C02-Visualization-Applying visual analytics
-
Upload
bioinformatics-open-source-conference -
Category
Education
-
view
577 -
download
0
description
Transcript of C02-Visualization-Applying visual analytics
Trackster(The Galaxy Track Browser)
Jeremy Goecks, Kanwei Li, The Galaxy Team, and James Taylor
1
Why another Genome Browser?
2
Genome Browser✦ physical depiction of data✦ visually identify correlations✦ find interesting regions, features
Galaxy (http://usegalaxy.org)
✦ Web-based, uses open standards✦ tool integration framework✦ sharing, publication framework✦ HTS/NGS focused
Trackster
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
Trackster
Simple, dynamic Web-based visualization for your HTS/NGS data
Supports visual analytics
Can share & publish working visualizations
4
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
6
7
8
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
Dynamic filtering on element properties here, FPKM for putative transcripts
Modifying Cufflinks parameters and locally reassembling
Compatible Tools
Filtering tools
Genomic interval tools
Modified Cufflinks
Key requirement: ✦ local model or✦ access to global model
12
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
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
Sharing Trackster Visualizations
15
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
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
Trackster Summary
Dynamic, configurable Web-based visualization for your HTS/NGS data
Supports visual analytics
Can share & publish working visualizations
18
Supported by the NHGRI (HG005542, HG004909, HG005133), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health
Dan Blankenberg Nate Coraor
Kelly Vincent
Greg von Kuster
Enis Afgan Dannon Baker
Kanwei Li
Jeremy Goecks
Anton NekrutenkoJames Taylor
Dave Clements Jennifer Jackson
19
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
20