From jw12 at sanger.ac.uk  Wed Nov  2 11:57:15 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Wed, 2 Nov 2011 15:57:15 +0000
Subject: [DAS] Java DAS hackathon 1st December.
Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E@sanger.ac.uk>

Hi

There are at least 4 of us meeting up on the Sanger/EBI genome campus  
(Thursday 1st December) to write some code for the new Java DAS  
library (JDAS http://code.google.com/p/jdas/).
The main focus will be on making sure the new library has all the  
"essential" capabilities of the old Dasobert library and some new  
features.

We would like to extend an open invitation to Java developers in the  
DAS community. If you would like to attend and contribute then please  
drop me a line. We would be especially interested in having someone  
with expertise/interest in DAS structure or Alignment clients.
If you have any suggestions or burning needs for support to be  
included in the JDAS library you can also write to me or post to the  
list.

For inclusion (some of which has/will be implemented by 1 December):
Support for concurrency (Threads and queue management).
Support for alignment and structure queries/responses.
JSON support.
Writeback functionality (xml and JSON).
Registry sources filtering support.
Support for reading/writing JSON.

As always any contributions and suggestions welcome.
After the hackathon we would also welcome any offers of testing in  
real world situations?

Many thanks

The Sanger/EBI DAS team.


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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jrmacias at cnb.csic.es  Thu Nov  3 12:32:46 2011
From: jrmacias at cnb.csic.es (Jose-Ramon Macias)
Date: Thu, 3 Nov 2011 17:32:46 +0100
Subject: [DAS] DAS Digest, Vol 59, Issue 2
In-Reply-To: <mailman.15.1320336006.24072.das@lists.open-bio.org>
References: <mailman.15.1320336006.24072.das@lists.open-bio.org>
Message-ID: <8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>

Hi Jonathan,
I won't be able to attend physically, but would be very interested in any development regarding JDAS and the replacement for DasObert. Could I contribute from the distance ? How ? I'll be eager to test the resulting stuff, anyway.


On Nov 3, 2011, at 17:00, das-request at lists.open-bio.org wrote:

> Send DAS mailing list submissions to
> 	das at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/das
> or, via email, send a message with subject or body 'help' to
> 	das-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	das-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of DAS digest..."
> 
> 
> Today's Topics:
> 
>   1. Java DAS hackathon 1st December. (Jonathan Warren)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 2 Nov 2011 15:57:15 +0000
> From: Jonathan Warren <jw12 at sanger.ac.uk>
> Subject: [DAS] Java DAS hackathon 1st December.
> To: das at biodas.org
> Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E at sanger.ac.uk>
> Content-Type: text/plain;	charset=US-ASCII;	format=flowed;	delsp=yes
> 
> Hi
> 
> There are at least 4 of us meeting up on the Sanger/EBI genome campus  
> (Thursday 1st December) to write some code for the new Java DAS  
> library (JDAS http://code.google.com/p/jdas/).
> The main focus will be on making sure the new library has all the  
> "essential" capabilities of the old Dasobert library and some new  
> features.
> 
> We would like to extend an open invitation to Java developers in the  
> DAS community. If you would like to attend and contribute then please  
> drop me a line. We would be especially interested in having someone  
> with expertise/interest in DAS structure or Alignment clients.
> If you have any suggestions or burning needs for support to be  
> included in the JDAS library you can also write to me or post to the  
> list.
> 
> For inclusion (some of which has/will be implemented by 1 December):
> Support for concurrency (Threads and queue management).
> Support for alignment and structure queries/responses.
> JSON support.
> Writeback functionality (xml and JSON).
> Registry sources filtering support.
> Support for reading/writing JSON.
> 
> As always any contributions and suggestions welcome.
> After the hackathon we would also welcome any offers of testing in  
> real world situations?
> 
> Many thanks
> 
> The Sanger/EBI DAS team.
> 
> 
> 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 Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> 
> 
> ------------------------------
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
> 
> 
> End of DAS Digest, Vol 59, Issue 2
> **********************************

Jose-Ramon Macias

Unidad de Biocomputaci?n
Centro Nacional de Biotecnolog?a (CNB-CSIC)
Darwin, 3. 28049 Madrid.



From jw12 at sanger.ac.uk  Thu Nov  3 13:25:59 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 3 Nov 2011 17:25:59 +0000
Subject: [DAS] DAS Digest, Vol 59, Issue 2
In-Reply-To: <8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>
References: <mailman.15.1320336006.24072.das@lists.open-bio.org>
	<8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>
Message-ID: <923B0411-5ED2-4696-A23E-ACC772C52EDA@sanger.ac.uk>

Hi Jose

Great Jose. If you don't mind using Skype I'm sure you can contribute  
remotely.
If you get in touch closer to the time we can sort it out.

Cheers

Jonathan.

On 3 Nov 2011, at 16:32, Jose-Ramon Macias wrote:

> Hi Jonathan,
> I won't be able to attend physically, but would be very interested  
> in any development regarding JDAS and the replacement for DasObert.  
> Could I contribute from the distance ? How ? I'll be eager to test  
> the resulting stuff, anyway.
>
>
> On Nov 3, 2011, at 17:00, das-request at lists.open-bio.org wrote:
>
>> Send DAS mailing list submissions to
>> 	das at lists.open-bio.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://lists.open-bio.org/mailman/listinfo/das
>> or, via email, send a message with subject or body 'help' to
>> 	das-request at lists.open-bio.org
>>
>> You can reach the person managing the list at
>> 	das-owner at lists.open-bio.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of DAS digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Java DAS hackathon 1st December. (Jonathan Warren)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 2 Nov 2011 15:57:15 +0000
>> From: Jonathan Warren <jw12 at sanger.ac.uk>
>> Subject: [DAS] Java DAS hackathon 1st December.
>> To: das at biodas.org
>> Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E at sanger.ac.uk>
>> Content-Type: text/plain;	charset=US-ASCII;	format=flowed;	delsp=yes
>>
>> Hi
>>
>> There are at least 4 of us meeting up on the Sanger/EBI genome campus
>> (Thursday 1st December) to write some code for the new Java DAS
>> library (JDAS http://code.google.com/p/jdas/).
>> The main focus will be on making sure the new library has all the
>> "essential" capabilities of the old Dasobert library and some new
>> features.
>>
>> We would like to extend an open invitation to Java developers in the
>> DAS community. If you would like to attend and contribute then please
>> drop me a line. We would be especially interested in having someone
>> with expertise/interest in DAS structure or Alignment clients.
>> If you have any suggestions or burning needs for support to be
>> included in the JDAS library you can also write to me or post to the
>> list.
>>
>> For inclusion (some of which has/will be implemented by 1 December):
>> Support for concurrency (Threads and queue management).
>> Support for alignment and structure queries/responses.
>> JSON support.
>> Writeback functionality (xml and JSON).
>> Registry sources filtering support.
>> Support for reading/writing JSON.
>>
>> As always any contributions and suggestions welcome.
>> After the hackathon we would also welcome any offers of testing in
>> real world situations?
>>
>> Many thanks
>>
>> The Sanger/EBI DAS team.
>>
>>
>> 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 Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>> End of DAS Digest, Vol 59, Issue 2
>> **********************************
>
> Jose-Ramon Macias
>
> Unidad de Biocomputaci?n
> Centro Nacional de Biotecnolog?a (CNB-CSIC)
> Darwin, 3. 28049 Madrid.
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jw12 at sanger.ac.uk  Thu Nov 17 07:15:35 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Nov 2011 12:15:35 +0000
Subject: [DAS] More info Survey on DAS projects
Message-ID: <C27EE4EF-1760-4BE1-82ED-F84F4B07D8CC@sanger.ac.uk>

I forgot to add:

If you are interested in giving a talk please reply by the 1st of  
December (2 weeks from now) as we will need to start organising the  
format of this years workshop.

Many thanks


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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jw12 at sanger.ac.uk  Thu Nov 17 07:11:14 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Nov 2011 12:11:14 +0000
Subject: [DAS] Survey on DAS projects
Message-ID: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From mc at manuelcorpas.com  Thu Nov 17 12:11:08 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Thu, 17 Nov 2011 17:11:08 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
Message-ID: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>

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
>


From jw12 at sanger.ac.uk  Fri Nov 18 05:15:18 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Fri, 18 Nov 2011 10:15:18 +0000
Subject: [DAS] Genotype MyDAS adapter
In-Reply-To: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
Message-ID: <3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>

Thanks Manuel, that's exactly the sort of reply we are hoping for.  
It's great if people want to publicise what they are doing on the list.

In addition I should add that if people wish to distribute 23AndMe  
data via DAS I have developed a very simple MyDAS adapter for this  
purpose that comes with the current myDAS download (http://code.google.com/p/mydas/ 
).
Comprehensive instructions for setting up the database and uploading  
the data file can be found here: http://biodasman.wordpress.com/2011/11/04/how-to-create-a-genotype-database-for-use-as-a-das-source/
The configuration for connecting to this database is also in MyDAS and  
the blog.

Obviously this isn't an automatic set-up via a pretty interface, but  
it's relatively simple for anyone with a degree of technical ability  
to do in the mean time.

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
>>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From mc at manuelcorpas.com  Fri Nov 18 05:28:13 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Fri, 18 Nov 2011 10:28:13 +0000
Subject: [DAS] Genotype MyDAS adapter
In-Reply-To: <3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>
Message-ID: <CALZuiYLCia_UzXzeSNR+6LAMHroLHyX59=Bb7UJ8MdAs6z0NCg@mail.gmail.com>

Hi Jonathan,

thanks, this is really helpful.

Please find in this link my genotype data* should anyone would like to
give it a try with real data:

http://mykaryoview.com/data/son.txt.zip

Manuel

*my genotype data has CC BY-SA 3.0 License: you are able to copy,
distribute and transmit the work as long as you acknowledge the
source.

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



On 18 November 2011 10:15, Jonathan Warren <jw12 at sanger.ac.uk> wrote:
> Thanks Manuel, that's exactly the sort of reply we are hoping for.?It's
> great if people want to publicise what they are doing on the list.
> In addition I should add that if people wish to distribute 23AndMe data via
> DAS I have developed a very simple MyDAS adapter for this purpose that comes
> with the current myDAS download (http://code.google.com/p/mydas/).
> Comprehensive instructions for setting up the database and uploading the
> data file can be found
> here:?http://biodasman.wordpress.com/2011/11/04/how-to-create-a-genotype-database-for-use-as-a-das-source/
> The configuration for connecting to this database is also in MyDAS and the
> blog.
> Obviously this isn't an automatic set-up via a pretty interface, but it's
> relatively simple for anyone with a degree of technical ability to do in the
> mean time.
> 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
>
>
> 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 Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>


From andy.jenkinson at ebi.ac.uk  Fri Nov 18 10:14:02 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 18 Nov 2011 15:14:02 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
Message-ID: <1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>

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
>> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das



From mc at manuelcorpas.com  Fri Nov 18 10:24:59 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Fri, 18 Nov 2011 15:24:59 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
Message-ID: <CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>

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
>>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
>


From andy.jenkinson at ebi.ac.uk  Fri Nov 18 18:33:51 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 18 Nov 2011 23:33:51 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
Message-ID: <C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>

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
>>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
>> 



From mc at manuelcorpas.com  Sat Nov 19 10:58:16 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Sat, 19 Nov 2011 15:58:16 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
	<C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
Message-ID: <CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>

> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>>
>
>


From jw12 at sanger.ac.uk  Thu Nov 24 12:19:37 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 24 Nov 2011 17:19:37 +0000
Subject: [DAS] DAS projects/Future of DAS
In-Reply-To: <CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
	<C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
	<CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>
Message-ID: <A8A35A85-A88F-492C-903E-BE5A505DA38A@sanger.ac.uk>

Hi Manuel

Thanks again for the input ;)

I agree with Andy that a generic DAS upload/server is going to be  
inherently complicated and will be limited by the upload across the  
internet. To a large degree the DAS system came about to stop large  
amounts of data needing to be uploaded or downloaded over the net.
However I can see that having DAS "nodes" such as the EBI and Sanger  
etc with tailor made upload user interfaces and servers for specific  
data types is a reasonable solution/addition to the DAS system. To  
this end, I'm already more than half way to a solution for your needs  
(which doesn't need a database) which we could use, subject to Sanger  
approval. This solution could also be made more generic for other data  
sources as well with a specific interface developed for each.

As to the future of DAS - I believe that over the last 3 years we have  
improved the DAS protocol and many of the associated implementations  
so that we now have dispensed with many if not all of the previous  
criticisms people have had of the DAS system (1.6E spec):
Validation has improved the level of conformity to the DAS spec and  
new servers (MyDAS and Proserver) now behave in the same way for both  
requests and responses.
You can now search DAS sources (MyDAS).
Next feature capability (in the spec and Proserver).
You can have alternative content that will require less bandwidth e.g  
JSON (the Registry serves this already and soon MyDAS  servers and  
proserver hopefully).
We have writeback servers (MyDAS)-(already implemented at the EBI for  
proteins and an example server available soon that will accept posts  
and puts at the Sanger for genomic sources).

Really we NEED the community to come together and put data up using  
these new servers and for major clients such as Ensembl to start  
supporting 1.6 spec servers and the newer "Extended" features. The  
Dalliance browser by Thomas Down proves how fast a DAS client can be.  
I believe there is a lot more potential for the DAS system and it's  
still a good solution for today's data distribution needs.

Cheers

Jonathan.



On 19 Nov 2011, at 15:58, Manuel Corpas wrote:

>> 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
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>
>>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jw12 at sanger.ac.uk  Wed Nov  2 15:57:15 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Wed, 2 Nov 2011 15:57:15 +0000
Subject: [DAS] Java DAS hackathon 1st December.
Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E@sanger.ac.uk>

Hi

There are at least 4 of us meeting up on the Sanger/EBI genome campus  
(Thursday 1st December) to write some code for the new Java DAS  
library (JDAS http://code.google.com/p/jdas/).
The main focus will be on making sure the new library has all the  
"essential" capabilities of the old Dasobert library and some new  
features.

We would like to extend an open invitation to Java developers in the  
DAS community. If you would like to attend and contribute then please  
drop me a line. We would be especially interested in having someone  
with expertise/interest in DAS structure or Alignment clients.
If you have any suggestions or burning needs for support to be  
included in the JDAS library you can also write to me or post to the  
list.

For inclusion (some of which has/will be implemented by 1 December):
Support for concurrency (Threads and queue management).
Support for alignment and structure queries/responses.
JSON support.
Writeback functionality (xml and JSON).
Registry sources filtering support.
Support for reading/writing JSON.

As always any contributions and suggestions welcome.
After the hackathon we would also welcome any offers of testing in  
real world situations?

Many thanks

The Sanger/EBI DAS team.


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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jrmacias at cnb.csic.es  Thu Nov  3 16:32:46 2011
From: jrmacias at cnb.csic.es (Jose-Ramon Macias)
Date: Thu, 3 Nov 2011 17:32:46 +0100
Subject: [DAS] DAS Digest, Vol 59, Issue 2
In-Reply-To: <mailman.15.1320336006.24072.das@lists.open-bio.org>
References: <mailman.15.1320336006.24072.das@lists.open-bio.org>
Message-ID: <8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>

Hi Jonathan,
I won't be able to attend physically, but would be very interested in any development regarding JDAS and the replacement for DasObert. Could I contribute from the distance ? How ? I'll be eager to test the resulting stuff, anyway.


On Nov 3, 2011, at 17:00, das-request at lists.open-bio.org wrote:

> Send DAS mailing list submissions to
> 	das at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.open-bio.org/mailman/listinfo/das
> or, via email, send a message with subject or body 'help' to
> 	das-request at lists.open-bio.org
> 
> You can reach the person managing the list at
> 	das-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of DAS digest..."
> 
> 
> Today's Topics:
> 
>   1. Java DAS hackathon 1st December. (Jonathan Warren)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 2 Nov 2011 15:57:15 +0000
> From: Jonathan Warren <jw12 at sanger.ac.uk>
> Subject: [DAS] Java DAS hackathon 1st December.
> To: das at biodas.org
> Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E at sanger.ac.uk>
> Content-Type: text/plain;	charset=US-ASCII;	format=flowed;	delsp=yes
> 
> Hi
> 
> There are at least 4 of us meeting up on the Sanger/EBI genome campus  
> (Thursday 1st December) to write some code for the new Java DAS  
> library (JDAS http://code.google.com/p/jdas/).
> The main focus will be on making sure the new library has all the  
> "essential" capabilities of the old Dasobert library and some new  
> features.
> 
> We would like to extend an open invitation to Java developers in the  
> DAS community. If you would like to attend and contribute then please  
> drop me a line. We would be especially interested in having someone  
> with expertise/interest in DAS structure or Alignment clients.
> If you have any suggestions or burning needs for support to be  
> included in the JDAS library you can also write to me or post to the  
> list.
> 
> For inclusion (some of which has/will be implemented by 1 December):
> Support for concurrency (Threads and queue management).
> Support for alignment and structure queries/responses.
> JSON support.
> Writeback functionality (xml and JSON).
> Registry sources filtering support.
> Support for reading/writing JSON.
> 
> As always any contributions and suggestions welcome.
> After the hackathon we would also welcome any offers of testing in  
> real world situations?
> 
> Many thanks
> 
> The Sanger/EBI DAS team.
> 
> 
> 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 Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> 
> 
> ------------------------------
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
> 
> 
> End of DAS Digest, Vol 59, Issue 2
> **********************************

Jose-Ramon Macias

Unidad de Biocomputaci?n
Centro Nacional de Biotecnolog?a (CNB-CSIC)
Darwin, 3. 28049 Madrid.




From jw12 at sanger.ac.uk  Thu Nov  3 17:25:59 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 3 Nov 2011 17:25:59 +0000
Subject: [DAS] DAS Digest, Vol 59, Issue 2
In-Reply-To: <8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>
References: <mailman.15.1320336006.24072.das@lists.open-bio.org>
	<8252CA57-DCEC-4CB2-B544-BA60EEDD2732@cnb.csic.es>
Message-ID: <923B0411-5ED2-4696-A23E-ACC772C52EDA@sanger.ac.uk>

Hi Jose

Great Jose. If you don't mind using Skype I'm sure you can contribute  
remotely.
If you get in touch closer to the time we can sort it out.

Cheers

Jonathan.

On 3 Nov 2011, at 16:32, Jose-Ramon Macias wrote:

> Hi Jonathan,
> I won't be able to attend physically, but would be very interested  
> in any development regarding JDAS and the replacement for DasObert.  
> Could I contribute from the distance ? How ? I'll be eager to test  
> the resulting stuff, anyway.
>
>
> On Nov 3, 2011, at 17:00, das-request at lists.open-bio.org wrote:
>
>> Send DAS mailing list submissions to
>> 	das at lists.open-bio.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://lists.open-bio.org/mailman/listinfo/das
>> or, via email, send a message with subject or body 'help' to
>> 	das-request at lists.open-bio.org
>>
>> You can reach the person managing the list at
>> 	das-owner at lists.open-bio.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of DAS digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Java DAS hackathon 1st December. (Jonathan Warren)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 2 Nov 2011 15:57:15 +0000
>> From: Jonathan Warren <jw12 at sanger.ac.uk>
>> Subject: [DAS] Java DAS hackathon 1st December.
>> To: das at biodas.org
>> Message-ID: <28054914-049C-4F9F-BC19-BD299DA41A3E at sanger.ac.uk>
>> Content-Type: text/plain;	charset=US-ASCII;	format=flowed;	delsp=yes
>>
>> Hi
>>
>> There are at least 4 of us meeting up on the Sanger/EBI genome campus
>> (Thursday 1st December) to write some code for the new Java DAS
>> library (JDAS http://code.google.com/p/jdas/).
>> The main focus will be on making sure the new library has all the
>> "essential" capabilities of the old Dasobert library and some new
>> features.
>>
>> We would like to extend an open invitation to Java developers in the
>> DAS community. If you would like to attend and contribute then please
>> drop me a line. We would be especially interested in having someone
>> with expertise/interest in DAS structure or Alignment clients.
>> If you have any suggestions or burning needs for support to be
>> included in the JDAS library you can also write to me or post to the
>> list.
>>
>> For inclusion (some of which has/will be implemented by 1 December):
>> Support for concurrency (Threads and queue management).
>> Support for alignment and structure queries/responses.
>> JSON support.
>> Writeback functionality (xml and JSON).
>> Registry sources filtering support.
>> Support for reading/writing JSON.
>>
>> As always any contributions and suggestions welcome.
>> After the hackathon we would also welcome any offers of testing in
>> real world situations?
>>
>> Many thanks
>>
>> The Sanger/EBI DAS team.
>>
>>
>> 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 Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>> End of DAS Digest, Vol 59, Issue 2
>> **********************************
>
> Jose-Ramon Macias
>
> Unidad de Biocomputaci?n
> Centro Nacional de Biotecnolog?a (CNB-CSIC)
> Darwin, 3. 28049 Madrid.
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 



From jw12 at sanger.ac.uk  Thu Nov 17 12:15:35 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Nov 2011 12:15:35 +0000
Subject: [DAS] More info Survey on DAS projects
Message-ID: <C27EE4EF-1760-4BE1-82ED-F84F4B07D8CC@sanger.ac.uk>

I forgot to add:

If you are interested in giving a talk please reply by the 1st of  
December (2 weeks from now) as we will need to start organising the  
format of this years workshop.

Many thanks


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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jw12 at sanger.ac.uk  Thu Nov 17 12:11:14 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Nov 2011 12:11:14 +0000
Subject: [DAS] Survey on DAS projects
Message-ID: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From mc at manuelcorpas.com  Thu Nov 17 17:11:08 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Thu, 17 Nov 2011 17:11:08 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
Message-ID: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>

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
>



From jw12 at sanger.ac.uk  Fri Nov 18 10:15:18 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Fri, 18 Nov 2011 10:15:18 +0000
Subject: [DAS] Genotype MyDAS adapter
In-Reply-To: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
Message-ID: <3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>

Thanks Manuel, that's exactly the sort of reply we are hoping for.  
It's great if people want to publicise what they are doing on the list.

In addition I should add that if people wish to distribute 23AndMe  
data via DAS I have developed a very simple MyDAS adapter for this  
purpose that comes with the current myDAS download (http://code.google.com/p/mydas/ 
).
Comprehensive instructions for setting up the database and uploading  
the data file can be found here: http://biodasman.wordpress.com/2011/11/04/how-to-create-a-genotype-database-for-use-as-a-das-source/
The configuration for connecting to this database is also in MyDAS and  
the blog.

Obviously this isn't an automatic set-up via a pretty interface, but  
it's relatively simple for anyone with a degree of technical ability  
to do in the mean time.

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
>>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From mc at manuelcorpas.com  Fri Nov 18 10:28:13 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Fri, 18 Nov 2011 10:28:13 +0000
Subject: [DAS] Genotype MyDAS adapter
In-Reply-To: <3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<3A134B95-E6BD-486D-B9D0-A8721B345C07@sanger.ac.uk>
Message-ID: <CALZuiYLCia_UzXzeSNR+6LAMHroLHyX59=Bb7UJ8MdAs6z0NCg@mail.gmail.com>

Hi Jonathan,

thanks, this is really helpful.

Please find in this link my genotype data* should anyone would like to
give it a try with real data:

http://mykaryoview.com/data/son.txt.zip

Manuel

*my genotype data has CC BY-SA 3.0 License: you are able to copy,
distribute and transmit the work as long as you acknowledge the
source.

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



On 18 November 2011 10:15, Jonathan Warren <jw12 at sanger.ac.uk> wrote:
> Thanks Manuel, that's exactly the sort of reply we are hoping for.?It's
> great if people want to publicise what they are doing on the list.
> In addition I should add that if people wish to distribute 23AndMe data via
> DAS I have developed a very simple MyDAS adapter for this purpose that comes
> with the current myDAS download (http://code.google.com/p/mydas/).
> Comprehensive instructions for setting up the database and uploading the
> data file can be found
> here:?http://biodasman.wordpress.com/2011/11/04/how-to-create-a-genotype-database-for-use-as-a-das-source/
> The configuration for connecting to this database is also in MyDAS and the
> blog.
> Obviously this isn't an automatic set-up via a pretty interface, but it's
> relatively simple for anyone with a degree of technical ability to do in the
> mean time.
> 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
>
>
> 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 Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>



From andy.jenkinson at ebi.ac.uk  Fri Nov 18 15:14:02 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 18 Nov 2011 15:14:02 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
Message-ID: <1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>

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
>> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From mc at manuelcorpas.com  Fri Nov 18 15:24:59 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Fri, 18 Nov 2011 15:24:59 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
Message-ID: <CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>

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
>>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
>



From andy.jenkinson at ebi.ac.uk  Fri Nov 18 23:33:51 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 18 Nov 2011 23:33:51 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
Message-ID: <C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>

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
>>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
>> 




From mc at manuelcorpas.com  Sat Nov 19 15:58:16 2011
From: mc at manuelcorpas.com (Manuel Corpas)
Date: Sat, 19 Nov 2011 15:58:16 +0000
Subject: [DAS] Survey on DAS projects
In-Reply-To: <C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
	<C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
Message-ID: <CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>

> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>>
>
>



From jw12 at sanger.ac.uk  Thu Nov 24 17:19:37 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 24 Nov 2011 17:19:37 +0000
Subject: [DAS] DAS projects/Future of DAS
In-Reply-To: <CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>
References: <4A0F0B2F-D98C-4B88-BC48-104607F9E526@sanger.ac.uk>
	<CALZuiYL6+p09nrCpQpMEitZcWd5mZjmDbD68OuLngo85coZq2A@mail.gmail.com>
	<1C57BEA4-3B0A-4CBE-8308-97D418D2F243@ebi.ac.uk>
	<CALZuiYKUj8sL8vic-5t7CmB30atVBquaXH1UCj-4SDBq=svnmg@mail.gmail.com>
	<C4DEEEE6-5A45-4594-9A02-EA4AB88F0904@ebi.ac.uk>
	<CALZuiYLHiDcs08h0Sjp27yvWvp6FHDMDEuH8Qf3rgwUMvss77w@mail.gmail.com>
Message-ID: <A8A35A85-A88F-492C-903E-BE5A505DA38A@sanger.ac.uk>

Hi Manuel

Thanks again for the input ;)

I agree with Andy that a generic DAS upload/server is going to be  
inherently complicated and will be limited by the upload across the  
internet. To a large degree the DAS system came about to stop large  
amounts of data needing to be uploaded or downloaded over the net.
However I can see that having DAS "nodes" such as the EBI and Sanger  
etc with tailor made upload user interfaces and servers for specific  
data types is a reasonable solution/addition to the DAS system. To  
this end, I'm already more than half way to a solution for your needs  
(which doesn't need a database) which we could use, subject to Sanger  
approval. This solution could also be made more generic for other data  
sources as well with a specific interface developed for each.

As to the future of DAS - I believe that over the last 3 years we have  
improved the DAS protocol and many of the associated implementations  
so that we now have dispensed with many if not all of the previous  
criticisms people have had of the DAS system (1.6E spec):
Validation has improved the level of conformity to the DAS spec and  
new servers (MyDAS and Proserver) now behave in the same way for both  
requests and responses.
You can now search DAS sources (MyDAS).
Next feature capability (in the spec and Proserver).
You can have alternative content that will require less bandwidth e.g  
JSON (the Registry serves this already and soon MyDAS  servers and  
proserver hopefully).
We have writeback servers (MyDAS)-(already implemented at the EBI for  
proteins and an example server available soon that will accept posts  
and puts at the Sanger for genomic sources).

Really we NEED the community to come together and put data up using  
these new servers and for major clients such as Ensembl to start  
supporting 1.6 spec servers and the newer "Extended" features. The  
Dalliance browser by Thomas Down proves how fast a DAS client can be.  
I believe there is a lot more potential for the DAS system and it's  
still a good solution for today's data distribution needs.

Cheers

Jonathan.



On 19 Nov 2011, at 15:58, Manuel Corpas wrote:

>> 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
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>
>>

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 Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.