Published on October 31, 2008
, Genome Browser 4 .
An Interview with Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10
•UCSC Human Genome Browser •50,000 Hit/Day •3,000 users/Day • •1,257 Hit/Day •10 users/Day
Code Name : Acuvue Objective: !
1 3 2
Google Maps API Presentation SNP Population Reference Link
•Part of Generic Model Organism Database Project •Lightweight & portable •Highly configurable •Clean user interface •Promotes data sharing
•Find your Favorite Gene •Find your Favorite Domain •Find your Favorite Oligo •Zoom - Low Magnification •Zoom - Medium Magnification •Zoom - High Magnification •Zoom - Highest Magnification •CustomTracks
•End-user •Turn tracks on and off, change order, change packing & labeling attributes(stored in cookie) •Data provider •Change fonts, colors, text. •Change overview-genetic map, contigs, coverage, karyotype. •Define new tracks using simple config file. •Tinker with track appearance to hearts content.
Glyphs DAS Adaptor Remote Source
•Add your own tracks •Add 3d party tracks •Distributed annotation system support
Glyphs DAS Adaptor UCSC Genome Browser
•Gbrowse on UCSC •Gbrowse on EnsEMBL •Gbrowse on both
Gbrowse 2 Gbrowse 1 Gbrowse 3 My Gbrowse
•BioPerl and Bio::Graphics Software Libraries •Bio::DB::GFF Database •GadFly Database •Plug-ins
seqid source type start end score strand phase attribute Chr1 dbsnp snp 200 300 . + . ID=SNP:rs1234;alleles:G/T Chr1 dbsnp snp 400 700 . + . ID=SNP:rs4321;alleles:G/T
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 A B C (1,2,3,7,8,9,10,11) (1,4,14,15,16,17) (1,5,20)
•“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix
Genome Browser 10 % 90 %
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