Hi Manuel, Since 2008 ProServer has had a BED format SourceAdaptor (called bed12, as it is intended to work with the 12-field BED format). It also supports Hydras, which are modules that are designed to automatically create DAS sources from a single config without restarting the server. This is how EasyDAS works with ProServer: there is one SourceAdaptor, and a Hydra to scan a relational database for new data.
I don't know what 23andme's data looks like, but the addition of a Hydra to scan directories for new files and automatically make them available as DAS sources would seem to be a trivial piece of work. I daresay a VCF adaptor would also be fairly easy, especially if there is a Perl API of some sort (BioPerl?). Cheers, Andy On 17 Nov 2011, at 17:11, Manuel Corpas wrote: > Dear Jonathan, > > I hope you do not mind me copying the DAS list in this email, as we > would be very keen to gather interest in the community regarding DAS > applications to whole genomes. > > We are interested in exploring DAS in the context of genomic variants > (SNPs, indels, CNVs) from personal genomes plus their integration with > relevant sources (genes, variation data, phenotypes). > > Currently we have done a lot of work with 23andMe (whole-genome) > genotypes but now we are expecting to extend our efforts further to > exome data. A critical tool we are currently missing is one that > allows automatic creation of DAS sources via an API directly from bed > format (used by 23andMe) or vcf (1000genomes). > > Anyone interested in discussing these topics please let me know. > > Kind regards, > Manuel > > Manuel Corpas, PhD > Tel: +44.122349.2372 > Web: http://manuelcorpas.com/about/ > Twitter: @manuelcorpas > > > > On 17 November 2011 12:11, Jonathan Warren <[email protected]> wrote: >> Hi >> >> As the 2012 DAS workshop is coming up at the end of February we would like >> to hear from people using DAS. >> We would be really grateful to receive just a short email from anyone using >> DAS or developing DAS with a brief summary about their project and how DAS >> fits in, especially if you have not spoken at the DAS workshops at any time. >> >> Please also say if you would be interested in giving a short presentation at >> the workshop in February even if you are not sure if you could make it. >> Previous years the presentations have been 15 minutes with 5 minutes for >> questions - however this year we intend to be more flexible and so if you >> would prefer to give a "lightning talk" of just 5 minutes to update people >> or give them a brief overview that will be fine. Links to the previous years >> talks can be found here http://www.biodas.org/wiki/DASWorkshop2011#Day_2 >> >> I must emphasise - please give us a summary even if you are not interested >> in giving a talk as we would like to know what is going on out there and we >> promise not to hound you to give a talk :) >> >> Thanks in advance >> >> The Sanger/EBI DAS people. >> >> >> Jonathan Warren >> Senior Developer and DAS coordinator >> blog: http://biodasman.wordpress.com/ >> [email protected] >> Ext: 2314 >> Telephone: 01223 492314 >> >> >> >> >> >> >> >> >> >> >> -- >> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a >> charity registered in England with number 1021457 and acompany registered in >> England with number 2742969, whose registeredoffice is 215 Euston Road, >> London, NW1 2BE._______________________________________________ >> DAS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/das >> > > _______________________________________________ > DAS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/das _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
