Do you use the DAS sequence/annotation tools in Jalview ?

Dear jalview-discuss

I'm interested in finding out who uses Jalview's DAS sequence and annotation tools.

DAS is the way in which Jalview discovers ENSEMBL and NCBI genome sequence and annotation tracks. These are shown in the 'Sequence Fetcher' database dialog, and also listed in the 'DAS Settings' tab of the 'Sequence Feature Settings' panel in the Desktop.

The reason I ask is that the DAS infrastructure, which is mostly maintained by the Sanger Centre in the UK, will no longer be supported after May 2015. Up until that time, DAS services may well become unreliable. If you rely on certain DAS services, please let us know so we can look at alternative ways for Jalview to maintain access to those services!

Hear from you soon!
Jim.

Jim,

We had hoped to use DAS to expose our InterMine-based plant genomic data in Jalview (once we invest the modest effort to build a DAS adaptor for InterMine) but it sounds like we should rethink that. Is Sanger’s planned phase out of DAS support posted/discussed anywhere else? I didn’t see any notices to that effect at http://www.sanger.ac.uk/resources/software/das/

thanks,

-David

David M. Goodstein, Ph.D.
Phytozome Team Lead

Eukaryotic Data Systems - Computational and Plant Genomics

U.S. Dept of Energy Joint Genome Institute

2800 Mitchell Dr.
Walnut Creek, CA USA 94598
http://phytozome.jgi.doe.gov

postbox-contact.jpg

···

Hi David.

Sorry if I’ve set alarm bells ringing! I had an unofficial heads up regarding these plans, and I understand that official announcements are currently being finalized.

I can say, however, that there are at least 12 months of support left, so this is not an emergency situation. Also, from Jalview’s perspective, we have no plans to drop DAS support from the desktop, and it would be quite straightforward to replace the current registry URL with one or more alternative defaults. What I’d like to do is work out what the best solution will be for Jalview users.

I anticipate there will be some discussion over at the biodas in the near future. I’ll post a message on this thread as and when I have more information.

Jim.

postbox-contact.jpg

···

Hi Jim,

The announcement of the DAS Registry closure in 2015 is on the website:
http://www.dasregistry.org/.

DAS itself is a protocol (see http://www.biodas.org/) and is implemented
in a number of DAS servers and systems with DAS service interfaces.
There are also many clients for DAS. So providing and consuming DAS
services will remain viable. It is just the central hub for DAS service
discovery that is going to go away.

FWIW I am aware of discussions in the past to integrate the DAS Registry
data in to other service registries. I don't know if the DAS Registry
are planning to discuss options with other service registries during
their phase out period, but for those interested in having a central
registry in future it may be worth letting them know about the other
service registries you are using and suggest that at least some data
about the services could be transferred before the final shutdown of the
DAS Registry service.

All the best,

Hamish

···

On 02/06/14 20:24, jprocter@compbio.dundee.ac.uk wrote:

Hi David.

Sorry if I've set alarm bells ringing! I had an unofficial heads up
regarding these plans, and I understand that official announcements are
currently being finalized.

I can say, however, that there are at least 12 months of support left,
so this is not an emergency situation. Also, from Jalview's perspective,
we have no plans to drop DAS support from the desktop, and it would be
quite straightforward to replace the current registry URL with one or
more alternative defaults. What I'd like to do is work out what the best
solution will be for Jalview users.

I anticipate there will be some discussion over at the biodas in the
near future. I'll post a message on this thread as and when I have more
information.

Jim.

Sent from my android device.

-----Original Message-----
From: "David M. Goodstein" <dmgoodstein@lbl.gov>
To: Jim Procter <jprocter@compbio.dundee.ac.uk>
Cc: "Jalview-discuss@jalview.org" <Jalview-discuss@jalview.org>
Sent: Mon, 02 Jun 2014 6:30 PM
Subject: Re: [Jalview-discuss] Do you use the DAS sequence/annotation
tools in Jalview ?

Jim,

  We had hoped to use DAS to expose our InterMine-based plant genomic
data in Jalview (once we invest the modest effort to build a DAS adaptor
for InterMine) but it sounds like we should rethink that. Is Sanger's
planned phase out of DAS support posted/discussed anywhere else? I
didn't see any notices to that effect at
http://www.sanger.ac.uk/resources/software/das/

thanks,

-David

David M. Goodstein, Ph.D.
Phytozome Team Lead
Eukaryotic Data Systems - Computational and Plant Genomics
U.S. Dept of Energy Joint Genome Institute
2800 Mitchell Dr.
Walnut Creek, CA USA 94598
http://phytozome.jgi.doe.gov <http://www.phytozome.net>

Jim Procter <mailto:jprocter@compbio.dundee.ac.uk>
June 2, 2014 at 6:42 AM
Dear jalview-discuss

I'm interested in finding out who uses Jalview's DAS sequence and
annotation tools.

DAS is the way in which Jalview discovers ENSEMBL and NCBI genome
sequence and annotation tracks. These are shown in the 'Sequence
Fetcher' database dialog, and also listed in the 'DAS Settings' tab of
the 'Sequence Feature Settings' panel in the Desktop.

The reason I ask is that the DAS infrastructure, which is mostly
maintained by the Sanger Centre in the UK, will no longer be supported
after May 2015. Up until that time, DAS services may well become
unreliable. If you rely on certain DAS services, please let us know so
we can look at alternative ways for Jalview to maintain access to those
services!

Hear from you soon!
Jim.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
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--

Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/

Hi Hamish.

The announcement of the DAS Registry closure in 2015 is on the website:
http://www.dasregistry.org/.

yes - it doesn't have all the details yet though. I'm waiting for a message to appear on das@biodas.org so the conversation can start.

It is just the central hub for DAS service
discovery that is going to go away.

Yes. That's kind of a problem, though, since DAS1.6 doesn't include support for multiple registries out of the box, and the 'DAS way' was to use a single default registry. Most likely, future versions of Jalview will use Jalview's own service registry to autodiscover DAS registry settings. (This may also have the side effect of allowing anyone to set up their own registry via a JABA server!).

FWIW I am aware of discussions in the past to integrate the DAS Registry
data in to other service registries. I don't know if the DAS Registry
are planning to discuss options with other service registries during
their phase out period, but for those interested in having a central
registry in future it may be worth letting them know about the other
service registries you are using and suggest that at least some data
about the services could be transferred before the final shutdown of the
DAS Registry service.

We'll wait and see what emerges! I can think of a few profitable routes here (perhaps involving http://www.elixir-europe.org/services/elixir-denmark ), but practically all of them depend on the actions of others :slight_smile:

Jim.

···

On 03/06/2014 08:48, Hamish McWilliam wrote: