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

[Brian Gilman]

Greg,

	Can I use the DAS2 server framework to write the Haploview service?

-B
--
Brian Gilman
President Panther Informatics Inc.
E-Mail: gilmanb at pantherinformatics.com
         gilmanb at jforge.net
AIM: gilmanb1

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On Oct 28, 2008, at 2:02 PM, Gregg Helt wrote:

> 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
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