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Jonathan Warren | 12 Apr 13:50
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ensembl das sources

http://das.ensembl.org/das/sources now contains a non redundant list of ensembl das sources that
points to archived ensembl instances using the new sources document specification and conforms to the
1.6 specification way of specifying data source uris
http://www.biodas.org/documents/spec-1.6.html#uris. This document is hosted by the Sanger but not
maintained by the ensembl project itself. The DAS data sources it points to are hosted by the ensembl
project however.

Any issues/suggestions then let me know.

Cheers

Jonathan.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 <at> sanger.ac.uk

--

-- 
 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.
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Jonathan Warren | 13 Mar 14:34
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DAS workshop outcomes 2012

Thanks to all those who attended the DAS workshop this year it was a great year in terms of developer outcomes
and we hope the tutorials on day 1 were useful for new users.

There is a section on the workshop page with outcomes of the workshop
http://www.biodas.org/wiki/DASWorkshop2012#Outcomes_from_workshop_2012 please feel free to add
further links and information there.
Thanks to David for all the great pictures available here
http://www.flickr.com/photos/davidmam/sets/72157629110016398/ looks to me like we were having a
good time :)

I'd personally like to thank the other tutors many of whom put in extra hours outside of work to make this a
successful workshop.

New users who attended the workshop my be interested to know that talks from last years workshop that
illustrate how DAS is being used in the wider community are available as video links from here: http://www.biodas.org/wiki/DASWorkshop2011#Day_2

Thanks again

Jonathan.

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
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Jim Procter | 22 Feb 12:08
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das developer day topics


Hi Jonathan and everyone.

I noticed that there are several topics listed on the developer day 
under 'developments since last meeting' for which there is no proposer 
(authentication/encryption in proserver is the one that caught my eye).

Who is going to talk about those topics ?

Jim.
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Jonathan Warren | 20 Jan 11:41
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DAS Workshop Registrations

Hi

If you are intending to come to the DAS workshop this year can you  
register soon as we would like to get an idea of numbers for the 3  
respective days (1st day tutorials and short talks, 2nd and 3rd day  
developers hackathon). This will then enable us to start firming up  
the schedule for the 3 days.
If you are not intending to come to the workshop can I ask for some  
feedback that may help us entice you in the future?

Many thanks

Jonathan.

See workshop email for you convenience below:

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes
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Dan Bolser | 12 Jan 19:09
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DAS2GFF3?

Hi,

Given a set of features in DAS format, what is the easiest way to
generate GFF3 format? Can most DAS server implementation be persuaded
to serve GFF3 in response to DAS feature requests?

Cheers,
Dan.
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Jonathan Warren | 12 Jan 14:21
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Personal genomics/Deploying a DAS server for Dummies/6 Easy steps

Hi

I've put some instructions for people with little or no technical  
ability and no access to IT personnel or servers, to be able to  
publish there genotype data from companies such as 23andme etc as a  
DAS source on the amazon cloud.

http://biodasman.wordpress.com/2012/01/12/easy-deployment-of-das-server-for-personal-genotype-data-to-the-amazon-cloud/

All someone needs is a tab delimited text file from one of these  
companies, a credit card and an internet connection. The instructions  
show them how to set up and deploy their server to the cloud in 6 easy  
steps and then view the data in Ensembl.

Example server can be accessed from here http://mychoiceofname.elasticbeanstalk.com/das/person1

Any comments suggestions welcomed.

Cheers

Jonathan.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 <at> sanger.ac.uk
Ext: 2314
Telephone: 01223 492314

--

--
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Jonathan Warren | 11 Jan 15:20
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Workshop 2012 format change

After some discussions and partly due to a lack of volunteers for  
talks we have decided to modify the DAS workshop format this year. The  
first day as per previous years will be tutorials and talks for new  
users of DAS. The second and third day will be for DAS developers as a  
hackathon to facilitate the implementation and updating of clients,  
servers and libraries to implement the latest 1.6E specifications.  
Thus for this year we are dispensing with the second day of talks  
which will hopefully be back in some form next year. The workshop  
registration page and registrations will be updated to reflect this  
change soon.

Any comments or suggestions please let us know.

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.
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Jonathan Warren | 5 Jan 10:49
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Registrations for DAS Workshop 2012

DAS is currently being used to share annotations on genomes, protein
alignments, structural and interaction information.

If you are interested in sharing biological information the DAS workshop
below may be of interest to you.

Learn of and contribute to current developments in DAS such as: DAS in  
the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative  
annotation projects, DAS alternative formats.

Registration is open for the 2012 DAS workshop (27-29 February) at the
Genome Campus, Hinxton UK. If you are interested in attending, please
find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html 
  and
register via the web link at the bottom of the page. This workshop will
cater for novice to expert DAS users as each day is optional.

Please register early as places will be limited. Registration closes  
10 February 2012 - 12:00.

If you are interested in giving a 15 minute talk on the second day  
please email Jonathan Warren using jonathan.warren <at> sanger.ac.uk

Many thanks

The Sanger/EBI DAS team.

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
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Jonathan Warren | 5 Jan 10:57
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workshop email

Hi DAS people.

I intend to circulate to other email lists the DAS workshop email just  
sent. If anyone has suggestions as to other email lists to post it to  
or would like to forward this email on to them (saves me registering  
on lots of lists :) ) then please do (but let me know so I don't  
duplicate posts).

List  I intend to use are:
gmod
biojava
ensembl
bioperl
Sanger/EBI campus

We could do with it being circulated around less developer focused  
lists e.g. plant focused user groups? More general biology lists?  
Suggestions?

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
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Jonathan Warren | 20 Dec 12:49
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DAS Workshop 2012 registration open

Please register at the link below if you are coming to the 2012 DAS  
workshop at the Sanger/EBI genome campus, Hinxton, Cambridge UK.
http://www.ebi.ac.uk/training/onsite/120227_DAS.html

If you would like to give a talk about work you have done/are doing  
with DAS please email me.

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.
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Jonathan Warren | 20 Dec 11:48
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Sanger DAS sources

If a client has the X-DAS-Version set to DAS/1.6E in the request  
header the Sanger DAS sources at http://das.sanger.ac.uk/das/sources  
will respond with 1.6 style XML responses. If no header is set for  
this or it does not contain the number 6 the DAS 1.53E xml responses  
will be returned (with the exception of about 10 data sources that are  
labelled 1.6E with a property in the sources response (<PROP  
name="spec" value="DAS/1.6E"/>).

In the future I hope that more genomic DAS clients will move to  
support DAS 1.6 but in the meantime this is the Sanger solution to  
backwards compatibility issues which normally will only effect data  
sources with groups/parent/parts. This way we can also support the  
clients that do offer support for DAS 1.6.

Any problems or suggestion as always feel free to email me.

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.
(Continue reading)

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