Dalliance
Thomas Down
http://www.biodalliance.org/
Genome browsers
- Can we have the best of both worlds?
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Technologies align
- Solid Javascript implementations
- Rich browser-based graphics (SVG/Canvas)
- Browser vendors focussing on performance (games!)
- DAS: Distributed Annotation System
- CORS: Cross-origin Resource Sharing
- HTML5
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Let's try it out
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What is CORS?
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More data...
- Data volumes increasing
- More datasets
- Larger datasets
- Experiments like:
- ChIP-seq.
- Exome resequencing.
- ...
- Small labs produce genome-wide data
- Few resources to help get data out
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How does this fit DAS?
- DAS XML has served us well
- Relatively rich data model (IDs, links, notes)
- ...but XML is verbose
<FEATURE id="why_oh_why?">
<START>30000000</START>
<END>30000001</END>
<TYPE id="density">read depth</TYPE>
...and more...
</FEATURE>
Requires a server deployment
...and someone to deploy that server
Relational DB backends don't always scale
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The binary solution
- Dense binary formats
bigbed
: general features
bigwig
: dense quantitative data
BAM
: short read alignments
- All have indices
- Therefore, random access is possible
- HTTP supports random access using
Range
.htaccess
file:
Header set Access-Control-Allow-Origin "*"
Header set Access-Control-Allow-Headers "Range"
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Binary Dalliance
- Latest Dalliance supports bigwig and bigbed
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Integrating binary data into DAS
- Alternative formats have been proposed for some time
- Not widely adopted
- Alternative solution
- Replace the
features
capability completely
<SOURCE title="K36me3-chip">
<COORDINATES .... >
<CAPABILITY type="xdas1:bigfile"
query_uri="http://chip.org/K36me3.bb">
<CAPABILITY type="das1:stylesheet"
query_uri="http://chip.org/stylesheet">
...
</SOURCE>
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Dalliance in 2011
- More data!
- More formats (BAM, others, please ask!)
- Adding data from local disk
- More interactivity
- Jump around quickly between interesting regions.
- Link to other tools.
- Connect with other biologists.
- Alignments (assembly mapping; comparative genomics)
- Performance (SVG -> Canvas?)
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Acknowledgements
- Tim Hubbard
- DAS Developers
- Dalliance testers
- My other life: Wellcome Trust.
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