1. Copyright OpenHelix. No use or reproduction without express written consent1

2. GBrowse Generic Genome Browser 1.x Series Materials prepared by: Mary E. Mangan, Ph.D. www.openhelix.com Updated: Q3 2010 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

4. Copyright OpenHelix. No use or reproduction without express written consent4 GBrowse Introduction GBrowse developed by GMOD Generic Model Organism Database generic Genome Browser web application to explore genomes free software goal: simplify & standardize MODs Model Organism Databases

5. Copyright OpenHelix. No use or reproduction without express written consent5 Browsing a Genome bird’s eye view......or zoom in for details colored glyphs (icons) customize it

6. Copyright OpenHelix. No use or reproduction without express written consent6 GBrowse as a Standard Human Genome Segmental Duplication Database

7. Copyright OpenHelix. No use or reproduction without express written consent7 Citation, Documentation, Mailing List PMID: 12368253 http://gmod.org/wiki/Gbrowse https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

8. Copyright OpenHelix. No use or reproduction without express written consent8 Administrator and Developer Resources

9. Copyright OpenHelix. No use or reproduction without express written consent9 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

10. Copyright OpenHelix. No use or reproduction without express written consent10 Universal GBrowse Layout Human Genome Segmental Duplication Database

11. Copyright OpenHelix. No use or reproduction without express written consent11 Mouse GBrowse banner instructions search description details tracks cookies overview region displayedinstructions search overview details

12. Copyright OpenHelix. No use or reproduction without express written consent12 Opening and Closing Sections Open ViewHidden View toggle (open) (hide) control sections you want to view

13. Copyright OpenHelix. No use or reproduction without express written consent13 Instructions what’s allowable for searches bookmark current view and settings for re-visits to page view Detail image in SVG format restore standard settings

14. Copyright OpenHelix. No use or reproduction without express written consent14 Search Gene symbols Gene IDs Sequence IDs Genetic markers Relative nucleotide coordinates Absolute nucleotide coordinates etc... click hoxd11sod* tyrosine kinase receptor

15. Copyright OpenHelix. No use or reproduction without express written consent15 Multiple Matches click

16. Copyright OpenHelix. No use or reproduction without express written consent16 Sod2, at 10 kb Sod2 pick-list

17. Copyright OpenHelix. No use or reproduction without express written consent17 Sod2, at 1 Mb Sod2

18. Copyright OpenHelix. No use or reproduction without express written consent18 Reports and Analysis Perform actions and “Go” Download sequences or features Configure features with options Choose restriction sites

19. Copyright OpenHelix. No use or reproduction without express written consent19 WormBase and v1.69 New features in v1.69 description instructions search overview details tracks

20. Copyright OpenHelix. No use or reproduction without express written consent20 Display Quantitative Data “Wiggle” tracks display type Plot data with different values http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks wiggle

21. Copyright OpenHelix. No use or reproduction without express written consent21 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

22. Copyright OpenHelix. No use or reproduction without express written consent22 Annotation Controls: Tracks

23. Copyright OpenHelix. No use or reproduction without express written consent23 Selecting Tracks

24. Copyright OpenHelix. No use or reproduction without express written consent24 Changing Tracks

25. Copyright OpenHelix. No use or reproduction without express written consent25 Updated Image mouse over and click 2 transcripts 3 phenotypes 2 SNPs 4 targeted alleles pick-list

26. Copyright OpenHelix. No use or reproduction without express written consent26 Updated Image, at 1 Mb Sod2

27. Copyright OpenHelix. No use or reproduction without express written consent27 Configuring Tracks

28. Copyright OpenHelix. No use or reproduction without express written consent28 “Show” and “Format” Configurations pick-list

29. Copyright OpenHelix. No use or reproduction without express written consent29 “Expand & Label” View BEFOREAFTER Auto format Expand & Label format transcripts are labeled and expanded

30. Copyright OpenHelix. No use or reproduction without express written consent30 “Limit” and “Order” Configurations pick PAGE RELOADS pick

31. Copyright OpenHelix. No use or reproduction without express written consent31 Altering Track Order

32. Copyright OpenHelix. No use or reproduction without express written consent32 New Track Order Displayed Track 1

33. Copyright OpenHelix. No use or reproduction without express written consent33 Annotation Controls: Display Settings

34. Copyright OpenHelix. No use or reproduction without express written consent34 “Image Width” 450 800

35. Copyright OpenHelix. No use or reproduction without express written consent35 “Key Position” “Key” between annotations“Key” beneath annotations

36. Copyright OpenHelix. No use or reproduction without express written consent36 “Track Name Table” alphabetical Tracks varied Tracks

37. Copyright OpenHelix. No use or reproduction without express written consent37 “Grid” and “Highlight Features” now glyph GeneID:20656_Sod2 is yellow highlighted glyphs NM_013671_MGI:98352_Sod2 are yellow highlighted edit

38. Copyright OpenHelix. No use or reproduction without express written consent38 “Highlight Regions” edit highlights the specified region

39. Copyright OpenHelix. No use or reproduction without express written consent39 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

40. Copyright OpenHelix. No use or reproduction without express written consent40 Add Your Own Tracks

41. Copyright OpenHelix. No use or reproduction without express written consent41 Add Your Own Tracks

42. Copyright OpenHelix. No use or reproduction without express written consent42 Sample Annotation Text File simple text file of annotations

43. Copyright OpenHelix. No use or reproduction without express written consent43 Uploading Personal Annotations Upload chemical annotations appear

44. Copyright OpenHelix. No use or reproduction without express written consent44 Configuring and Editing Your Own Tracks customize your glyphs to any color and shape

45. Copyright OpenHelix. No use or reproduction without express written consent45 Use any Data as an Annotation overlaid with TAF1 promoter binding skeleton phenotypes Discover genes that map to both sets of annotations.

46. Copyright OpenHelix. No use or reproduction without express written consent46 Add Remote Annotations

47. Copyright OpenHelix. No use or reproduction without express written consent47 Data Sharing: SNPedia --> HapMap GBrowse www.snpedia.com SNPedia data overlaid on HapMap GBrowse add remote URLs

48. Copyright OpenHelix. No use or reproduction without express written consent48 Bookmark and Share GBrowse

49. Copyright OpenHelix. No use or reproduction without express written consent49 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

50. Copyright OpenHelix. No use or reproduction without express written consent50 WormBase Tour Data Source Expression data

51. Copyright OpenHelix. No use or reproduction without express written consent51 “Reports & Analysis” feature pick-list

52. Copyright OpenHelix. No use or reproduction without express written consent52 FlyBase Tour Data Source 12 fly genomes

53. Copyright OpenHelix. No use or reproduction without express written consent53 Comparative Genome Analysis C. elegans D. melanogaster orthologs

54. Copyright OpenHelix. No use or reproduction without express written consent54 HGSDD Tour Human Genome Segmental Duplication Database map genomic diseases to duplications disease duplications

55. Copyright OpenHelix. No use or reproduction without express written consent55 DictyBase Tour

56. Copyright OpenHelix. No use or reproduction without express written consent56 Personal Genomes jimwatsonsequence.cshl.edu jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence

57. Copyright OpenHelix. No use or reproduction without express written consent57 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

58. Copyright OpenHelix. No use or reproduction without express written consent58 GBrowse: Universal & Unique GBrowse -- free software by GMOD -- standardize MODs -- universal and unique U N I V E R S A L A P P E A R A N C EU N I Q U E A P P E A R A N C E Tracks

59. Copyright OpenHelix. No use or reproduction without express written consent59 GBrowse: Sequences & Annotations intuitive searches genomic sequence annotated data

60. Copyright OpenHelix. No use or reproduction without express written consent60 GBrowse: Tracks & Customization choose data you want to see customize data the way you want to see it

61. Copyright OpenHelix. No use or reproduction without express written consent61 GBrowse: Add Your Data upload your own annotation files

62. Copyright OpenHelix. No use or reproduction without express written consent62 GBrowse: Tours Human Genome Segmental Duplication Database photo: NIH

63. Copyright OpenHelix. No use or reproduction without express written consent63 GBrowse Agenda Introduction and Credits Layout and Basic Search Basic Annotation Controls Advanced Annotation Controls Tours Summary Exercises GBrowse: http://gmod.org/wiki/Gbrowse

64. Copyright OpenHelix. No use or reproduction without express written consent64