[DAS] Important : 1.6 Specification release

[Jonathan Warren]

Hello fellow DAS developers.

We are now approaching the 2010 DAS workshop (April 7-9th  http://www.ebi.ac.uk/training/onsite/DAS_070410.html) 
  being held at the Sanger/EBI genome campus.
The DAS 1.6 specification ( http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html 
  ) has been written over the past year and we are approaching what we  
hope will be the final draft especially related to genomic DAS. It is  
our hope that client developers and data providers alike will develop  
and test the new 1.6 spec over the next couple of months. At the  
workshop we can discuss issues/improvements and decide on an official  
release date or just accept the new spec as official and release it.

DAS clients will need to be able to handle the new 1.6 sources in some  
way - these sources should be identified by the correct header X-DAS- 
Version being sent (DAS/1.6 or DAS/1.6E) with any responses from a 1.6  
server.

The main change that will affect developers is the parent/parts usage  
instead of Group, but there are many other improvements and  
consolidations which the community had agreed last year would be  
useful. A list of changes taken from the spec is listed at the end of  
this email.

Development so far:

We have 1.6 specification development versions of Proserver (svn co https://proserver.svn.sourceforge.net/svnroot/proserver/branches/1.6-spec) 
  and Dazzle (svn co http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle) 
  available from SVN available for testing and development. The  
registry will now validate and accept 1.6 specification DAS sources, a  
list of which can be found using the web interface or requests to http://www.dasregistry.org/das1.6/sources 
  note at the moment 1.6 sources will not be listed in the standard  
sources request (http://www.dasregistry.org/das/sources ) until the  
specification is official. Please register any new 1.6 sources you  
have created as examples to others.

A new version of Dasobert will soon be available as part of the  
Biojava Version 3 development and a new version of Bio::Das::Lite.

Some specimen 1.6 sources will be available in the registry soon as  
examples.



CHANGES:
    This version mainly introduces concepts and extensions that are  
already in use but yet to be incorporated into the specification.

Nonpositional annotations are now supported.
Introduced the concept of "coordinate systems" and the DAS Registry.
Relaxed the constraints on data source names.
Clarified the use of HTTP and DAS status codes.
Added requirement for clients to include specific request headers.
All command responses are now described by RELAX NG schemas.
New commands: sources, structure and alignment. These commands are  
taken from DAS 1.53E, with some changes.
Deprecated commands: dsn, dna and link.
Entry points command gained "paging", and other minor changes.
Features command gained hierarchical referencing, in favour of groups.
Several elements in the features command response are now optional.
Features command gained "maxbins".
Unified the format of segment XML across all commands.
Added support for using ontologies in annotations.
Stylesheets now support histograms, colour gradients and line plots,  
more colours, and are better characterised. The "toomany" glyph is  
deprecated.
Clarified the content of attributes across several commands, such as  
segment versions.

Thanks

Jonathan Warren, Andy Jenkinson and the DAS developers at the Sanger/ 
EBI.



Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk








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