[DAS] Survey on DAS projects
andy.jenkinson at ebi.ac.uk
Fri Nov 18 15:14:02 UTC 2011
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?).
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 Corpas, PhD
> Tel: +44.122349.2372
> Web: http://manuelcorpas.com/about/
> Twitter: @manuelcorpas
> On 17 November 2011 12:11, Jonathan Warren <jw12 at sanger.ac.uk> wrote:
>> 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/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
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>> England with number 2742969, whose registeredoffice is 215 Euston Road,
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