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 Taylor1
  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 Webbrowser for everything: analysis, workflows, sharing,publication, and visualizationA public web service (http://usegalaxy.org) integrating awealth of tools, compute resources, terabytes of referencedata and permanent storageOpen source software that makes integrating your owntools and data and customizing for your own site simple 3
  4. 4. TracksterSimple, dynamic Web-based visualizationfor your HTS/NGS dataSupports visual analyticsCan share & publish working visualizations 4
  5. 5. HTS Datasets on the WebHTS datasets are often GBs, so cannotload them all at onceMultiple indices needed to load data ondemand 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 ToolsFiltering toolsGenomic interval toolsModified CufflinksKey requirement: ✦ local model or ✦ access to global model 12
  13. 13. Your Tools with TracksterIntegrate tools with Galaxy using simple, XMLdefinitionLocal model ✦ just add <trackster_conf/> to tool definitionGlobal model ✦ store and retrieve global model ✦ support filtering -- decorate data with attributes 13
  14. 14. Sharing VisualizationsCommunication paramount ✦ biomedical/genomics research is collaborative ✦ majority of publications use visualization“A picture is worth a 1000 words.”A fully-interactive visualization is worthmany more words 14
  15. 15. Sharing Trackster Visualizations 15
  16. 16. ImplementationClient: OO JavaScript, HTML5 canvas ✦ Web standards ✦ dynamic, customizable, tools, filters, ...Server: uses existing Galaxy functionality ✦ tool integration ✦ data indexing and aggregation ✦ sharing and publicationCustom Builds! 16
  17. 17. Modular and ExtensibleData exchange uses JSON, not tied to GalaxydatatypesClient UI (browser) components not tied to Galaxy UI ✦ rendering components are CommonJS modules that can be reused in any JS environmentEverything is extensible: displays, track types,element rendering, data providers... 17
  18. 18. Trackster SummaryDynamic, configurable Web-basedvisualization for your HTS/NGS dataSupports visual analyticsCan 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 NekrutenkoSupported 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.orgBOSC BOF Session: Galaxy-Taverna integrationjeremy.goecks@emory.edu 20