reduced species richness by 2.5 species on average (28%. Deer browsing in the partial exclosure was more selective than deer + moose browsing together, perhaps contributing to the decline in species richness in the former treatment and the lack of additional decline in the latter. Moose used the control plots at roughly the same frequency as deer (as determined by remote camera traps, suggesting that the much larger moose was the dominant browser species in terms of animal biomass in these cuts. A lack of functional redundancy with respect to foraging behavior between sympatric large herbivores may explain combined browsing effects that were

  20. Prototype of Multifunctional Full-text Library in the Architecture Web-browser / Web-server / SQL-server

    Science.gov (United States)

    Lyapin, Sergey; Kukovyakin, Alexey

    Within the framework of the research program "Textaurus" an operational prototype of multifunctional library T-Libra v.4.1. has been created which makes it possible to carry out flexible parametrizable search within a full-text database. The information system is realized in the architecture Web-browser / Web-server / SQL-server. This allows to achieve an optimal combination of universality and efficiency of text processing, on the one hand, and convenience and minimization of expenses for an end user (due to applying of a standard Web-browser as a client application), on the other one. The following principles underlie the information system: a) multifunctionality, b) intelligence, c) multilingual primary texts and full-text searching, d) development of digital library (DL) by a user ("administrative client"), e) multi-platform working. A "library of concepts", i.e. a block of functional models of semantic (concept-oriented) searching, as well as a subsystem of parametrizable queries to a full-text database, which is closely connected with the "library", serve as a conceptual basis of multifunctionality and "intelligence" of the DL T-Libra v.4.1. An author's paragraph is a unit of full-text searching in the suggested technology. At that, the "logic" of an educational / scientific topic or a problem can be built in a multilevel flexible structure of a query and the "library of concepts", replenishable by the developers and experts. About 10 queries of various level of complexity and conceptuality are realized in the suggested version of the information system: from simple terminological searching (taking into account lexical and grammatical paradigms of Russian) to several kinds of explication of terminological fields and adjustable two-parameter thematic searching (a [set of terms] and a [distance between terms] within the limits of an author's paragraph are such parameters correspondingly).

  1. Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser

    National Research Council Canada - National Science Library

    Cline, Melissa S; Craft, Brian; Swatloski, Teresa; Goldman, Mary; Ma, Singer; Haussler, David; Zhu, Jingchun

    2013-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) offers interactive visualization and exploration of TCGA genomic, phenotypic, and clinical data, as produced by the Cancer Genome Atlas Research Network...

  2. Database Description - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Open TG-GATEs Database Description General information of database Database name Open TG-GAT...onomy ID: 9606 Database description Toxicogenomics Project (TGP) is a government-private companies collabora... available URL of Web services - Need for user registration - About This Database Database Descript...ion Download License Update History of This Database Site Policy | Contact Us Database Description - Open TG-GATEs | LSDB Archive ...

  3. Database Description - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AT Atlas Database Description General information of database Database name AT Atlas Alterna.... coli, wheat, human, yeast et al. as organisms using protein biosynthesis. Database description AT Atlas wi...eb services - Need for user registration Not available About This Database Database Descript...ion Download License Update History of This Database Site Policy | Contact Us Database Description - AT Atlas | LSDB Archive ...

  4. Database Description - Gene Name Thesaurus | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Gene Name Thesaurus Database Description General information of database Database name Gene ...lus subtilis Taxonomy ID: 1423 Database description Gene names and gene family names were collected for 9 di...f Web services - Need for user registration - About This Database Database Description Download License Upda...te History of This Database Site Policy | Contact Us Database Description - Gene Name Thesaurus | LSDB Archive ...

  5. A Policy Based Approach for the Management of Web Browser Resources to Prevent Anonymity Attacks in Tor

    Science.gov (United States)

    Navarro-Arribas, Guillermo; Garcia-Alfaro, Joaquin

    Web browsers are becoming the universal interface to reach applications and services related with these systems. Different browsing contexts may be required in order to reach them, e.g., use of VPN tunnels, corporate proxies, anonymisers, etc. By browsing context we mean how the user browsers the Web, including mainly the concrete configuration of its browser. When the context of the browser changes, its security requirements also change. In this work, we present the use of authorisation policies to automatise the process of controlling the resources of a Web browser when its context changes. The objective of our proposal is oriented towards easing the adaptation to the security requirements of the new context and enforce them in the browser without the need for user intervention. We present a concrete application of our work as a plug-in for the adaption of security requirements in Mozilla/Firefox browser when a context of anonymous navigation through the Tor network is enabled.

  6. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

    Science.gov (United States)

    Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony; Ballester, Benoit

    2018-01-04

    With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. A Protocol, a standard and a (PULI) database for quantitative micro-FTIR measurements of water in nominally anhydrous minerals: an update

    Science.gov (United States)

    Kovacs, Istvan; Udvardi, Beatrix; Pintér, Zsanett; Hidas, Károly; Kutassy, Lászlóné; Falus, György; Lendvay, Pál; István, Török; Zelei, Tamás; Fancsik, Tamás; Gál, Tamás; Mihály, Judith; Németh, Csaba; Ingrin, Jannick; Xia, Qunke; Hermann, Jörg; Stalder, Roland; Perucchi, Andrea; Kamarás, Katalin; Szekrényes, Zsolt

    2014-05-01

    numerous infrared spectra. To keep up with this rising numbers of infrared spectra an electronic spectral database would be desirable. This was the motivation why we have constructed the Pannon Uniform Lithosheric Infrared (PULI) spectral database ( puli.mfgi.hu ), which by now include over a 1000 spectra of olivine and pyroxenes from the shallow upper mantle. The spectra were collected in uniform electronic formats (txt or xls) which will facilitate the comparison and quantitative re-evaluation.

  8. AMDIS and CHART update. 1

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, I.; Kato, T. [National Inst. for Fusion Science, Toki, Gifu (Japan); Igarashi, A. [Miyazaki Univ., Miyazaki (JP)] [and others

    2002-10-01

    A working group for updating atomic and molecular collision data in the NIFS database AMDIS (electron scattering) and CHART (ion scattering) has been organized. This group has searched and reviewed literatures for collecting relevant atomic data with are to be included into the database. This is a summary report of the activities of this working group. (author)

  9. Comcutejs: A Web Browser Based Platform For Large-Scale Computations

    Directory of Open Access Journals (Sweden)

    Roman Debski

    2013-01-01

    Full Text Available The paper presents a new, cost effective, volunteer computing based platform.It utilizes volunteers’ web browsers as computational nodes. The computationaltasks are delegated to the browsers and executed in the background (indepen-dently of any user interface scripts making use of the HTML5 web workerstechnology. The capabilities of the platform have been proved by experimentsperformed in a wide range of numbers of computational nodes (1–400.

  10. Living City, a Collaborative Browser-based Massively Multiplayer Online Game

    OpenAIRE

    Ferrara, Emilio; Fiumara, Giacomo; Pagano, Francesco

    2010-01-01

    This work presents the design and implementation of our Browser-based Massively Multiplayer Online Game, Living City, a simulation game fully developed at the University of Messina. Living City is a persistent and real-time digital world, running in the Web browser environment and accessible from users without any client-side installation. Today Massively Multiplayer Online Games attract the attention of Computer Scientists both for their architectural peculiarity and the close interconnectio...

  11. How Far Can Client-Only Solutions Go for Mobile Browser Speed?

    OpenAIRE

    Wang, Zhen; Lin, Felix Xiaozhu; Zhong, Lin; Chishtie, Mansoor

    2011-01-01

    Mobile browser is known to be slow because of the bottleneck in resource loading. Client-only solutions to improve resource loading are attractive because they are immediately deployable, scalable, and secure. We present the first publicly known treatment of client-only solutions to understand how much they can improve mobile browser speed without infrastructure support. Leveraging an unprecedented set of web usage data collected from 24 iPhone users continuously over one year, we examine the...

  12. A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

    Science.gov (United States)

    Naito, O.

    A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

  13. A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

    Directory of Open Access Journals (Sweden)

    O. Naito

    2017-01-01

    Full Text Available A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

  14. Software to provide security for Web Browser Cookies and Passwords using Trusted Computing Technology

    OpenAIRE

    Kannamanani, R.

    2008-01-01

    For further development and enhancement of browser security, there is need to develop something new which provides the better security for the user credential information which will be stored in user PC through the web browser. Although we have many softwares which provide the security functionalities for system, there are many vulnerabilities, so for this there is need to use some functions and specifications mentioned by Trusted Computing group. Therefore, the goal of this semester thesis w...

  15. Steam Properties Database

    Science.gov (United States)

    SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

  16. OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

    Science.gov (United States)

    Chen, Wei-Hua; Lu, Guanting; Chen, Xiao; Zhao, Xing-Ming; Bork, Peer

    2017-01-04

    OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased numbers of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Browser impacts in Mapungubwe National Park, South Africa: Should we be worried?

    Directory of Open Access Journals (Sweden)

    Corli Coetsee

    2016-03-01

    Full Text Available This study explores the impact of browsers on vegetation types within the Mapungubwe National Park and specifically whether rocky outcrops or ridges in the park serve as refugia from browsers, particularly elephants. We sampled 80 transects at 20 sites and recorded 1740 plants comprising 65 species. We found that a high proportion (> 80% of the woody vegetation sampled indicated browser utilisation. Although certain woody species (e.g. Albizia harveyi, Boscia albitrunca, Lannea schweinfurthii appeared to be preferred by browsers, browsing levels were relatively high among all woody species. High levels of browsing by herbivores other than elephants suggest that they have a significant impact on the park’s vegetation. We did not find that rocky ridges acted as refugia to browsers, but instead found that vegetation in rocky ridges was more severely impacted by browsers than vegetation in flat areas, despite vegetation being more accessible in flat areas. If elephant numbers continue to increase at the current rate (e.g. elephant numbers doubled between 2007 and 2010, we predict that some of the heavily utilised species will become locally rare over time.Conservation implications: High levels of browsing by both elephant and smaller herbivores contribute to significant impacts on vegetation away from rivers in Mapungubwe National Park. Without management interventions that address both types of impact, structural and species diversity are bound to decrease over the short to medium term.

  18. The HuRef Browser: a web resource for individual human genomics.

    Science.gov (United States)

    Axelrod, Nelson; Lin, Yuan; Ng, Pauline C; Stockwell, Timothy B; Crabtree, Jonathan; Huang, Jiaqi; Kirkness, Ewen; Strausberg, Robert L; Frazier, Marvin E; Venter, J Craig; Kravitz, Saul; Levy, Samuel

    2009-01-01

    The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at http://huref.jcvi.org.

  19. An Asynchronous P300-Based Brain-Computer Interface Web Browser for Severely Disabled People.

    Science.gov (United States)

    Martinez-Cagigal, Victor; Gomez-Pilar, Javier; Alvarez, Daniel; Hornero, Roberto

    2017-08-01

    This paper presents an electroencephalographic (EEG) P300-based brain-computer interface (BCI) Internet browser. The system uses the "odd-ball" row-col paradigm for generating the P300 evoked potentials on the scalp of the user, which are immediately processed and translated into web browser commands. There were previous approaches for controlling a BCI web browser. However, to the best of our knowledge, none of them was focused on an assistive context, failing to test their applications with a suitable number of end users. In addition, all of them were synchronous applications, where it was necessary to introduce a "read-mode" command in order to avoid a continuous command selection. Thus, the aim of this study is twofold: 1) to test our web browser with a population of multiple sclerosis (MS) patients in order to assess the usefulness of our proposal to meet their daily communication needs; and 2) to overcome the aforementioned limitation by adding a threshold that discerns between control and non-control states, allowing the user to calmly read the web page without undesirable selections. The browser was tested with sixteen MS patients and five healthy volunteers. Both quantitative and qualitative metrics were obtained. MS participants reached an average accuracy of 84.14%, whereas 95.75% was achieved by control subjects. Results show that MS patients can successfully control the BCI web browser, improving their personal autonomy.

  20. An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.

    Directory of Open Access Journals (Sweden)

    Debbie Winter

    Full Text Available BACKGROUND: The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. METHODOLOGY/PRINCIPAL FINDINGS: In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph - or eFP - Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser, data for subcellular localization of Arabidopsis proteins (Cell eFP Browser, and mouse tissue atlas microarray data (Mouse eFP Browser. CONCLUSIONS/SIGNIFICANCE: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.

  1. Memory disorders associated with consumption of drugs: updating through a case/noncase study in the French PharmacoVigilance Database

    Science.gov (United States)

    Chavant, Francois; Favrelière, Sylvie; Lafay-Chebassier, Claire; Plazanet, Caroline; Pérault-Pochat, Marie-Christine

    2011-01-01

    AIMS To investigate putative associations of reports of memory disorders and suspected drugs. METHODS We used the case/noncase method in the French PharmacoVigilance Database (FPVD). Cases were reports of memory loss in the FPVD between January 2000 and December 2009. Noncases were all other reports during the same period. To assess the association between memory impairment and drug intake, we calculated an odds ratio with its 95% confidence interval. RESULTS Among the 188 284 adverse drug reactions recorded, we identified 519 cases of memory loss. The sex ratio was 0.6 and the median age was 54 years (range 4–93). The maximal number of cases occurred between 40–49 and 50–59 years. Evolution was favourable in 63% of the cases. We found significant odds ratios for benzodiazepines (alprazolam, bromazepam, prazepam, clonazepam etc.), benzodiazepine-like hypnotics (zolpidem and zopiclone), antidepressants (fluoxetine, paroxetine and venlafaxine), analgesics (morphine, nefopam and tramadol), anticonvulsants (topiramate, pregabalin, levetiracetam etc.), antipsychotics (aripiprazole and lithium) and other drugs, such as trihexyphenidyl, ciclosporin and isotretinoin. CONCLUSIONS Our study confirmed an association between memory disorders and some drugs, such as benzodiazepines and anticonvulsants. However, other drugs, such as benzodiazepine-like hypnotics, newer anticonvulsants, serotonin reuptake inhibitor antidepressants, isotretinoin and ciclosporin were significantly associated with memory disorders, although this was not described or poorly described in the literature. Taking account of the limits of this study in the FPVD (under-reporting, notoriety bias etc.), the case/noncase method allows assessment and detection of associations between exposure to drugs and a specific adverse drug reaction, such as memory disorders, and could thus generate signals and orientate us to further prospective studies to confirm such associations. PMID:21557759

  2. Memory disorders associated with consumption of drugs: updating through a case/noncase study in the French PharmacoVigilance Database.

    Science.gov (United States)

    Chavant, Francois; Favrelière, Sylvie; Lafay-Chebassier, Claire; Plazanet, Caroline; Pérault-Pochat, Marie-Christine

    2011-12-01

    To investigate putative associations of reports of memory disorders and suspected drugs. We used the case/noncase method in the French PharmacoVigilance Database (FPVD). Cases were reports of memory loss in the FPVD between January 2000 and December 2009. Noncases were all other reports during the same period. To assess the association between memory impairment and drug intake, we calculated an odds ratio with its 95% confidence interval. Among the 188,284 adverse drug reactions recorded, we identified 519 cases of memory loss. The sex ratio was 0.6 and the median age was 54 years (range 4-93). The maximal number of cases occurred between 40-49 and 50-59 years. Evolution was favourable in 63% of the cases. We found significant odds ratios for benzodiazepines (alprazolam, bromazepam, prazepam, clonazepam etc.), benzodiazepine-like hypnotics (zolpidem and zopiclone), antidepressants (fluoxetine, paroxetine and venlafaxine), analgesics (morphine, nefopam and tramadol), anticonvulsants (topiramate, pregabalin, levetiracetam etc.), antipsychotics (aripiprazole and lithium) and other drugs, such as trihexyphenidyl, ciclosporin and isotretinoin. Our study confirmed an association between memory disorders and some drugs, such as benzodiazepines and anticonvulsants. However, other drugs, such as benzodiazepine-like hypnotics, newer anticonvulsants, serotonin reuptake inhibitor antidepressants, isotretinoin and ciclosporin were significantly associated with memory disorders, although this was not described or poorly described in the literature. Taking account of the limits of this study in the FPVD (under-reporting, notoriety bias etc.), the case/noncase method allows assessment and detection of associations between exposure to drugs and a specific adverse drug reaction, such as memory disorders, and could thus generate signals and orientate us to further prospective studies to confirm such associations. © 2011 The Authors. British Journal of Clinical Pharmacology © 2011

  3. RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database

    Directory of Open Access Journals (Sweden)

    Pestaña Ángel

    2005-11-01

    Full Text Available Abstract Background Retinoblastoma, a prototype of hereditary cancer, is the most common intraocular tumour in children and potential cause of blindness from therapeutic eye ablation, second tumours in germ line carrier's survivors, and even death when left untreated. The molecular scanning of RB1 in search of germ line mutations lead to the publication of more than 900 mutations whose knowledge is important for genetic counselling and the characterization of phenotypic-genotypic relationships. Results A searchable database (RBGMdb has been constructed with 932 published RB1 mutations. The spectrum of these mutations has been analyzed with the following results: 1 the retinoblastoma protein is frequently inactivated by deletions and nonsense mutations while missense mutations are the main inactivating event in most genetic diseases. 2 Near 40% of RB1 gene mutations are recurrent and gather in sixteen hot points, including twelve nonsense, two missense and three splicing mutations. The remainder mutations are scattered along RB1, being most frequent in exons 9, 10, 14, 17, 18, 20, and 23. 3 The analysis of RB1 mutations by country of origin of the patients identifies two groups in which the incidence of nonsense and splicing mutations show differences extremely significant, and suggest the involvement of predisposing ethnic backgrounds. 4 A significant association between late age at diagnosis and splicing mutations in bilateral retinoblastoma patients suggests the occurrence of a delayed-onset genotype. 5 Most of the reported mutations in low-penetrance families fall in three groups: a Mutations in regulatory sequences at the promoter resulting in low expression of a normal Rb; b Missense and in-frame deletions affecting non-essential sequence motifs which result in a partial inactivation of Rb functions; c Splicing mutations leading to the reduction of normal mRNA splicing or to alternative splicing involving either true oncogenic or defective

  4. An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases

    Directory of Open Access Journals (Sweden)

    Oh Jeongsu

    2008-12-01

    Full Text Available Abstract Background Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. Results To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. Conclusion Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for

  5. License - RGP physicalmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available nse Update History of This Database Site Policy | Contact Us License - RGP physicalmap | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us RGP physi...calmap License License to Use This Database Last updated : 2015/07/07 You may use t

  6. A user-centred evaluation framework for the Sealife semantic web browsers.

    Science.gov (United States)

    Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

    2009-10-01

    Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

  7. Navigating protected genomics data with UCSC Genome Browser in a Box.

    Science.gov (United States)

    Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

    2015-03-01

    Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

  8. Optimal database locks for efficient integrity checking

    DEFF Research Database (Denmark)

    Martinenghi, Davide

    2004-01-01

    In concurrent database systems, correctness of update transactions refers to the equivalent effects of the execution schedule and some serial schedule over the same set of transactions. Integrity constraints add further semantic requirements to the correctness of the database states reached upon...... the execution of update transactions. Several methods for efficient integrity checking and enforcing exist. We show in this paper how to apply one such method to automatically extend update transactions with locks and simplified consistency tests on the locked entities. All schedules produced in this way...... are conflict serializable and preserve consistency. For certain classes of databases we also guarantee that the amount of locked database entities is minimal....

  9. Update to the legend of the reconnaissance soil map of Espírito Santo state and the implementation of Geobases interface for data usage in GIS

    Directory of Open Access Journals (Sweden)

    Alexson de Mello Cunha

    2016-12-01

    Full Text Available The objective of this study was the upgrade of soil mapping units defined in surveys published by the Radambrasil/ IBGE in 1983 and 1987, with the main focus on the clas - ses of soils. To accomplish this, data from representative soil profiles of those surveys were used to classify them in the current Brazilian Classification System. The mapping units which do not have representative profiles were updated based solely on the direct correlation between the denomination used in the old and current classification. This work has also updated the legend of the reconnaissance soil map. The layer of information related to soil, in shape format, containing an attribute table with data regarding mapping units and the respective updated legends (taxonomy, symbols and colors is currently available and can be downloaded by the general public using the Geobases browser. A specific geographic interface for the partners of Geobases dedicated to soil studies has also been created. This interface allows the analysis, acquisition and input of new data, which contributes to the non-duplication of efforts and financial resources on activities of surveying, registering and maintenance of geospatial database related to soils in the State

  10. HITRAN2008 and Current Updates

    Science.gov (United States)

    Rothman, Laurence; Gordon, Iouli

    2010-05-01

    The current edition of the HITRAN molecular spectroscopic database1 appeared in 2008. In the intervening period to the present, there have been several important updates. The archived database, as described in the HITRAN paper, is available at a public ftp site, while critical updates are posted in the HITRAN website (www.cfa.harvard.edu/hitran/updates.html). An international committee meets at least once per year and discusses the many issues involved in improving the database. These issues encompass not only acquisition of new data (both experimental and theoretical), but validation, new directions, etc. In this presentation, we review highlight some of the successes of the current edition of HITRAN. We also discuss new directions. This effort has been supported by the NASA Earth Observing System (EOS) program, under the grant NAG5-13534.

  11. Database Description - Metabolonote | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Metabol...onote Database Description General information of database Database name Metabolonote... for managing information on experimental methods (metadata) which is accompanied with the experimental data obtained from metabol...omics studies. This system aims to promote the publication and utilization of metabolo... design of the system contributes to accelarate publication of metabolomics data.

  12. ECR Browser: A Tool For Visualizing And Accessing Data From Comparisons Of Multiple Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Loots, G G; Ovcharenko, I; Stubbs, L; Nobrega, M A

    2004-01-06

    The increasing number of vertebrate genomes being sequenced in draft or finished form provide a unique opportunity to study and decode the language of DNA sequence through comparative genome alignments. However, novel tools and strategies are required to accommodate this increasing volume of genomic information and to facilitate experimental annotation of genome function. Here we present the ECR Browser, a tool that provides an easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignment of any user-submitted sequence to the genome of choice. The interconnection of the ECR browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.

  13. A framework for web browser-based medical simulation using WebGL.

    Science.gov (United States)

    Halic, Tansel; Ahn, Woojin; De, Suvranu

    2012-01-01

    This paper presents a web browser-based software framework that provides accessibility, portability, and platform independence for medical simulation. Typical medical simulation systems are restricted to the underlying platform and device, which limits widespread use. Our framework allows realistic and efficient medical simulation using only the web browser for anytime anywhere access using a variety of platforms ranging from desktop PCs to tablets. The framework consists of visualization, simulation, and hardware integration modules that are fundamental components for multimodal interactive simulation. Benchmark tests are performed to validate the rendering and computing performance of our framework with latest web browsers including Chrome and Firefox. The results are quite promising opening up the possibility of developing web-based medical simulation technology.

  14. DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

    Directory of Open Access Journals (Sweden)

    Liu Guozhen

    2008-10-01

    Full Text Available Abstract Background Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. Description DroID, the Drosophila Interactions Database, is a comprehensive interactions database designed specifically for Drosophila. DroID houses published physical protein interactions, genetic interactions, and computationally predicted interactions, including interologs based on data for other model organisms and humans. All interactions are annotated with original experimental data and source information. DroID can be searched and filtered based on interaction information or a comprehensive set of gene attributes from Flybase. DroID also contains gene expression and expression correlation data that can be searched and used to filter datasets, for example, to focus a study on sub-networks of co-expressed genes. To address the inherent noise in interaction data, DroID employs an updatable confidence scoring system that assigns a score to each physical interaction based on the likelihood that it represents a biologically significant link. Conclusion DroID is the most comprehensive interactions database available for Drosophila. To facilitate downstream analyses, interactions are annotated with original experimental information, gene expression data, and confidence scores. All data in

  15. Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

    Science.gov (United States)

    Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

    2006-01-01

    The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

  16. Rfam: updates to the RNA families database

    DEFF Research Database (Denmark)

    Gardner, Paul P; Daub, Jennifer; Tate, John G

    2008-01-01

    Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination wit...

  17. Database for Hydraulically Conductive Fractures. Update 2010

    Energy Technology Data Exchange (ETDEWEB)

    Tammisto, E.; Palmen, J. (Poeyry Finland Oy, Espoo (Finland))

    2011-02-15

    Posiva flow logging (PFL) with 0.5 m test interval and made in 10 cm steps can be used for exact depth determination of hydraulically conductive fractures. Together with drillhole wall images and fracture data from core logging PFL provides possibilities to detect single conductive fractures. In this report, the results of PFL are combined to the fracture data in drillholes OL-KR49 .. OL-KR53, OL-KR50B, OL-KR52B and OLKR53B and pilot holes ONK-PH11 - ONK-PH13. The results are used mainly in development of hydroDFN- models. The conductive fractures were first recognised from the PFL data and digital drillhole images and then the fractures from the core logging corresponding to the ones picked from the digital drillhole images were identified. The conductive fractures were recognised from the images primarily based on openness of fractures or a visible flow in the image. In most of the cases of measured flow, no tails of flow were seen in the image. In these cases, the conductive fractures were recognised from the image based on openness of fractures and a matching depth. According to the results the hydraulically conductive fractures/zones can be distinguished from the drillhole wall images in most cases. An important phase in the work is to calibrate the depth of the image and the flow logging with the sample length. The hydraulic conductivity is clearly higher in the upper part of the bedrock in the depth range 0-150 m below sea level than deeper in the bedrock. The frequency of hydraulically conductive fractures detected in flow logging (T > 10 -10-10-9 m2/s) in depth range 0-150 m varies from 0.07 to 0.84 fractures/meter of sample length. Deeper in the rock the conductive fractures are less frequent, but occur often in groups of few fractures. In drillholes OL-KR49 .. OL-KR53, OL-KR50B, OL-KR52B and OL-KR53B about 8.5 % of all fractures and 4.4 % of the conductive fractures are within HZ-structures. (orig.)

  18. Database for hydraulically conductive fractures. Update 2009

    Energy Technology Data Exchange (ETDEWEB)

    Palmen, J.; Tammisto, E.; Ahokas, H. (Poeyry Finland Oy, Espoo (Finland))

    2010-03-15

    Posiva flow logging (PFL) with a 0.5 m test interval and made in 10 cm steps can be used for the determination of the depth of hydraulically conductive fractures. Together with drillhole wall images and fracture data from core logging, PFL provides possibilities to detect individual conductive fractures. In this report, the results of PFL are combined with fracture data on drillholes OL-KR41 - OL-KR48, OL-KR41B - OLKR45B and pilot holes ONK-PH8 - ONK-PH10. In addition, HTU-data measured by 2 m section length and 2 m steps in holes OL-KR39 and OL-KR40 at depths 300-700 m were analyzed and combined with fracture data in a similar way. The conductive fractures were first recognised from PFL data and digital drillhole images and then the fractures from the core logging that correspond to the ones picked from the digital drillhole images were identified. The conductive fractures were primarily recognised in the images based on the openness of fractures or a visible flow in the image. In most of the cases, no tails of flow were seen in the image. In these cases the conductive fractures were recognised in the image based on the openness of fractures and a matching depth. On the basis of the results hydraulically conductive fractures/zones could in most cases be distinguished in the drillhole wall images. An important phase in the work is the calibration of the depth of the image, flow logging and the HTU logging with the sample length. In addition to results of PFL-correlation, Hydraulic Testing Unit (HTU) data measured by 2 m section length and 2 m steps was studied at selected depths for holes OL-KR39, OL-KR40, OL-KR42 and OL-KR45. Due to low HTU section depth accuracy the conducting fractures were successfully correlated with Fracture Data Base (FDB) fractures only in drillholes OL-KR39 and OL-KR40. HTU-data depth matching in these two drillholes was performed using geophysical Single Point Resistance (SPR) data both from geophysical and PFL measurements as a depth reference. (orig.)

  19. Modeling the HTML DOM and Browser API in Static Analysis of JavaScript Web Applications

    DEFF Research Database (Denmark)

    Jensen, Simon Holm; Madsen, Magnus; Møller, Anders

    2011-01-01

    such technologies to the domain of JavaScript web applications is challenging. In this paper, we discuss the challenges, which include the dynamic aspects of JavaScript and the complex interactions between JavaScript, HTML, and the browser. From this, we present the first static analysis that is capable...... of reasoning about the flow of control and data in modern JavaScript applications that interact with the HTML DOM and browser API. One application of such a static analysis is to detect type-related and dataflow-related programming errors. We report on experiments with a range of modern web applications...

  20. An open source browser-based software tool for graph drawing and visualisation

    OpenAIRE

    Vogt, Veit-Dieter

    2014-01-01

    In this research work we searched for open source libraries which supports graph drawing and visualisation and can run in a browser. Subsequent these libraries were evaluated to find out which one is the best for this task. The result was the d3.js is that library which has the greatest functionality, flexibility and customisability. Afterwards we developed an open source software tool where d3.js was included and which was written in JavaScript so that it can run browser-based. En este tr...

  1. Black-Box Security Testing of Browser-Based Security Protocols

    OpenAIRE

    Sudhodanan, Avinash

    2017-01-01

    Millions of computer users worldwide use the Internet every day for consuming web-based services (e.g., for purchasing products from online stores, for storing sensitive files in cloud-based file storage web sites, etc.). Browser-based security protocols (i.e. security protocols that run over the Hypertext Transfer Protocol and are executable by commercial web-browsers) are used to ensure the security of these services. Multiple parties are often involved in these protocols. For instance, a b...

  2. License - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database License License to Use This Database Last updated : 2017/02/27 You may use this database...cense specifies the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative ...Commons Attribution-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database...ative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you ar

  3. Download - eSOL | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Database Description Download License Update History of This Database Site Policy | Contact Us Download - eSOL | LSDB Archive ...

  4. Database of Literature on Guided Imagery and Music and Related Topics

    DEFF Research Database (Denmark)

    Bonde, Lars Ole

    2015-01-01

    A March 2015 update of the largest international database on literature on Guided Imagery and Music and related topics.......A March 2015 update of the largest international database on literature on Guided Imagery and Music and related topics....

  5. Download - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ion Download License Update History of This Database Site Policy | Contact Us Download - SSBD | LSDB Archive ...

  6. Download - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Download License Update History of This Database Site Policy | Contact Us Download - RPSD | LSDB Archive ...

  7. Download - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...base Description Download License Update History of This Database Site Policy | Contact Us Download - DGBY | LSDB Archive ...

  8. License - DMPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ownload License Update History of This Database Site Policy | Contact Us License - DMPD | LSDB Archive ...

  9. Download - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - Plabrain DB | LSDB Archive ...

  10. Locus - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...URL: ftp://ftp.biosciencedbc.jp/archive/astra/LATEST/astra_locus.zip File size: 887 KB Simple search URL htt...icing type (ex. cassette) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Locus - ASTRA | LSDB Archive ...

  11. Alignment - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e URL: ftp://ftp.biosciencedbc.jp/archive/sahg/LATEST/sahg_alignment.zip File size: 12.0 MB Simple search UR...s Database Database Description Download License Update History of This Database Site Policy | Contact Us Alignment - SAHG | LSDB Archive ...

  12. Exon - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ontents Exons in variants Data file File name: astra_exon.zip File URL: ftp://ftp.biosciencedbc.jp/archive/a... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Exon - ASTRA | LSDB Archive ...

  13. Reference - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ailable. Data file File name: place_reference.zip File URL: ftp://ftp.biosciencedbc.jp/archive/place/LATEST/...ber About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Reference - PLACE | LSDB Archive ...

  14. Flat Files - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... Data file File name: jsnp_flat_files File URL: ftp://ftp.biosciencedbc.jp/archiv...his Database Database Description Download License Update History of This Database Site Policy | Contact Us Flat Files - JSNP | LSDB Archive ...

  15. Download - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data .... If it is, access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - RPD | LSDB Archive ...

  16. Spot table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...d_spot.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_spot.zip F... cDNA. (multiple entries) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Spot table - RPD | LSDB Archive ...

  17. Main data - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ftp://ftp.biosciencedbc.jp/archive/rmg/LATEST/rmg_main.zip File size: 1 KB Simple search URL http://togodb.b... This Database Database Description Download License Update History of This Database Site Policy | Contact Us Main data - RMG | LSDB Archive ...

  18. Download - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data .... If it is, access [here]. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - JSNP | LSDB Archive ...

  19. Complex Modeling - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available lex Modeling Data detail Data name Complex Modeling DOI 10.18908/lsdba.nbdc01193-00.... About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Complex Modeling - SAHG | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us SAHG Comp

  20. Enhancers - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...d - Data analysis method CAGE Number of data entries 9 files - About This Database Database Description Download License Update Histo...ry of This Database Site Policy | Contact Us Enhancers - FANTOM5 | LSDB Archive ...

  1. ORF information - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_orf_infomation.zip File size: 526 KB Simple s...ut This Database Database Description Download License Update History of This Database Site Policy | Contact Us ORF information - KOME | LSDB Archive ...

  2. Toppar: An interactive browser for viewing association study results.

    Science.gov (United States)

    Juliusdottir, Thorhildur; Banasik, Karina; Robertson, Neil R; Mott, Richard; McCarthy, Mark I

    2018-01-08

    Data integration and visualization help geneticists make sense of large amounts of data. To help facilitate interpretation of genetic association data we developed Toppar, a customizable visualization tool that stores results from association studies and enables browsing over multiple results, by combining features from existing tools and linking to appropriate external databases. Detailed information on Toppar's features and functionality are on our website http://mccarthy.well.ox.ac.uk/toppar/docs along with instructions on how to download, install and run Toppar. Our online version of Toppar is accessible from the website and can be test-driven using Firefox, Safari or Chrome on sub-sets of publicly available genome-wide association study (GWAS) anthropometric waist and body mass index (BMI) data (Locke, et al., 2015; Shungin, et al., 2015) from the Genetic Investigation of ANthropometric Traits (GIANT) consortium. totajuliusd@gmail.com.

  3. Website updates

    Data.gov (United States)

    National Aeronautics and Space Administration — Updates to Website: (Please add new items at the top of this description with the date of the website change) May 9, 2012: Uploaded experimental data in matlab...

  4. Circular Updates

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Circular Updates are periodic sequentially numbered instructions to debriefing staff and observers informing them of changes or additions to scientific and specimen...

  5. Cybersecurity Update

    CERN Document Server

    Heagerty, Denise

    2008-01-01

    An update on recent security issues and vulnerabilities affecting Windows, Linux and Mac platforms. This talk is based on contributions and input from a range of colleagues both within and outside CERN. It covers clients, servers and control systems.

  6. Important update of CERN Mail Services

    CERN Multimedia

    IT Department

    2009-01-01

    The CERN Mail Services are evolving. In the course of June and July 2009, all CERN mailboxes will be updated with a new infrastructure for hosting mailboxes, running Exchange 2007. This update is taking place in order to provide the capacity upgrade for the constantly growing volume of CERN mailboxes. It is also the opportunity to provide a number of improvements to CERN mailboxes: new and improved Outlook Web Access (the web interface used to access your mailbox from a web browser, also known as "webmail"), new features in the Out-of-Office auto-reply assistant, easier spam management... The update will preserve the mailbox configuration and no specific action is required by users. During the next weeks, each mailbox will be individually notified of the upcoming update the day before it takes place. We invite all users to carefully read this notification as it will contain the latest information for this update. The mailbox will be unavailable for a short time during the ni...

  7. Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

    Science.gov (United States)

    Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio

    2015-03-01

    In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.

  8. Enhancing Independent Internet Access for Individuals with Mental Retardation through Use of a Specialized Web Browser: A Pilot Study.

    Science.gov (United States)

    Davies, Daniel K.; Stock, Steven E.; Wehmeyer, Michael L.

    2001-01-01

    In this study, a prototype web browser, called Web Trek, that utilizes multimedia to provide access for individuals with cognitive disabilities was developed and pilot-tested with 12 adults with mental retardation. The Web Trek browser provided greater independence in accessing the Internet compared to Internet Explorer. (Contains references.)…

  9. Hawaii bibliographic database

    Science.gov (United States)

    Wright, Thomas L.; Takahashi, Taeko Jane

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and s or (if no ) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  10. Hawaii bibliographic database

    Science.gov (United States)

    Wright, T.L.; Takahashi, T.J.

    1998-01-01

    The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

  11. Nuclear Science References Database

    Energy Technology Data Exchange (ETDEWEB)

    Pritychenko, B., E-mail: pritychenko@bnl.gov [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Běták, E. [Institute of Physics, Slovak Academy of Sciences, 84511 Bratislava (Slovakia); Singh, B. [Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada L8S 4M1 (Canada); Totans, J. [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

    2014-06-15

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energy Agency (http://www-nds.iaea.org/nsr)

  12. New Perspectives on Popular Culture, Science and Technology: Web Browsers and the New Illiteracy

    Science.gov (United States)

    Charters, Elizabeth

    2004-01-01

    Analysts predict that the knowledge economy of the near future will require people to be both computer literate and print literate. However, some of the reading and thinking habits of current college students suggest that electronic media such as web browsers may be limiting the new generation's ability to absorb and process what they read. Their…

  13. Temporal Manipulation and Sharing of Presentation State in Browser-Embedded Multimedia Documents

    NARCIS (Netherlands)

    D.C.A. Bulterman (Dick); A.J. Jansen (Jack); P.S. Cesar Garcia (Pablo Santiago)

    2008-01-01

    htmlabstractThis paper describes an approach to defining, manipulating and sharing state variables between a web browser and a multimedia presentation engine in functionally compound XML-based documents. This framework, which we call smilState: the SMIL XML State Architecture, is a fully

  14. Piracy Versus Privacy: An Analysis of Values Encoded in the PirateBrowser

    NARCIS (Netherlands)

    Bodó, B.

    2015-01-01

    The Piratebrowser is a web browser which utilizes the Privacy Enhancing Technology Tor to circumvent nationally implemented internet filters blocking the access to the Pirate Bay. The article analyzes the possible consequences of a mass influx of copyright pirates into the privacy domain. It

  15. A Freely-Available Authoring System for Browser-Based CALL with Speech Recognition

    Science.gov (United States)

    O'Brien, Myles

    2017-01-01

    A system for authoring browser-based CALL material incorporating Google speech recognition has been developed and made freely available for download. The system provides a teacher with a simple way to set up CALL material, including an optional image, sound or video, which will elicit spoken (and/or typed) answers from the user and check them…

  16. A browser-based event display for the CMS experiment at the LHC

    Science.gov (United States)

    Hategan, M.; McCauley, T.; Nguyen, P.

    2012-12-01

    The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d. The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.

  17. MediaMill: Fast and effective video search using the ForkBrowser

    NARCIS (Netherlands)

    de Rooij, O.; Snoek, C.G.M.; Worring, M.

    2008-01-01

    In this technical demonstration we showcase the MediaMill ForkBrowser for video retrieval. It embeds multiple query methods into a single browsing environment. We show that users can switch query methods on demand without the need to adapt to a different interface. This allows for fast and effective

  18. Web Browser History Detection as a Real-World Privacy Threat

    CERN Document Server

    Janc, A

    2010-01-01

    Web browser history detection using CSS $visited$ styles has long been dismissed as an issue of marginal impact. However, due to recent changes in Web usage patterns, coupled with browser performance improvements, the long-standing issue has now become a significant threat to the privacy of Internet users. In this paper we analyze the impact of CSS-based history detection and demonstrate the feasibility of conducting practical attacks with minimal resources. We analyze Web browser behavior and detectability of content loaded via standard protocols and with various HTTP response codes. We develop an algorithm for efficient examination of large link sets and evaluate its performance in modern browsers. Compared to existing methods our approach is up to 6 times faster, and is able to detect up to 30,000 visited links per second. We present a novel Web application capable of effectively detecting clients’ browsing histories and discuss real-world results obtained from 271,576 Internet users. Our results indicat...

  19. A browser-based event display for the CMS experiment at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Hategan, M. [Chicago U.; McCauley, T. [Fermilab; Nguyen, P. [Fermilab

    2012-01-01

    The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d. The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.

  20. C# Database Basics

    CERN Document Server

    Schmalz, Michael

    2012-01-01

    Working with data and databases in C# certainly can be daunting if you're coming from VB6, VBA, or Access. With this hands-on guide, you'll shorten the learning curve considerably as you master accessing, adding, updating, and deleting data with C#-basic skills you need if you intend to program with this language. No previous knowledge of C# is necessary. By following the examples in this book, you'll learn how to tackle several database tasks in C#, such as working with SQL Server, building data entry forms, and using data in a web service. The book's code samples will help you get started

  1. Real Time Baseball Database

    Science.gov (United States)

    Fukue, Yasuhiro

    The author describes the system outline, features and operations of "Nikkan Sports Realtime Basaball Database" which was developed and operated by Nikkan Sports Shimbun, K. K. The system enables to input numerical data of professional baseball games as they proceed simultaneously, and execute data updating at realtime, just-in-time. Other than serving as supporting tool for prepareing newspapers it is also available for broadcasting media, general users through NTT dial Q2 and others.

  2. SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

    Science.gov (United States)

    Bakhtiari, M

    2012-06-01

    Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

  3. Database Description - ChIP-Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us ChIP-Atlas Database Description General information of database Database name ChIP-Atlas Alt...ucleotide Sequence Databases - Transcriptional regulator sites and transcription ...axonomy ID: 6239 Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database description ChIP-Atlas i...ble URL of Web services - Need for user registration Not available About This Database Database Description ...Download License Update History of This Database Site Policy | Contact Us Database Description - ChIP-Atlas | LSDB Archive ...

  4. Database Description - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name AcEST Alternative n...hi, Tokyo-to 192-0397 Tel: +81-42-677-1111(ext.3654) E-mail: Database classificat...eneris Taxonomy ID: 13818 Database description This is a database of EST sequences of Adiantum capillus-vene...(3): 223-227. External Links: Original website information Database maintenance site Plant Environmental Res...base Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - AcEST | LSDB Archive ...

  5. The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

    Science.gov (United States)

    Galperin, Michael Y; Fernández-Suárez, Xosé M

    2012-01-01

    The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

  6. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

    Science.gov (United States)

    Mei, Shenglin; Qin, Qian; Wu, Qiu; Sun, Hanfei; Zheng, Rongbin; Zang, Chongzhi; Zhu, Muyuan; Wu, Jiaxin; Shi, Xiaohui; Taing, Len; Liu, Tao; Brown, Myles; Meyer, Clifford A; Liu, X Shirley

    2017-01-04

    Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Browser App Approach: Can It Be an Answer to the Challenges in Cross-Platform App Development?

    Directory of Open Access Journals (Sweden)

    Minh Q. Huynh

    2017-02-01

    Full Text Available Aim/Purpose: As smartphones proliferate, many different platforms begin to emerge. The challenge to developers as well as IS educators and students is how to learn the skills to design and develop apps to run on cross-platforms. Background: For developers, the purpose of this paper is to describe an alternative to the complex native app development. For IS educators and students, the paper provides a feasible way to learn and develop fully functional mobile apps without technical burdens. Methodology: The methods used in the development of browser-based apps is prototyping. Our proposed approach is browser-based, supports cross-platforms, uses open-source standards, and takes advantage of “write-once-and-run-anywhere” (WORA concept. Contribution: The paper illustrates the application of the browser-based approach to create a series of browser apps without high learning curve. Findings: The results show the potentials for using browser app approach to teach as well as to create new apps. Recommendations for Practitioners\t: Our proposed browser app development approach and example would be useful to mobile app developers/IS educators and non-technical students because the source code as well as documentations in this project are available for downloading. Future Research: For further work, we discuss the use of hybrid development framework to enhance browser apps.

  8. Status Update

    Science.gov (United States)

    Hernandez, Arelis

    2010-01-01

    This article offers some updates on the share of the higher education institutions in the billion-worth stimulus package and how institutions were assisted through this funding. Since the $787 billion stimulus package, formally known as the American Reinvestment and Recovery Act (ARRA), was signed into law in 2009, an estimated $50 billion to $75…

  9. The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species.

    Science.gov (United States)

    Dang, Ha X; Pryor, Barry; Peever, Tobin; Lawrence, Christopher B

    2015-03-25

    Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The

  10. Advantages to Geoscience and Disaster Response from QuakeSim Implementation of Interferometric Radar Maps in a GIS Database System

    Science.gov (United States)

    Parker, Jay; Donnellan, Andrea; Glasscoe, Margaret; Fox, Geoffrey; Wang, Jun; Pierce, Marlon; Ma, Yu

    2015-08-01

    High-resolution maps of earth surface deformation are available in public archives for scientific interpretation, but are primarily available as bulky downloads on the internet. The NASA uninhabited aerial vehicle synthetic aperture radar (UAVSAR) archive of airborne radar interferograms delivers very high resolution images (approximately seven meter pixels) making remote handling of the files that much more pressing. Data exploration requiring data selection and exploratory analysis has been tedious. QuakeSim has implemented an archive of UAVSAR data in a web service and browser system based on GeoServer (http://geoserver.org). This supports a variety of services that supply consistent maps, raster image data and geographic information systems (GIS) objects including standard earthquake faults. Browsing the database is supported by initially displaying GIS-referenced thumbnail images of the radar displacement maps. Access is also provided to image metadata and links for full file downloads. One of the most widely used features is the QuakeSim line-of-sight profile tool, which calculates the radar-observed displacement (from an unwrapped interferogram product) along a line specified through a web browser. Displacement values along a profile are updated to a plot on the screen as the user interactively redefines the endpoints of the line and the sampling density. The profile and also a plot of the ground height are available as CSV (text) files for further examination, without any need to download the full radar file. Additional tools allow the user to select a polygon overlapping the radar displacement image, specify a downsampling rate and extract a modest sized grid of observations for display or for inversion, for example, the QuakeSim simplex inversion tool which estimates a consistent fault geometry and slip model.

  11. Database Description - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 4751 Database description MicrobeDB.jp is an integrated database of several micr...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Mi...crobeDB.jp Database Description General information of database Database name MicrobeDB.jp...hiba Creator Affiliation: National Institute for Basic Biology Journal Search: Creator Name: Nozomi...me: Hiroyo Nishide Creator Affiliation: National Institute for Basic Biology Contact address 1111 Yata, Mish

  12. On Simplification of Database Integrity Constraints

    DEFF Research Database (Denmark)

    Christiansen, Henning; Martinenghi, Davide

    2006-01-01

    Without proper simplification techniques, database integrity checking can be prohibitively time consuming. Several methods have been developed for producing simplified incremental checks for each update but none until now of sufficient quality and generality for providing a true practical impact,...

  13. Database Dump - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us fRNAdb Database Dump Data detail Data name Database Dump DOI 10.18908/lsdba.nbdc00452-002 De... data (tab separeted text) Data file File name: Database_Dump File URL: ftp://ftp....biosciencedbc.jp/archive/frnadb/LATEST/Database_Dump File size: 673 MB Simple search URL - Data acquisition...s. Data analysis method - Number of data entries 4 files - About This Database Database Description Download... License Update History of This Database Site Policy | Contact Us Database Dump - fRNAdb | LSDB Archive ...

  14. Self-study program on HTML browser--application to Clinical Nursing General Remarks Course.

    Science.gov (United States)

    Ochiai, N; Sota, Y; Ezumi, H

    1997-01-01

    We created a self-study program using HTML browser on the Clinical Nursing General Remarks Course, Eighty-three students each selected a published book on a personal history (written personal reflections from individuals who had undergone medical treatment and hospitalization), read it and submitted reports of their impressions of the histories. Their reports were arranged from a nursing perspective and entered on the home page of our college using HTML browser. We intended that the students would become more interested in reading of the personal histories, and that they would acquire new self-study skills and increase their interest in Internet through use of our program. In addition, we hoped that this program would encourage positive communication and mutual sharing of information. The students were able to easily refer to a personal history according to their interest from a nursing perspective. Therefore this program realized the mutual learning among students and other users.

  15. The Open Anatomy Browser: A Collaborative Web-Based Viewer for Interoperable Anatomy Atlases.

    Science.gov (United States)

    Halle, Michael; Demeusy, Valentin; Kikinis, Ron

    2017-01-01

    The Open Anatomy Browser (OABrowser) is an open source, web-based, zero-installation anatomy atlas viewer based on current web browser technologies and evolving anatomy atlas interoperability standards. OABrowser displays three-dimensional anatomical models, image cross-sections of labeled structures and source radiological imaging, and a text-based hierarchy of structures. The viewer includes novel collaborative tools: users can save bookmarks of atlas views for later access and exchange those bookmarks with other users, and dynamic shared views allow groups of users can participate in a collaborative interactive atlas viewing session. We have published several anatomy atlases (an MRI-derived brain atlas and atlases of other parts of the anatomy) to demonstrate OABrowser's functionality. The atlas source data, processing tools, and the source for OABrowser are freely available through GitHub and are distributed under a liberal open source license.

  16. jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

    Science.gov (United States)

    de Leeuw, Joshua R

    2015-03-01

    Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

  17. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  18. ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

    Science.gov (United States)

    Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

    2012-01-01

    Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

  19. Formats and Network Protocols for Browser Access to 2D Raster Data

    Science.gov (United States)

    Plesea, L.

    2015-12-01

    Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

  20. ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

    Directory of Open Access Journals (Sweden)

    Jonas S Almeida

    2012-01-01

    Full Text Available Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results : Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH′s popular ImageJ application. Conclusions : The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without

  1. CPTAC 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 via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

  2. The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

    Directory of Open Access Journals (Sweden)

    Norman E Davey

    2014-12-01

    Full Text Available Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

  3. License - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Plabrain... Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Plabrain...of this database (http://dbarchive.lifesciencedb.jp/english/en/plabrain-db/desc.html) in the article or pape...se Description Download License Update History of This Database Site Policy | Contact Us License - Plabrain DB | LSDB Archive ...

  4. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease.

    Science.gov (United States)

    Eppig, Janan T; Blake, Judith A; Bult, Carol J; Kadin, James A; Richardson, Joel E

    2015-01-01

    The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse-human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human-Mouse: Disease Connection, allows users to explore gene-phenotype-disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

    Directory of Open Access Journals (Sweden)

    Michael Bensch

    2007-01-01

    Full Text Available We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links. Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications.

  6. Nessi: an EEG-controlled web browser for severely paralyzed patients.

    Science.gov (United States)

    Bensch, Michael; Karim, Ahmed A; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

    2007-01-01

    We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications.

  7. A Lifelog Browser for Visualization and Search of Mobile Everyday-Life

    Directory of Open Access Journals (Sweden)

    Keum-Sung Hwang

    2014-01-01

    Full Text Available Mobile devices can now handle a great deal of information thanks to the convergence of diverse functionalities. Mobile environments have already shown great potential in terms of providing customized service to users because they can record meaningful and private information continually for long periods of time. The research for understanding, searching and summarizing the everyday-life of human has received increasing attention in recent years due to the digital convergence. In this paper, we propose a mobile life browser, which visualizes and searches human's mobile life based on the contents and context of lifelog data. The mobile life browser is for searching the personal information effectively collected on his/her mobile device and for supporting the concept-based searching method by using concept networks and Bayesian networks. In the experiments, we collected the real mobile log data from three users for a month and visualized the mobile lives of the users with the mobile life browser developed. Some tests on searching tasks confirmed that the result using the proposed concept-based searching method is promising.

  8. EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Jia Peng

    2011-10-01

    Full Text Available Abstract Background Escherichia coli has been extensively studied as a prokaryotic model organism whose whole genome was determined in 1997. However, it is difficult to identify all the gene products involved in diverse functions by using whole genome sequencesalone. The high-resolution transcriptome mapping using tiling arrays has proved effective to improve the annotation of transcript units and discover new transcripts of ncRNAs. While abundant tiling array data have been generated, the lack of appropriate visualization tools to accommodate and integrate multiple sources of data has emerged. Findings EcoBrowser is a web-based tool for visualizing genome annotations and transcriptome data of E. coli. Important tiling array data of E. coli from different experimental platforms are collected and processed for query. An AJAX based genome browser is embedded for visualization. Thus, genome annotations can be compared with transcript profiling and genome occupancy profiling from independent experiments, which will be helpful in discovering new transcripts including novel mRNAs and ncRNAs, generating a detailed description of the transcription unit architecture, further providing clues for investigation of prokaryotic transcriptional regulation that has proved to be far more complex than previously thought. Conclusions With the help of EcoBrowser, users can get a systemic view both from the vertical and parallel sides, as well as inspirations for the design of new experiments which will expand our understanding of the regulation mechanism.

  9. Winning by a neck: tall giraffes avoid competing with shorter browsers.

    Science.gov (United States)

    Cameron, Elissa Z; du Toit, Johan T

    2007-01-01

    With their vertically elongated body form, giraffes generally feed above the level of other browsers within the savanna browsing guild, despite having access to foliage at lower levels. They ingest more leaf mass per bite when foraging high in the tree, perhaps because smaller, more selective browsers deplete shoots at lower levels or because trees differentially allocate resources to promote shoot growth in the upper canopy. We erected exclosures around individual Acacia nigrescens trees in the greater Kruger ecosystem, South Africa. After a complete growing season, we found no differences in leaf biomass per shoot across height zones in excluded trees but significant differences in control trees. We conclude that giraffes preferentially browse at high levels in the canopy to avoid competition with smaller browsers. Our findings are analogous with those from studies of grazing guilds and demonstrate that resource partitioning can be driven by competition when smaller foragers displace larger foragers from shared resources. This provides the first experimental support for the classic evolutionary hypothesis that vertical elongation of the giraffe body is an outcome of competition within the browsing ungulate guild.

  10. plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

    Science.gov (United States)

    Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

    2014-12-01

    Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

  11. License - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available y use this database in compliance with the terms and conditions of the license described below. The license ...List Contact us SKIP Stemcell Database License License to Use This Database Last updated : 2017/03/13 You ma

  12. Specialist Bibliographic Databases

    Science.gov (United States)

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  13. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  14. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  15. KEUNTUNGAN PENGGUNAAN EXTERNAL FUNCTION PADA DATABASE POSTGRESQL

    Directory of Open Access Journals (Sweden)

    Nahrun Hartono

    2015-02-01

    Full Text Available Database id a central data for an information system, there were many database system applications that revolve both paid and free. PostgreSQL is one of the free database system and it has the powerful feature, one of the feature that make it different with others sysem is a function features, where the users can make their function by them selves by using spesific programming language, then it can be called return for executed. In this research the writer tries for conducting additional data testing by using INSERT Query and External Function Query on the terminal/command prompt and web browser. From the result of the trial, the research found that the average of time in additional data processing on the terminal/command prompt by using INSERT Query was 185.293 ms and the average of time External Function Query proccess was 129.52 ms, while the average of time in additional data processing on web browser by using INSERT Query was 168.363 ms and External Function Query was 145.64 ms. There was a difference both of the query, but the important thing and should be noted that external function is a command was defined by stand alone by the user, this matter lets the user to determine a specify command that they need.

  16. WGE: a CRISPR database for genome engineering.

    Science.gov (United States)

    Hodgkins, Alex; Farne, Anna; Perera, Sajith; Grego, Tiago; Parry-Smith, David J; Skarnes, William C; Iyer, Vivek

    2015-09-15

    The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. The WGE database is freely available at www.sanger.ac.uk/htgt/wge : vvi@sanger.ac.uk or skarnes@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  17. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  18. Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

  19. Database resources of the National Center for Biotechnology Information

    OpenAIRE

    Wheeler, David L.; Church, Deanna M.; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Pontius, Joan U.; Schuler, Gregory D.; Schriml, Lynn M.; Tatusova, Tatiana A.; Wagner, Lukas; Rapp, Barbara A.

    2001-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Homol...

  20. License - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PLACE License License to Use This Database Last updated : 2014/07/17 You may use this database...ense terms regarding the use of this database and the requirements you must follow in using this database. The license for this datab...re Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follows: ... ...re . With regard to this database, you are licensed to: freely access part or whole of this database, and ac...quire data; freely redistribute part or whole of the data from this database; and freely create and distribute database

  1. Main - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ntents List of datasets Data file File name: kome_main.zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome...ase Database Description Download License Update History of This Database Site Policy | Contact Us Main - KOME | LSDB Archive ...

  2. PREIMS - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Targeted Proteins Research Program (TPRP). Data file File name: at_atlas_preims.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...base Database Description Download License Update History of This Database Site Policy | Contact Us PREIMS - AT Atlas | LSDB Archive ...

  3. EST data - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...st.zip File URL: ftp://ftp.biosciencedbc.jp/archive/red/LATEST/red_est.zip File size: 629 KB Simple search U...ase Database Description Download License Update History of This Database Site Policy | Contact Us EST data - RED | LSDB Archive ...

  4. Strategic Access: Government/Defense Online Databases.

    Science.gov (United States)

    Kline, Eileen

    1987-01-01

    This overview of the available government and defense online databases divides them into the categories of research and development and market intelligence and describes the contents of each database. A listing of the online producers and providers, starting dates of files, and update frequency is provided. (CLB)

  5. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ....18908/lsdba.nbdc01194-02-006.V002 Version V2 10.18908/lsdba.nbdc01194-02-006.V002 Update History V1 10.1890...ower taxon Next infrageneric taxon About This Database Database Description Download License Update History

  6. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ....18908/lsdba.nbdc01194-02-003.V002 Version V2 10.18908/lsdba.nbdc01194-02-003.V002 Update History V1 10.1890...ower taxon Next infrageneric taxon About This Database Database Description Download License Update History

  7. Knowledge extraction from the behaviour of players in a web browser game

    OpenAIRE

    Alves, João Miguel Pereira

    2013-01-01

    Dissertação de mestrado em Informatics Engineering The analysis of the player’s behaviour is a requirement with growing popularity in the traditional computer games segment and has been proven to aid the developers create better and more profitable games. There is now interest in trying to replicate this attainment in a less conventional genre of games known as web browser games. The main objective of this work is to analyse and create a technique for the analysis of the beh...

  8. Professional iOS database application programming

    CERN Document Server

    Alessi, Patrick

    2013-01-01

    Updated and revised coverage that includes the latest versions of iOS and Xcode Whether you're a novice or experienced developer, you will want to dive into this updated resource on database application programming for the iPhone and iPad. Packed with more than 50 percent new and revised material - including completely rebuilt code, screenshots, and full coverage of new features pertaining to database programming and enterprise integration in iOS 6 - this must-have book intends to continue the precedent set by the previous edition by helping thousands of developers master database

  9. License - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PSCDB License License to Use This Database Last updated : 2016/11/30 You may use this database...ense terms regarding the use of this database and the requirements you must follow in using this database. The license for this datab...re Alike 4.0 International . If you use data from this database, please be sure attribute this database as f... Alike 4.0 International is found here . With regard to this database, you are licensed to: freely access part or whole of this datab... of the data from this database; and freely create and distribute database and other adapted materials based

  10. License - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RPSD License License to Use This Database Last updated : 2014/11/10 You may use this database...nse terms regarding the use of this database and the requirements you must follow in using this database. The license for this databa...e Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: S...ke 2.1 Japan is found here . With regard to this database, you are licensed to: freely access part or whole of this database..., and acquire data; freely redistribute part or whole of the data from this database; and fr

  11. License - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AT Atlas License License to Use This Database Last updated : 2013/11/19 You may use this database...license terms regarding the use of this database and the requirements you must follow in using this database...Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follow...ase, you are licensed to: freely access part or whole of this database, and acquire... data; freely redistribute part or whole of the data from this database; and freely create and distribute database

  12. License - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RMG License License to Use This Database Last updated : 2013/08/07 You may use this database...se terms regarding the use of this database and the requirements you must follow in using this database. The license for this databas... Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follows: Ric...Japan is found here . With regard to this database, you are licensed to: freely access part or whole of this database..., and acquire data; freely redistribute part or whole of the data from this database; and freely create and distribute datab

  13. License - TP Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us TP Atlas License License to Use This Database Last updated : 2013/10/18 You may use this database...license terms regarding the use of this database and the requirements you must follow in using this database...Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follow...ase, you are licensed to: freely access part or whole of this database, and acquire... data; freely redistribute part or whole of the data from this database; and freely create and distribute database

  14. License - KEGG MEDICUS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us KEGG MEDICUS License License to Use This Database Last updated : 2014/04/03 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion-NonCommercial-NoDerivs 2.1 Japan. If you use data from this database, please be sure attribute this database...NoDerivs 2.1 Japan is found here . With regard to this database, you are licensed to: freely access part or whole of this database

  15. License - RGP gmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RGP gmap License License to Use This Database Last updated : 2014/10/31 You may use this database...license terms regarding the use of this database and the requirements you must follow in using this database...Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follow...ution-Share Alike 2.1 Japan is found here . With regard to this database, you are licensed to: freely access... part or whole of this database, and acquire data; freely redistribute part or whole of the data from this database

  16. License - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us KOME License License to Use This Database Last updated : 2013/07/30 You may use this database...nse terms regarding the use of this database and the requirements you must follow in using this database. The license for this databa...e Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follows: ... K...pan is found here . With regard to this database, you are licensed to: freely access part or whole of this database..., and acquire data; freely redistribute part or whole of the data from this database; and freely create and distribute databas

  17. License - Society Catalog | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Society Catalog License License to Use This Database Last updated : 2012/01/17 You may use this database...es the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attri...bution-Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as...is found here . With regard to this database, you are licensed to: freely access part or whole of this database

  18. License - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RMOS License License to Use This Database Last updated : 2015/10/27 You may use this database...nse terms regarding the use of this database and the requirements you must follow in using this database. The license for this databa...e Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: R...pan is found here . With regard to this database, you are licensed to: freely access part or whole of this database..., and acquire data; freely redistribute part or whole of the data from this database; and freely create and distribute databas

  19. License - RGP caps | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us RGP caps License License to Use This Database Last updated : 2015/05/12 You may use this database...license terms regarding the use of this database and the requirements you must follow in using this database...Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follow...ommons Attribution-Share Alike 2.1 Japan is found here . With regard to this database, you are licensed to: ...freely access part or whole of this database, and acquire data; freely redistribute part or whole of the data from this database

  20. Update of the FANTOM web resource

    DEFF Research Database (Denmark)

    Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad

    2017-01-01

    Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptio...... for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives....

  1. The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection.

    Science.gov (United States)

    Fernández-Suárez, Xosé M; Galperin, Michael Y

    2013-01-01

    The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year's highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein-protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI's dbVar and EBI's DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein-ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

  2. NPIDB: nucleic acid?protein interaction database

    OpenAIRE

    Kirsanov, Dmitry D.; Zanegina, Olga N.; Aksianov, Evgeniy A.; Spirin, Sergei A.; Karyagina, Anna S.; Alexeevski, Andrei V

    2012-01-01

    The Nucleic acid?Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA?protein and RNA?protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid?Protein Interaction DataBase is an upgrade ...

  3. Database resources of the National Center for Biotechnology Information

    OpenAIRE

    Wheeler, David L.; Chappey, Colombe; Lash, Alex E.; Leipe, Detlef D.; Madden, Thomas L.; Schuler, Gregory D.; Tatusova, Tatiana A.; Rapp, Barbara A.

    2000-01-01

    In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide...

  4. PSCID List - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pscdb/LATEST/pscdb_pscid_list.zip File size: 24.4 KB Simp...nd-binding sites About This Database Database Description Download License Update History of This Database Site Policy | Contact Us PSCID List - PSCDB | LSDB Archive ...

  5. gEVAL - a web-based browser for evaluating genome assemblies.

    Science.gov (United States)

    Chow, William; Brugger, Kim; Caccamo, Mario; Sealy, Ian; Torrance, James; Howe, Kerstin

    2016-08-15

    For most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. Although gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including from Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly. Web Browser: http://geval.sanger.ac.uk, Plugin: http://wchow.github.io/wtsi-geval-plugin kj2@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  6. LightWAVE: Waveform and Annotation Viewing and Editing in a Web Browser.

    Science.gov (United States)

    Moody, George B

    2013-09-01

    This paper describes LightWAVE, recently-developed open-source software for viewing ECGs and other physiologic waveforms and associated annotations (event markers). It supports efficient interactive creation and modification of annotations, capabilities that are essential for building new collections of physiologic signals and time series for research. LightWAVE is constructed of components that interact in simple ways, making it straightforward to enhance or replace any of them. The back end (server) is a common gateway interface (CGI) application written in C for speed and efficiency. It retrieves data from its data repository (PhysioNet's open-access PhysioBank archives by default, or any set of files or web pages structured as in PhysioBank) and delivers them in response to requests generated by the front end. The front end (client) is a web application written in JavaScript. It runs within any modern web browser and does not require installation on the user's computer, tablet, or phone. Finally, LightWAVE's scribe is a tiny CGI application written in Perl, which records the user's edits in annotation files. LightWAVE's data repository, back end, and front end can be located on the same computer or on separate computers. The data repository may be split across multiple computers. For compatibility with the standard browser security model, the front end and the scribe must be loaded from the same domain.

  7. HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.

    Science.gov (United States)

    Kim, Jong Hyun; Kim, Woo-Cheol; Waterman, Michael S; Park, Sanghyun; Li, Lei M

    2009-09-15

    Haplotype assembly is becoming a very important tool in genome sequencing of human and other organisms. Although haplotypes were previously inferred from genome assemblies, there has never been a comparative haplotype browser that depicts a global picture of whole-genome alignments among haplotypes of different organisms. We introduce a whole-genome HAPLotype brOWSER (HAPLOWSER), providing evolutionary perspectives from multiple aligned haplotypes and functional annotations. Haplowser enables the comparison of haplotypes from metagenomes, and associates conserved regions or the bases at the conserved regions with functional annotations and custom tracks. The associations are quantified for further analysis and presented as pie charts. Functional annotations and custom tracks that are projected onto haplotypes are saved as multiple files in FASTA format. Haplowser provides a user-friendly interface, and can display alignments of haplotypes with functional annotations at any resolution. Haplowser, written in Java, supports multiple platforms including Windows and Linux. Haplowser is publicly available at http://embio.yonsei.ac.kr/haplowser .

  8. NemaCount: quantification of nematode chemotaxis behavior in a browser.

    Science.gov (United States)

    O'Halloran, Damien M

    2016-06-01

    Nematodes such as Caenorhabditis elegans offer a very effective and tractable system to probe the underlying mechanisms of diverse sensory behaviors. Numerous platforms exist for quantifying nematode behavior and often require separate dependencies or software. Here I describe a novel and simple tool called NemaCount that provides a versatile solution for the quantification of nematode chemotaxis behavior. The ease of installation and user-friendly interface makes NemaCount a practical tool for measuring diverse behaviors and image features of nematodes such as C. elegans. The main advantage of NemaCount is that it operates from within a modern browser such as Google Chrome or Apple Safari. Any features that change in total number, size, shape, or angular distance between control and experimental preparations are suited to NemaCount for image analysis, while commonly used chemotaxis assays can be quantified, and statistically analyzed using a suite of functions from within NemaCount. NemaCount also offers image filtering options that allow the user to improve object detection and measurements. NemaCount was validated by examining nematode chemotaxis behavior; angular distances of locomotory tracks in C. elegans; and body lengths of Heterorhabditis bacteriophora nematodes. Apart from a modern browser, no additional software is required to operate NemaCount, making NemaCount a cheap, simple option for the analysis of nematode images and chemotaxis behavior.

  9. Networked telepresence system using web browsers and omni-directional video streams

    Science.gov (United States)

    Ishikawa, Tomoya; Yamazawa, Kazumasa; Sato, Tomokazu; Ikeda, Sei; Nakamura, Yutaka; Fujikawa, Kazutoshi; Sunahara, Hideki; Yokoya, Naokazu

    2005-03-01

    In this paper, we describe a new telepresence system which enables a user to look around a virtualized real world easily in network environments. The proposed system includes omni-directional video viewers on web browsers and allows the user to look around the omni-directional video contents on the web browsers. The omni-directional video viewer is implemented as an Active-X program so that the user can install the viewer automatically only by opening the web site which contains the omni-directional video contents. The system allows many users at different sites to look around the scene just like an interactive TV using a multi-cast protocol without increasing the network traffic. This paper describes the implemented system and the experiments using live and stored video streams. In the experiment with stored video streams, the system uses an omni-directional multi-camera system for video capturing. We can look around high resolution and high quality video contents. In the experiment with live video streams, a car-mounted omni-directional camera acquires omni-directional video streams surrounding the car, running in an outdoor environment. The acquired video streams are transferred to the remote site through the wireless and wired network using multi-cast protocol. We can see the live video contents freely in arbitrary direction. In the both experiments, we have implemented a view-dependent presentation with a head-mounted display (HMD) and a gyro sensor for realizing more rich presence.

  10. EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

    Science.gov (United States)

    Loman, Nicholas J; Pallen, Mark J

    2010-06-21

    Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

  11. JavaScript Access to DICOM Network and Objects in Web Browser.

    Science.gov (United States)

    Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

    2017-10-01

    Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

  12. EntrezAJAX: direct web browser access to the Entrez Programming Utilities

    Directory of Open Access Journals (Sweden)

    Pallen Mark J

    2010-06-01

    Full Text Available Abstract Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

  13. Database design and SQL for DB2

    CERN Document Server

    Cooper, James

    2013-01-01

    Thorough and updated coverage of database design and SQL for DB2 are the focus of this guide for the relational database-management system used on IBM i computer systems. Suitable for classroom instruction or self-study, this book explains the most widely used database language and the way that language is implemented on a variety of computer platforms. Topics covered include database concepts, SQL inquiries, web applications, and database security, and the material is reinforced by numerous illustrations, examples, and exercises.

  14. High Performance Database Management for Earth Sciences

    Science.gov (United States)

    Rishe, Naphtali; Barton, David; Urban, Frank; Chekmasov, Maxim; Martinez, Maria; Alvarez, Elms; Gutierrez, Martha; Pardo, Philippe

    1998-01-01

    The High Performance Database Research Center at Florida International University is completing the development of a highly parallel database system based on the semantic/object-oriented approach. This system provides exceptional usability and flexibility. It allows shorter application design and programming cycles and gives the user control via an intuitive information structure. It empowers the end-user to pose complex ad hoc decision support queries. Superior efficiency is provided through a high level of optimization, which is transparent to the user. Manifold reduction in storage size is allowed for many applications. This system allows for operability via internet browsers. The system will be used for the NASA Applications Center program to store remote sensing data, as well as for Earth Science applications.

  15. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  16. GRIP Database original data - GRIPDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us GRIPDB GRIP Database original data Data detail Data name GRIP Database original data DOI 10....18908/lsdba.nbdc01665-006 Description of data contents GRIP Database original data It consists of data table...s and sequences. Data file File name: gripdb_original_data.zip File URL: ftp://ftp.biosciencedbc.jp/archive/gripdb/LATEST/gripdb_orig...e Database Description Download License Update History of This Database Site Policy | Contact Us GRIP Database original data - GRIPDB | LSDB Archive ... ...inal_data.zip File size: 779 KB Simple search URL - Data

  17. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  18. TARGISOL: An ISOL-database on the web

    Science.gov (United States)

    Tengblad, O.; Turrion, M.; Fraile, L. M.

    2005-09-01

    An essential requisite for an efficient production of short-lived nuclei in an Isotope Separation On-Line (ISOL) facility is the fast release and extraction of the radioactive isotopes. In order to control the variables affecting the design and development of the target matrices and ion-sources, a database management system, called DifEfIsol, containing the relevant information of this diffusion-effusion process has been built. The Oracle database is constructed within an Open-URL framework directly reachable from any Web-browser at http://www.targisol.csic.es. The database includes the diffusion and desorption data of most elements in a range of materials. About 2400 entries are presently stored in the database. These data are used as input to a Monte Carlo simulation program that presently is being tested. This paper presents the database and the Web application as a tool for diffusion-effusion studies.

  19. Download - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... Download License Update History of This Database Site Policy | Contact Us Download - TogoTV | LSDB Archive ...

  20. License - eSOL | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...iption Download License Update History of This Database Site Policy | Contact Us License - eSOL | LSDB Archive ...

  1. Download - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...Download License Update History of This Database Site Policy | Contact Us Download - fRNAdb | LSDB Archive ...

  2. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  3. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  4. Movie collection - TogoTV | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ols. Data file File name: movie File URL: ftp://ftp.biosciencedbc.jp/archive/togotv/movie/ File size: 200 GB...ata entries 1169 entries - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Movie collection - TogoTV | LSDB Archive ...

  5. cDNA table - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ile URL: ftp://ftp.biosciencedbc.jp/archive/rpd/LATEST/rpd_cdna.zip File size: 15 KB Simple search URL http:...age About This Database Database Description Download License Update History of This Database Site Policy | Contact Us cDNA table - RPD | LSDB Archive ...

  6. Hematology - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ivo tests. Data file File name: open_tggates_hematology.zip File URL: ftp://ftp.biosciencedbc.jp/archive/ope...en About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Hematology - Open TG-GATEs | LSDB Archive ...

  7. Complex Model Structure - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available lex Model Structure Data detail Data name Complex Model Structure DOI 10.18908/lsdb...ntries - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Complex Model Structure - SAHG | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us SAHG Comp

  8. Cell sample - Open TG-GATEs | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Open...y About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Cell sample - Open TG-GATEs | LSDB Archive ...

  9. Memsat search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...rection of 5' end About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Memsat search result - KOME | LSDB Archive ...

  10. Raw Data (FASTA format) - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ... (Mar. 31, 1997) About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Raw Data (FASTA format) - PLACE | LSDB Archive ...

  11. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  12. The Innate Immune Database (IIDB

    Directory of Open Access Journals (Sweden)

    Zak Daniel

    2008-03-01

    -wide chromatin immnuopreciptation (ChIP-chip results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at http://db.systemsbiology.net/IIDB.

  13. Database Description - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available pecific and subcellular-localized proteins from rice. Reference(s) Article title: Rice proteome database: a ... Sep;59(1):179-90. External Links: Article title: Rice proteomics: a step toward functional analysis of the ...ell Proteomics. 2003 Jan;2(1):2-10. External Links: Article title: Rice Proteome Database based on two-dimen...t Genomics. 2004 Jun;271(5):566-76. Epub 2004 Apr 7. External Links: Article title: Proteome analysis of ric...485-96. Epub 2003 Nov 21. External Links: Article title: Update and challenges on

  14. License - BodyParts3D | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us BodyParts...on-Share Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follows: BodyParts... +81-3-5841-8090 E-mail : About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - BodyParts3D | LSDB Archive ...

  15. Literature searches on Ayurveda: An update.

    Science.gov (United States)

    Aggithaya, Madhur G; Narahari, Saravu R

    2015-01-01

    The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand

  16. License - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 License License to Use This Database Last updated : 2017/03/14 You may use this database...icense terms regarding the use of this database and the requirements you must follow in using this database. The license for this dat....0 International . If you use data from this database, please be sure attribute this database as follows: FA...tion 4.0 International is found here . With regard to this database, you are lice...nsed to: freely access part or whole of this database, and acquire data; freely redistribute part or whole of the data from this data

  17. License - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us TMFunction License License to Use This Database Last updated : 2017/01/23 You may use this database...e license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attributio...n-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database...ion-Share Alike 4.0 International is found here . With regard to this database, you are licensed to: freely

  18. License - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SSBD License License to Use This Database Last updated : 2016/07/25 You may use this database...nse terms regarding the use of this database and the requirements you must follow in using this database. The license for this databa...e Alike 4.0 International . If you use data from this database, please be sure attribute this database as fo...tive Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you are... licensed to: freely access part or whole of this database, and acquire data; freely redistribute part or wh

  19. License - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us GETDB License License to Use This Database Last updated : 2010/02/17 You may use this database...ense terms regarding the use of this database and the requirements you must follow in using this database. The license for this datab...re Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: ...ry of the Creative Commons Attribution-Share Alike 2.1 Japan is found here . With regard to this database..., you are licensed to: freely access part or whole of this database, and acquire dat

  20. License - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Taxonomy Icon License License to Use This Database Last updated : 2013/3/21 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Taxon...ative Commons Attribution 2.1 Japan is found here . With regard to this database,