[DAS] Survey on DAS projects

Sat Nov 19 15:58:16 UTC 2011

> Having said all this, I am a little confused about what you are trying to achieve. In your first mail you said you wanted to create sources via an API, in the second you say you want to do it via a click. Obviously the requirements for both are very different.

Both API and 1-click DAS source creation would be extremely helpful in
my view. The fact that this functionality is not available is
seriously affecting many of our users' ability to create DAS sources
with their 23andMe genotypes.

The fact that these facilities do not exist has stopped new potential
users from utilizing DAS. If DAS is truly going to survive as a
standard, automatic creation of data sources needs to be easier.

Manuel

Manuel Corpas, PhD
Tel:      +44.122349.2372
Web:    http://manuelcorpas.com/about/
Twitter: @manuelcorpas

On 18 November 2011 23:33, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> wrote:
> Hi Manuel,
>
> It would be nice to be able to create a DAS source from any type of data you happen to have with a click or two, but I don't think it is realistic. Even in this email you have just told me what all the columns mean, what the assembly is, what kind of file it is. Any application would need to know the same things (and more).
>
> That is not to say that it is difficult to build something to let you do this if it is specifically designed for the exact type of data you are using, just that it does not already exist and so you have to actually create it. Either MyDas or ProServer would seem to offer you a starting point to do that, but only a starting point. EasyDAS is the closest thing to what you want but obviously it has to cater for any type of data so has to ask you a lot more questions. Its web-based architecture obviously limits the size of data files you can process quickly too, but that is the trade off you make by not needing an Internet-visible web server of your own to run a DAS server from. I daresay if you wanted to create something that an individual can use to make a DAS source from their personal BED/VCF file then it would have to be web based, will always be restricted by the speed of the Internet, but the interface could be much simpler than EasyDAS and a database might not be needed (EasyDAS loads file contents into a database to standardise them, which slows things down).
>
> Having said all this, I am a little confused about what you are trying to achieve. In your first mail you said you wanted to create sources via an API, in the second you say you want to do it via a click. Obviously the requirements for both are very different.
>
> Cheers,
> Andy
>
> On 18 Nov 2011, at 15:24, Manuel Corpas wrote:
>
>> Hi Andy,
>>
>> thanks for the info. Having a bed DAS adaptor is part of the problem,
>> the other is not having to worry about having to deal with the DAS
>> server directly. easyDAS manages to do this but unfortunately it is
>> not obvious for people who do not know DAS how to operate it. Also if
>> the file is very big and the connection slow it can take up to an hour
>> to create a DAS source.
>>
>> Wouldn't it be nice to create a DAS source just with one click or two?
>>
>> Please see below a snippet of a few SNPs in my chromosome 16 just as
>> you would get them from 23andMe (NCBI36 assembly; columns mean
>> SNP_id/chr/position/genotype).
>>
>> Cheers,
>> Manuel
>>
>> rs7763        16      544555  TT
>> rs763158      16      546105  GG
>> rs7190878     16      549131  AG
>> rs4984890     16      552699  CT
>> rs710925      16      573355  AG
>> rs2017567     16      577213  CT
>> rs4144003     16      585969  CT
>> rs7190358     16      590789  AG
>> rs7203694     16      592942  AG
>> rs11248940    16      595687  TT
>> rs7204088     16      601143  TT
>> rs4984677     16      611683  AG
>> rs9929621     16      619413  CT
>> rs11642546    16      641657  CC
>> rs3752496     16      650256  TT
>> rs2301426     16      651906  GG
>> rs1044662     16      655061  CC
>> rs9934288     16      656288  AC
>> rs3752493     16      657524  TT
>> rs1139897     16      660987  GG
>> rs1045763     16      664085  CC
>> rs3830140     16      665336  AA
>> rs8056588     16      666190  CC
>> rs6597        16      671726  TT
>>
>>
>> Manuel Corpas, PhD
>> Tel:      +44.122349.2372
>> Web:    http://manuelcorpas.com/about/
>> Twitter: @manuelcorpas
>>
>>
>>
>> On 18 November 2011 15:14, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> wrote:
>>> 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 <jw12 at sanger.ac.uk> 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/
>>>>> jw12 at sanger.ac.uk
>>>>> 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
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>
>>>>
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>>>
>
>