Genome Browser

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This document discusses GenomeBrowser. It mentions that the UCSC Human Genome Browser receives 50,000 hits per day and 3,000 users per day, while another receives 1,257 hits per day and 10 users per day. It also discusses various features of GenomeBrowser like being lightweight, configurable, and promoting data sharing.

Technology Education

GenomeBrowser
GenomeBrowser

Center for Genome Science, NIH, KCDC
Hong ChangBum
hongiiv@gmail.com

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

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.

•Add your own tracks
•Add 3d party tracks
•Distributed annotation system support

•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

4.*(#/,'(5
Hong ChangBum
Center for Genome Science
NIH, KCDC !quot;0*$1,.23quot;'
hongiiv@gmail.com
!quot;#quot;$%"'()*&$+,-.#/,'(
!quot;#$%&'()*!'+,-.#&
http://socmaster.homelinux.org/~hongiiv
/++0122quot;3#4-!'5*quot;#$%&'(-(*+

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Genome Browser

1. GenomeBrowser GenomeBrowser Center for Genome Science, NIH, KCDC Hong ChangBum hongiiv@gmail.com

3. , Genome Browser 4 .

6. An Interview with Ewan Birney: Keynote Speaker at O’Relly’s Bioinformatics Technology Conference 2001/10

10.

11.

12.    

13.

14.    

15.    

16.   •UCSC Human Genome Browser •50,000 Hit/Day •3,000 users/Day • •1,257 Hit/Day •10 users/Day

17. Code Name : Acuvue Objective: !

18.    

19.    

20.    

21. 1 3 2  

22.  

23. Google Maps API Presentation SNP Population Reference Link

24.       

25.   •Part of Generic Model Organism Database Project •Lightweight & portable •Highly configurable •Clean user interface •Promotes data sharing

26.           •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

27.   •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.

28.   Glyphs DAS Adaptor Remote Source

29.   •Add your own tracks •Add 3d party tracks •Distributed annotation system support

30.      

31.

32.      

33.       Glyphs DAS Adaptor UCSC Genome Browser

34. •Gbrowse on UCSC •Gbrowse on EnsEMBL •Gbrowse on both

35.

36.   Gbrowse 2 Gbrowse 1 Gbrowse 3 My Gbrowse

37.   •BioPerl and Bio::Graphics Software Libraries •Bio::DB::GFF Database •GadFly Database •Plug-ins

38.       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

39.   !quot;    !quot;#$ #$%&'%(      )%&%          

40.   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)

41.  

42.  

43. •“One Click” install on Macintosh OSX •“Three Click” install onWindows XP •“Tippity-tappity-tap” install on Linux/Solaris/BSD Unix

44. Genome Browser 10 % 90 %

45. 4.*(#/,'(5 Hong ChangBum Center for Genome Science NIH, KCDC !quot;0*$1,.23quot;' hongiiv@gmail.com !quot;#quot;$%"'()*&$+,-.#/,'( !quot;#$%&'()*!'+,-.#& http://socmaster.homelinux.org/~hongiiv /++0122quot;3#4-!'5*quot;#$%&'(-(*+

Genome Browser

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