[DAS2] Trellis/Ivy: DAS1 --> DAS2 transformational proxy

[Gregg Helt]

I'm pleased to announce I've got a DAS1 to DAS2 transformational proxy
working.  I'm calling it Trellis/Ivy.  Trellis is the overall DAS2 server
framework, and Ivy is the DAS1 proxy plugin.  The source code is available
via SVN at http://code.google.com/p/genomancer/ .  This should definitely be
considered a beta release, there are plenty of features that aren't yet
implemented and I'm sure still some bugs in what is implemented.

I'm hoping a stable version of this can eventually be set up close to or
integrated with the DAS1 registry.  For current testing I've deployed an
instance of Trellis/Ivy at genomancer.org in the Amazon EC2 cloud.  It's
hardwired to proxy for the Sanger DAS1
registry<http://www.dasregistry.org/das1/sources>.
Some example DAS2 queries and the DAS1 queries they proxy for:

All DAS1 registry sources:
http://www.dasregistry.org/das1/sources
All DAS1 registry sources --> DAS1+2 sources
http://www.genomancer.org/das2/das1_proxy/sources

DAS1 filtered sources
http://www.dasregistry.org/das1/sources?type=Chromosome&capability=types
DAS1 filtered sources --> DAS1+2 filtered sources
http://www.genomancer.org/das2/das1_proxy/sources?type=Chromosome&capability=types

Ensembl DAS1 entry points
http://www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points
Ensembl DAS1 entry points --> DAS2 segments
http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.reference/entry_points

Uniprot DAS1 types
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types
Uniprot DAS1 types --> DAS2 types:
http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/types

Uniprot DAS1 features (from UniProt DAS home page example)
http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502
UniProt DAS1 features --> DAS2 features
http://www.genomancer.org/das2/das1_proxy/www.ebi.ac.uk/das-srv/uniprot/das/uniprot/features?segment=O35502

Ensembl DAS1 features (from Ensembl DAS home page example)
http://www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13:31787617,31871806
Ensembl DAS1 features --> DAS2 features
http://www.genomancer.org/das2/das1_proxy/www.ensembl.org/das/Homo_sapiens.NCBI36.transcript/features?segment=13;overlaps=31787616:31871806

UCSC-Gencode segment/overlap/type-filtered, URL-encoded, DAS2 feature
request (copied from IGB testing):
http://www.genomancer.org/das2/das1_proxy/hgwdev-gencode.cse.ucsc.edu/cgi-bin/das/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2F21;overlaps=26014828%3A26071595;type=http%3A%2F%2Fwww.genomancer.org%2Fdas2%2Fdas1_proxy%2Fhgwdev-gencode.cse.ucsc.edu%2Fcgi-bin%2Fdas%2Fhg18%2FknownGene


Basic DAS1.53 query --> DAS2.0 conversions not yet implemented:
    DAS1 sequence --> DAS2 segments
    DAS1 dsn --> DAS2 sources
    DAS1 stylesheet --> DAS2 stylesheet
I'll post a summary of plans for these queries and other features soon, but
I wanted to at least send out this announcement so people who are interested
can check out the examples.  Please let me know what you think.

    Gregg