Bluejay 1.0: Genome browsing and comparison with rich customization provision and dynamic resource linking

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Soh, Jung ^a   Gordon, Paul M K ^a   Taschuk, Morgan L ^a   Dong, Anguo ^a   Ah Seng, Andrew C ^a   Turinsky, Andrei L ^b   Sensen, Christoph W ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; COMPARATIVE GENOMICS; DYNAMIC RESOURCES; GENE EXPRESSION PROFILING; GENOMIC INFORMATION; PERSONALIZED RECOMMENDATION; SCALABLE VECTOR GRAPHICS; USER RELEVANCE FEEDBACKS;

GENE EXPRESSION; WEB SERVICES;

COMPUTER GRAPHICS;

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; FEEDBACK SYSTEM; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC REGULATION; GENOME; INFORMATION PROCESSING; MOLECULAR EVOLUTION; WEB BROWSER; ANIMAL; HUMAN; METHODOLOGY; NUCLEIC ACID DATABASE; SEQUENCE ALIGNMENT;

ANIMALS; DATABASES, NUCLEIC ACID; GENOME; HUMANS; SEQUENCE ALIGNMENT;

EID: 57049116993     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-450     Document Type: Article

References (31)

1. Soh J Gordon PM Ah-Seng AC Turinsky AL Taschuk M Borowski K Sensen CW Bluejay: A highly scalable and integrative visual environment for genome exploration Proc 2007 IEEE Congress on Services: July 2007 Salt Lake City 2007, 92-98
2. Turinsky AL Ah-Seng AC Gordon PM Stromer JN Taschuk ML Xu EW Sensen CW Bioinformatics visualization and integration with open standards: The Bluejay genomic browser Silico Biol 2005, 5(2):187-198 15972014
3. The BioMoby Consortium Interoperability with Moby 1.0 - It's better than sharing your toothbrush! Briefings in Bioinformatics 2008 18238804
4. W3C Document Object Model (DOM) http://www.w3c.org/DOM
5. Gordon PM Sensen CW Seahawk: Moving beyond HTML in Web-based bioinformatics analysis BMC Bioinformatics 2007, 8:208 17577405 17577405 1906838
6. Saeed AI Sharov V White J Li J Liang W Bhagabati N Braisted J Klapa M Currier T Thiagarajan M Sturn A Snuffin M Rezantsev A Popov D Ryltsov A Kostukovich E Borisovsky I Liu Z Vinsavich A Trush V Quackenbush J TM4: a free, open-source system for microarray data management and analysis Biotechniques 2003, 34(2):374-378 12613259
7. XSL Transformations (XSLT) Version 1.0 http://www.w3.org/TR/xslt
8. Bluejay: A Browser for Linear Units in Java http://bluejay.ucalgary.ca
9. The Apache Software Foundation http://www.apache.org
10. Turinsky AL Gordon PM Xu EW Stromer JN Sensen CW Genomic data representation through images: The MAGPIE/Bluejay system Handbook of Genome Research Weinheim: Wiley-VCH Sensen CW 2005, 187-198
11. MAGPIE: Multipurpose Automated Genome Project Investigation Environment http://magpie.ucalgary.ca
12. XML Linking Language (XLink) Version 1.0 http://www.w3.org/TR/xlink
13. Scalable Vector Graphics (SVG) 1.1 Specification http://www.w3.org/TR/SVG
14. Gene Ontology Home http://www.geneontology.org
15. Stephens RS Kalman S Lammel C Fan J Marathe R Aravind L Mitchell W Olinger L Tatusov RL Zhao Q Koonin EV Davis RW Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis Science 1998, 282(5389):754-9 9784136 9784136
16. Dehal P Boore JL Two rounds of whole genome duplication in the ancestral vertebrate PLoS Biology 2005, 3(10):e314 16128622 16128622 1197285
17. Burke R Hybrid recommender systems: Survey and experiments User Modeling and User-Adapted Interaction 2002, 12(4):331-370
18. Salton G Buckley C Term-weighting approaches in automatic text retrieval Information Processing and Management 1988, 24(5):513-523
19. Likert R A technique for the measurement of attitudes Archives of Psychology 1932, 140:1-55
20. Adomavicius G Tuzhilin A Toward the next generation of recommender systems: A survey of the state-of-the-art and possible extensions IEEE Transactions on Knowledge and Data Engineering 2005, 17(6):734-749
21. Altschul SF Madden TL Schäffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402 9254694 9254694 146917
22. Delcher AL Phillippy A Carlton J Salzberg SL Fast algorithms for large-scale genome alignment and comparison Nucleic Acids Res 2002, 30(11):2478-2483 12034836 12034836 117189
23. Treangen TJ Messeguer X M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species BMC Bioinformatics 2006, 7:433 17022809 17022809 1629028
24. Hubbard TJ Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Down T Dyer SC Fitzgerald S Fernandez-Banet J Graf S Haider S Hammond M Herrero J Holland R Howe K Howe K Johnson N Kahari A Keefe D Kokocinski F Kulesha E Lawson D Longden I Melsopp C Megy K Meidl P Ouverdin B Parker A Prlic A Rice S Rios D Schuster M Sealy I Severin J Slater G Smedley D Spudich G Trevanion S Vilella A Vogel J White S Wood M Cox T Curwen V Durbin R Fernandez-Suarez XM Flicek P Kasprzyk A Proctor G Searle S Smith J Ureta-Vidal A Birney E Ensembl 2007 Nucleic Acids Res 2007, 35 Database D610-D617 17148474 17148474 1761443
25. Kawai M Nakao K Uchiyama I Kobayashi I How genomes rearrange: Genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms Gene 2006, 383:52-63 16949772 16949772
26. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A Lewis S The generic genome browser: A building block for a model organism system database Genome Res 2002, 12(10):1599-1610 12368253 12368253 187535
27. Kuhn RM Karolchik D Zweig AS Trumbower H Thomas DJ Thakkapallayil A Sugnet CW Stanke M Smith KE Siepel A Rosenbloom KR Rhead B Raney BJ Pohl A Pedersen JS Hsu F Hinrichs AS Harte RA Diekhans M Clawson H Bejerano G Barber GP Baertsch R Haussler D Kent WJ The UCSC genome browser database: Update 2007 Nucleic Acids Res 2007, 35 Database D668-D673 17142222 17142222 1669757
28. Dowell RD Jokerst RM Day A Eddy SR Stein L The distributed annotation system BMC Bioinformatics 2001, 2:7 11667947 11667947 58584
29. Feolo M Helmberg W Sherry S Maglott DR NCBI genetic resources supporting immunogenetic research Rev Immunogenet 2000, 2(4):461-467 12361089 12361089
30. Fröls S Gordon PMK Panlilio M Duggin IG Bell SD Sensen CW Schleper C Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage Journal of Bacteriology 2007, 189(23):8708-8718 17905990 2168930
31. Fröls S Gordon PM Panlilio MA Schleper C Sensen CW Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays Virology 2007, 365(1):48-59 17467765 17467765