1. bioinf.scri.ac.uk/flapjack

2. Introduction Barley genotyping Visualizing the data Flapjack overview Performance issues Other features Future work

3. bioinf.scri.ac.uk/flapjack Barley (Hordeum vulgare)

4. bioinf.scri.ac.uk/flapjack Barley (Hordeum vulgare)

5. bioinf.scri.ac.uk/flapjack Genetic Markers & Genotyping Marker technology lets us look at genetic diversity across a large number of varieties They provide a genetic framework against which we can anchor traits, such as disease resistance, yield, or malting quality Flapjack’s data is provided from Illumina SNP markers

6. bioinf.scri.ac.uk/flapjack From Database to Screen M1 M2 M3 M4 M5 M6 M7 M8 M9 M1 M2 M3 M4 M5 M6 M7 M8 M9 Line1 G T A - G A A/G G G Line2 G A/T A G G A G G A Line3 G G/C G G/C G/C A/T G G G Line4 - A G G G A - A A Line5 A T/A G C C G C G/C G Barley SNP data provided to Flapjack currently consists of: –3856 lines –4608 markers

7. bioinf.scri.ac.uk/flapjack Visualizing Squares

8. bioinf.scri.ac.uk/flapjack Visualizing Squares

9. bioinf.scri.ac.uk/flapjack Visualizing Squares

10. bioinf.scri.ac.uk/flapjack G AC T Homozygotes/heterozygotes A G

11. bioinf.scri.ac.uk/flapjack

21. Flapjack provides several different ways of colouring the data –(Default) nucleotide 4-colour model Colour Schemes

22. bioinf.scri.ac.uk/flapjack Flapjack provides several different ways of colouring the data –2-colour model for A/B data Colour Schemes

23. bioinf.scri.ac.uk/flapjack Flapjack provides several different ways of colouring the data –Colour by similarity to a comparison line Colour Schemes

24. bioinf.scri.ac.uk/flapjack Colour Schemes Flapjack provides several different ways of colouring the data –Colour by similarity to a comparison marker

25. bioinf.scri.ac.uk/flapjack Colour Schemes Flapjack provides several different ways of colouring the data –By frequency of rare alleles

26. bioinf.scri.ac.uk/flapjack Colour Schemes Flapjack provides several different ways of colouring the data –Random

27. bioinf.scri.ac.uk/flapjack

29. Performance

30. bioinf.scri.ac.uk/flapjack Reducing Memory G T A - G A A/G G G G A/T A G G A G G A G G/C G G/C G/C A/T G G G - A G G G A - A A A T/A G C C G C G/C G 0 – 1 G 2 T 3 A 4 A/G 5 A/T 6 G/C 7 C 1 2 3 0 1 3 4 1 1 1 5 3 1 1 3 1 1 3 1 6 1 6 6 5 1 1 1 0 3 1 1 1 3 0 3 3 3 5 1 7 7 1 7 6 1

31. bioinf.scri.ac.uk/flapjack Full back buffer (if memory allows) Screen buffer Selective Rendering & Buffering all markers all lines

32. bioinf.scri.ac.uk/flapjack Rubber Stamping On a 1920x1200 resolution screen, Flapjack may be drawing between 500,000 and 1,000,000 squares – per refresh Each square – if drawn in real-time – requires calculations for: –Its allele type and location on screen –Its colour gradient –Anti-aliased text A AAAAAAAAAAAAAA

33. bioinf.scri.ac.uk/flapjack Multi-threaded Rendering 2s Chromosome map Overviews Canvas back-buffer Real-time render (visible region) 0s Time (in seconds)

34. bioinf.scri.ac.uk/flapjack Rendering Issues canvas size memory render time square size back buffer creation possible:

35. bioinf.scri.ac.uk/flapjack Rendering Issues canvas size memory render time square size back buffer creation possible: render time

36. bioinf.scri.ac.uk/flapjack Features

37. bioinf.scri.ac.uk/flapjack Interaction Rapidly re-arrange the display to suit the user –CTRL+click and drag up/down to move lines –CTRL+click and drag left/right to move markers –CTRL+double click to temporarily hide lines or markers –Insert “dummy” lines to help break the display into regions –Click and drag selection of lines and markers –All with multiple undo/redo support

38. bioinf.scri.ac.uk/flapjack Searching Standard and regular expression based searches

39. bioinf.scri.ac.uk/flapjack Bookmarks Bookmark multiple regions of interest to aid navigation

40. bioinf.scri.ac.uk/flapjack Highlight Heterozygotes Toggle on or off highlighting of heterozygous alleles –Helps to rapidly identify rare alleles or mis-scored markers

41. bioinf.scri.ac.uk/flapjack Trait/phenotype Data

42. bioinf.scri.ac.uk/flapjack Sorting Sort lines by their similarity to a comparison line Sort lines by trait values (up to three)

43. bioinf.scri.ac.uk/flapjack Views Define multiple custom views of the same data sets Export views (or subsets of views) back to disk in data or image formats

44. bioinf.scri.ac.uk/flapjack Installer (install4j) Microsoft Windows Mac OS X Linux Solaris

45. bioinf.scri.ac.uk/flapjack Regional Bilingual: English and German versions (single install)

46. bioinf.scri.ac.uk/flapjack Online Help & Documentation

47. bioinf.scri.ac.uk/flapjack And Finally…

48. bioinf.scri.ac.uk/flapjack Future Work Pedigrees Clustering (with dendrogram view) QTL visualization LD visualization Haplotype block viewer Support for non-diploid visualizations, e.g. tetraploid (potatoes)

49. bioinf.scri.ac.uk/flapjack Team - Iain MilneMicha Bayer Paul ShawLinda CardleDavid Marshall

50. bioinf.scri.ac.uk/flapjack Other Demos CurlyWhirly Yumyum

51. bioinf.scri.ac.uk/flapjack European Spring Barley Pedigrees