[DAS] plans for 1.6 release

Jonathan Warren jw12 at sanger.ac.uk
Fri Sep 3 10:02:32 UTC 2010

Hi Thomas and Andy

Thanks for posting this to the list.
I don't think from our brief discussions at the Sanger/EBI that people  
here would object to moving to the DAS2 way for parents/parts. My  
impression of the DAS2 spec was that it was thought about and  
discussed in great detail and thus there would be very good reasons  
for doing it this way? Also an advantage of moving to this way is that  
it has been tested by people implementing DAS2 extensively already?
As the DAS 1.6 spec is in pretty much every other respect (apart from  
minor things like cvIds) a consolidation of the way DAS "IS" being  
used in the community surely it has been tested already?

The main principles of the 1.6 spec have been largely unchanged for  
over a year and were agreed by everyone at the 3rd day of the workshop  
in 2009- most changes say over the last 6 months I believe have  
largely been clarifications. The last year or so the DAS1.6 spec was  
supposed to be in a testing phase - but I agree that maybe not many  
clients have tested it yet. There has been much work at the EBI on  
clients and servers for proteins with 1.6.

I would like the spec to be set in stone, but I don't think it needs  
to be that way and I don't see that it can't be tweaked if needs be  
shortly after initial release. I think by releasing the spec we are  
saying "this is how the DAS community  think the system should work  
and we have provided servers that conform to that spec, code that will  
help clients process the xml and a registry that can validate and hold  
1.6 data sources". Given the lack of testing buy clients so far, I'm  
not sure how we can move DAS forward any other way?

The current situation is that Andy has kindly agreed to postpone the  
release for another week or so for developers to look at the spec and  
preferably do some testing with it.

It would be really great to get some more feedback from client  
developers and some  more 1.6 clients out there using 1.6 - thanks for  
your wise words Thomas.

On 2 Sep 2010, at 17:35, Thomas Down wrote:

> On Tue, Aug 31, 2010 at 5:28 PM, Andy Jenkinson <andy.jenkinson at ebi.ac.uk 
> >wrote:
>> Hi all,
>> As many of you know, DAS version 1.6 has been in development for a  
>> while
>> now, and we would really like to get it out of the door and  
>> "official". To
>> this end, we aim to do the following:
>> 1. resolve the remaining questions over the current draft  
>> (principally,
>> alignments and categorize) *
>> 2. ensure core Java and Perl software libraries support the  
>> specification
>> **
>> 3. officially switch over ***
>> 4. developers of solid client and server implementations will  
>> announce
>> dates for 1.6 support
> I agree that it'll be nice to get this out, although I'm still kind-of
> nervous about setting changes in stone when there aren't already
> implementations out there (client-side, in particular).  Are there any
> client developers who've had a good poke around and can reassure me?
> The other concern (which I've only just noticed, and had some  
> discussions
> off-list with Andy) is that -- in the new PART/PARENT system -- it is
> explicitly stated that you'll only get features overlapping the query
> region.  Features outside the query region will be excluded even if  
> they're
> PARTs of something that is included (e.g., you'll only get a subset  
> of exons
> for a gene).
> To my mind, the biggest advantage of a feature hierarchy system over  
> the
> GROUP system it replaces is that you can guarantee that you'll get the
> complete dataset for a complex feature in a single fetch.  I note  
> that the
> DAS/2 spec (which has a very similar PART/PARENT system) takes the  
> opposite
> approach and states that you'll always get complete graphs of  
> features back.
> Given that this is a new (to DAS/1) system, is there any reason not  
> to do
> things the DAS/2 way?
>               Thomas.
> _______________________________________________
> 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. 

More information about the DAS mailing list