DAS registry is no longer available

Jalview Discussion
1

For information: the DAS (Distributed Annotation Service) is no longer supported at the Wellcome Trust Sanger Institute.

The end of this service was notified last year and has now arrived.

See http://www.dasregistry.org/

Implications for Jalview:

  1. the Sequence Fetcher (menu option File | Fetch Sequences…) now only offers a reduced list of (non-DAS) database sources:

EMBL, EMBL CDS, PDB, PFAM (Full/Seed), RFAM (Full/Seed), UNIPROT

  1. Web Service | Fetch DB References also now has a restricted selection list:

EMBL, EMBL CDS, PDB, UNIPROT, UNIPROT_NAME

If you were to open Tools | Java Console you may see an error message

GET request for “http://www.dasregistry.org/das//sources” resulted in 410 (Gone)

If any other related problems are noticed, please post to this list.

Thanks,

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

2

Hi All.

Here is how to reinstate your DAS settings. The URL below is a temporary fix provided courtesy of the EMBL-EBI, until the community has decided on the location for a new DAS registry.

1. Save your work and close any running Jalview instances

2. Open a new Jalview destkop and browse to the Jalview desktop preferences dialog (Tools->Preferences). Then, select the DAS Settings tab (you may need to hit the right-arrow icon at the top of the dialog on on a Mac to scroll to the tab).

3. Enter the following URL in the 'Use registry' field:
http://www.ebi.ac.uk/das-srv/registry/das/

4. Hit refresh. Jalview should now show a number of DAS sources.

5. Hit OK - your settings will be saved.

6. Close Jalview, then restart it again, and open the File->Fetch Sequences option from the Desktop menu bar or the alignment window if you have jalview configured to open a default file. You should find that the the set of available DAS datasources in the Sequence fetcher will now be fully populated.

As usual, please let us know if you experience any problems!
Jim.

···

On 01/05/2015 15:03, Mungo Carstairs (Staff) wrote:

For information: the DAS (Distributed Annotation Service) is no longer supported at the Wellcome Trust Sanger Institute.

The end of this service was notified last year and has now arrived.

See http://www.dasregistry.org/

Implications for Jalview:

1) the Sequence Fetcher (menu option /*File | Fetch Sequences...*/) now only offers a reduced list of (non-DAS) database sources:

EMBL, EMBL CDS, PDB, PFAM (Full/Seed), RFAM (Full/Seed), UNIPROT

2) */Web Service | Fetch DB References /*also now has a restricted selection list:

EMBL, EMBL CDS, PDB, UNIPROT, UNIPROT_NAME

If you were to open */Tools | Java Console/* you may see an error message

GET request for "http://www.dasregistry.org/das//sources" resulted in 410 (Gone)

If any other related problems are noticed, please post to this list.

Thanks,

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org <http://www.jalview.org/&gt;
www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/&gt;

The University of Dundee is a registered Scottish Charity, No: SC015096

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