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

1. Trackster
(The Galaxy Track Browser)
Jeremy Goecks, Kanwei Li, The
Galaxy Team, and James Taylor
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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
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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
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4. Trackster
Simple, dynamic Web-based visualization
for your HTS/NGS data
Supports visual analytics
Can share & publish working visualizations
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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
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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
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10. Dynamic filtering on element properties here, FPKM for putative transcripts

11. Modifying Cufflinks parameters and locally reassembling

12. Compatible Tools
Filtering tools
Genomic interval tools
Modified Cufflinks
Key requirement:
✦ local model or
✦ access to global model
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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
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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
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15. Sharing Trackster Visualizations
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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!
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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...
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18. Trackster Summary
Dynamic, configurable Web-based
visualization for your HTS/NGS data
Supports visual analytics
Can share & publish working visualizations
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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
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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
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