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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

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

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  • 1. The  Galaxy  Visual  Analysis   Framework Jeremy  Goecks,  The  Galaxy  Team,  Anton   Nekrutenko,  and  James  Taylor 1
  • 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 http://usegalaxy.org http://galaxyproject.org 2
  • 3. GoalAn  open,  Web-­‐based  approach  for  making  highly  interactive  visual  analysis  tools  for  NGS  datasets 3
  • 4. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for  making  highly  interactive  visual  analysis  tools  for  NGS  datasets 4
  • 5. Goal distributed,  extendable,  sharable,  fastAn  open,  Web-­‐based  approach  for   flexible,  customizablemaking  highly  interactive  visual  analysis  tools  for  NGS  datasets 5
  • 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. 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. Demo 8
  • 9. Trackster 9
  • 10. Paramamonster 10
  • 11. Circster 11
  • 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. 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. CircsterCircos-­‐like  visualization  that  provides  genome-­‐wide  viewsComplements  TracksterVery  much  a  work  in  progress 14
  • 15. ArchitectureWebbrowser Galaxy HTML UIGalaxy Tools ... Datasets ... 15
  • 16. ArchitectureWebbrowser Galaxy HTML UI Data ProvidersGalaxy Tools ... Datasets ... 16
  • 17. Architecture VisualizationsWeb d3.js (SVG)browser HTML5: Canvas, CSS Galaxy HTML UI Data Managers ... Data ProvidersGalaxy Tools ... Datasets ... 17
  • 18. Future  DirectionsNon-­‐genomic  visualizations ✦ phylogenetic  trees ✦ scatterplotsIntegration  of  multiple  visualizations ✦ multiple  views  in  same  visualization ✦ views  in  different  visualizations 18
  • 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. Thanks!  Questions?http://galaxyproject.orgGalaxy  publications:  http://galaxyproject.org/wiki/CitingTech  Track  Talk  (TT08):  Sunday,  2:30pjeremy.goecks@emory.edu 20