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 _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
