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C02-Visualization-Applying visual analytics

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Applying visual analytics to extend the genome browser from visualisation tool to analysis tool (Jeremy Goecks)

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C02-Visualization-Applying visual analytics

  1. 1. Trackster (The Galaxy Track Browser) Jeremy Goecks, Kanwei Li, The Galaxy Team, and James Taylor 1
  2. 2. Why another Genome Browser? Galaxy (http://usegalaxy.org) ✦ Web-based, uses open standards ✦ tool integration framework ✦ sharing, publication framework ✦ HTS/NGS focused Trackster Genome Browser ✦ physical depiction of data ✦ visually identify correlations ✦ find interesting regions, features 2
  3. 3. What is Galaxy? Web-based GUI for genomics that requires only a Web browser for everything: analysis, workflows, sharing, publication, and visualization A public web service (http://usegalaxy.org) integrating a wealth of tools, compute resources, terabytes of reference data and permanent storage Open source software that makes integrating your own tools and data and customizing for your own site simple 3
  4. 4. Trackster Simple, dynamic Web-based visualization for your HTS/NGS data Supports visual analytics Can share & publish working visualizations 4
  5. 5. HTS Datasets on the Web HTS datasets are often GBs, so cannot load them all at once Multiple indices needed to load data on demand at different levels of detail ✦ IGV and Savant on the desktop... ...and now Trackster on the Web 5
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  9. 9. Supporting Visual Analytics Visual analytics: using interactive visualization to reason about and solve problems Increasingly complex genomic tools require parameter experimentation ✦ visual feedback aids exploration Galaxy provides abstract interfaces to tools 9
  10. 10. Dynamic filtering on element properties here, FPKM for putative transcripts
  11. 11. Modifying Cufflinks parameters and locally reassembling
  12. 12. Compatible Tools Filtering tools Genomic interval tools Modified Cufflinks Key requirement: ✦ local model or ✦ access to global model 12
  13. 13. Your Tools with Trackster Integrate tools with Galaxy using simple, XML definition Local model ✦ just add <trackster_conf/> to tool definition Global model ✦ store and retrieve global model ✦ support filtering -- decorate data with attributes 13
  14. 14. Sharing Visualizations Communication paramount ✦ biomedical/genomics research is collaborative ✦ majority of publications use visualization “A picture is worth a 1000 words.” A fully-interactive visualization is worth many more words 14
  15. 15. Sharing Trackster Visualizations 15
  16. 16. Implementation Client: OO JavaScript, HTML5 canvas ✦ Web standards ✦ dynamic, customizable, tools, filters, ... Server: uses existing Galaxy functionality ✦ tool integration ✦ data indexing and aggregation ✦ sharing and publication Custom Builds! 16
  17. 17. Modular and Extensible Data exchange uses JSON, not tied to Galaxy datatypes Client UI (browser) components not tied to Galaxy UI ✦ rendering components are CommonJS modules that can be reused in any JS environment Everything is extensible: displays, track types, element rendering, data providers... 17
  18. 18. Trackster Summary Dynamic, configurable Web-based visualization for your HTS/NGS data Supports visual analytics Can share & publish working visualizations 18
  19. 19. Enis Afgan Dannon Baker Dan Blankenberg Nate Coraor Dave Clements Jeremy Goecks Jennifer Jackson Greg von Kuster Kanwei Li James Taylor Kelly Vincent Anton Nekrutenko Supported by the NHGRI (HG005542, HG004909, HG005133), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health 19
  20. 20. Thanks! Questions? http://usegalaxy.org/visualization/list_published ✦ http://usegalaxy.org/u/jeremy/v/trackster-demo-1-viewing-and-navigating ✦ http://usegalaxy.org/u/jeremy/v/trackster-demo-2-dynamic-filtering ✦ (Running tools demo very slow on main due to high NGS tools usage; faster demo coming soon.) Galaxy ✦ public server: http://usegalaxy.org ✦ download and run: http://getgalaxy.org BOSC BOF Session: Galaxy-Taverna integration jeremy.goecks@emory.edu 20

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