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J Goecks - The Galaxy Visual Analysis Framework


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Presentation at BOSC2012 by J Goecks - The Galaxy Visual Analysis Framework

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J Goecks - The Galaxy Visual Analysis Framework

  1. 1. The  Galaxy  Visual  Analysis   Framework Jeremy  Goecks,  The  Galaxy  Team,  Anton   Nekrutenko,  and  James  Taylor 1
  2. 2. What  is  Galaxy?Web-based GUI for genomics ✦ for  complete  analyses:  obtain  and  integrate  data,  analyze,   visualize,  share,  publishA tool integration framework that makes it simpleto chain tool usage together step-by-step or createcomplex workflowsOpen source software  that  makes  it  simple  to   ✦ integrate  your  own  tools  and  data ✦ customize  and  run  on  your  own  resources 2
  3. 3. GoalAn  open,  Web-­‐based  approach  for  making  highly  interactive  visual  analysis  tools  for  NGS  datasets 3
  4. 4. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for  making  highly  interactive  visual  analysis  tools  for  NGS  datasets 4
  5. 5. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for   flexible,  customizablemaking  highly  interactive  visual  analysis  tools  for  NGS  datasets 5
  6. 6. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for   flexible,  customizable visualization  +  toolsmaking  highly  interactive  visual  analysis  tools  for  NGS  datasets 6
  7. 7. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for   flexible,  customizable visualization  +  toolsmaking  highly  interactive  visual  analysis   needs  to  scale  to  huge  datasets  tools  for  NGS  datasets 7
  8. 8. Demo 8
  9. 9. Trackster 9
  10. 10. Paramamonster 10
  11. 11. Circster 11
  12. 12. TracksterCompletely  Web-­‐based ✦ no  downloads,  no  add-­‐ons,  no  FlashSupports  arbitrarily  large  NGS  datasets ✦ SAM/BAM,  BED,  GFF/GTF,  VCF,  WIGHighly  flexible ✦ e.g.  custom  rainbow  tracksIntegrated  with  Galaxy  tool  framework ✦ dynamic  filtering ✦ re-­‐running  tools 12
  13. 13. ParamamonsterVisualization  for ✦ tool  parameter  space ✦ outputs  from  different  settingsCan  easily  find  good  settings  by  visual  inspection ✦ for  many  settings,  across  multiple  regionsCan  explore  parameter  space  systematically  or  ad-­‐hoc 13
  14. 14. CircsterCircos-­‐like  visualization  that  provides  genome-­‐wide  viewsComplements  TracksterVery  much  a  work  in  progress 14
  15. 15. ArchitectureWebbrowser Galaxy HTML UIGalaxy Tools ... Datasets ... 15
  16. 16. ArchitectureWebbrowser Galaxy HTML UI Data ProvidersGalaxy Tools ... Datasets ... 16
  17. 17. Architecture VisualizationsWeb d3.js (SVG)browser HTML5: Canvas, CSS Galaxy HTML UI Data Managers ... Data ProvidersGalaxy Tools ... Datasets ... 17
  18. 18. Future  DirectionsNon-­‐genomic  visualizations ✦ phylogenetic  trees ✦ scatterplotsIntegration  of  multiple  visualizations ✦ multiple  views  in  same  visualization ✦ views  in  different  visualizations 18
  19. 19. Enis Afgan Dannon Baker Dan Blankenberg Nate Coraor Dave Clements Jeremy Goecks Jennifer Jackson Greg von Kuster James Taylor Anton NekrutenkoSupported by the NHGRI (HG005542, HG004909, HG005133, HG006620), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health 19
  20. 20. Thanks!  Questions?http://galaxyproject.orgGalaxy  publications:  Track  Talk  (TT08):  Sunday, 20