[DAS2] [DAS] DAS workshop presentations
Steve Chervitz
Steve_Chervitz at affymetrix.com
Wed Apr 2 23:20:21 UTC 2008
Ewan Birney wrote on Wed, 2 Apr 2008 08:28:01 +0100:
> On 2 Apr 2008, at 02:03, Steve Chervitz wrote:
>
>> You're right. The bifurcation that has me concerned is really:
>>
>> DAS/1 --> genome & protein
>> DAS/2 --> genome only
>>
>> Though DAS/2 can be used for protein sequence annotations, it has
>> so far
>> mainly (only?) been used for serving genome annotations. The
>> retrieval DAS/2
>> spec itself is very genome-centric and could be updated/generalized to
>> include protein examples.
>>
>> So I guess it's not so much a bifurcation but a disparity in level of
>> support and usage patterns that distinguishes the 1 vs 2 versions
>> of the
>> spec, and this disparity seems destined to ensure the co-existence
>> incompatible DAS 1 & 2 clients and servers.
>>
>> DAS/1 has a large installed base of servers and clients and the DAS/
>> 1 spec
>> has more extensive support for protein sequence annotations.
>>
>> DAS/2 has some enhancements including support for alternative
>> formats and an
>> incipient writeback (annotation editing) facility. Usage as so far
>> been
>> confined to genome browsers.
>>
>
> One important thing in my mind is that "writeback" is a really huge
> additional concept that carries so many semantic issues which many servers
> just cannot implement (for sure, Ensembl is not going to be implementing
> a writeback server in the near term).
>
> For me, DAS's sweet spot is a "dumb server, smart client" mode, where
> there a few clients and many servers, and servers are easy to put up
> etc. Write back requires smart(er) servers.
>
> So I would also advocate splitting the DAS/2 discussing into "read-only"
> and "read-write" scenarios. I know this is implicitly there but I would
> argue worth formalising at a higher level, and would stress the servers
> can still be dumb.
Agreed. Lots of issues involved with writeback. That portion of the DAS/2
spec is clearly segregated from the retrieval portion, and was still in the
experimental stage when it was last worked on (~summer 2007). The future of
this aspect of the spec isn't so clear to me. It would take a significant
amount of developer time and community interest to make it fly.
So I would de-emphasize the writeback stuff when discussing what DAS/2
brings to the table. Seems to me to be more important to first address how
to best align the DAS/2 - DAS/1 work within the read-only world before
getting into writeback, and only then if there's significant interest &
funding.
> It is also worth noting that DAS/1 has evolved as a "de facto", working
> standard around the hinxton campus and we've really made good use and
> built up momentum around it. It takes a long time bizarrely for people
> to pick up technology and use it, and I want to make sure DAS/2
> discussion doesn't scare the growing set of people picking up and using
> DAS/1 - which is very useful, pragmatic and critically has working
> servers and clients now.
The growth in DAS users is a good thing and should be encouraged since it
helps realize the distributed annotation vision, and hooks up more people
with more data. Whether DAS/1 or DAS/2 or DAS/n is used under the hood is a
technical issue. One can always construct smarter clients that know how to
speak whatever DAS flavor, though that's not necessarily a good long-term
solution.
It's clear that there is evolutionary pressure on the DAS spec, both in the
existence of DAS/2 and in the modifications to DAS/1. What's less clear is
how to channel these forces so that the innovative ideas on both sides of
the pond can come together.
Steve
>> [ BTW: there isn't a good document describing these DAS/2
>> enhancements and
>> how DAS/2 diverges from DAS/1. I'll try and put something up on the
>> biodas.org wiki about this. In the meantime, there is a brief
>> summary here:
>> http://biodas.org/documents/das2/das2_protocol.html ]
>>
>> I agree with your ultimate goal for DAS. Getting there will take some
>> effort, but promoting that vision is a important step. Resuming the
>> conference calls as Ann mentioned will help.
>>
>> Cheers,
>> Steve
>>
>>
>>> From: Andreas Prlic <ap3 at sanger.ac.uk>
>>> Date: Tue, 1 Apr 2008 22:37:18 +0100
>>> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>
>>> Cc: DAS/2 Discussion <das2 at lists.open-bio.org>, <das at biodas.org>
>>> Subject: Re: [DAS] DAS workshop presentations
>>>
>>> Hi Steve,
>>>
>>> I don't really see the bifurcation between protein and genome DAS
>>> that you mention. We use DAS/1 nicely for both genome and protein
>>> clients.
>>> Also the DAS/1 extensions have been designed with being able to work
>>> with both worlds.
>>>
>>> The real bifurcation I see is the geographical split between the US
>>> and Europe as DAS is used in different ways here and there. Europe is
>>> very much organized around DAS/1.
>>>
>>> The ultimate goal of DAS is to separate data provision from
>>> visualization. As such a goal for us all should be that a DAS source
>>> can be shown in a similar fashion in all (genome) browsers. At the
>>> present this is not possible. In order to achieve such a standard it
>>> still will require a lot of collaboration, standardization and
>>> convincing between the different client and server-providers.
>>>
>>> Andreas
>>>
>>>>
>>>> There are perhaps are a handful of sites in the U.S. that have (or
>>>> are planning to) deploy DAS/2 servers in production environments,
>>>> though I don't have any official numbers. We've been tracking them
>>>> here: http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers
>>>>
>>>> Since the DAS/2 retrieval spec stabilized, there has been some work
>>>> on the writeback portion of the spec (for creating/editing
>>>> annotations), but that has not been finalized. As far as I know, it
>>>> hasn't progressed since the original grant for DAS/2 spec
>>>> development ended in Oct 2007. There was some good work done on the
>>>> writeback spec as well as some early implementations and it would
>>>> be good to see it congeal eventually.
>>>>
>>>> I know there's been continued development of the DAS/1 spec: http://
>>>> www.dasregistry.org/spec_1.53E.jsp
>>>>
>>>> This has stirred up some thoughts I've been chewing on recently
>>>> regarding where DAS is headed. Comments welcome. Here goes:
>>>>
>>>> While it would be nice to see a single DAS spec to simplify the
>>>> lives of people writing clients and to unite development efforts, I
>>>> wonder if this is reasonable expect yet. The genome vs. protein
>>>> annotation bifurcation that we have now may reflect a natural
>>>> division that might be difficult to unite into a single spec.
>>>> However, I think the current state is more a matter of the large
>>>> amount of inertia behind DAS/1 -- the shear number of existing DAS/
>>>> 1 servers and DAS/1 client code out there -- coupled with the fact
>>>> that DAS/2 is not backward compatible. Code doesn't rewrite itself.
>>>>
>>>> I know one of the early roadblocks for getting protein annotation
>>>> support into DAS/2 was that protein features were not described by
>>>> the Sequence Ontology (SO), but this has since been rectified. I've
>>>> learned that since August 2007, all of the protein features in the
>>>> bioSapiens project have been incorporated into SO ( http://
>>>> www.dasregistry.org/extension_ontology.jsp ).
>>>>
>>>> The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on
>>>> ( http://lists.open-bio.org/pipermail/das2/2006-October/
>>>> 000268.html ) could help with DAS/2 migration. But that project
>>>> never fully matured. Continued development of DAS/1 could
>>>> complicate the development of such an adapter.
>>>>
>>>> Regarding the genome-vs-protein DAS split, certainly there are many
>>>> commonalities at the level of annotations along a linear sequence
>>>> which apply equally well to nucleotide and protein sequences. Maybe
>>>> it would help to have a partitionable DAS spec to separate core
>>>> things from extensions that are nucleotide or protein-specific?
>>>> This could help isolate the more stable, low-level things from
>>>> higher-level functionality that is specific to nucleotide or
>>>> protein sequences, and could evolve without impacting the core
>>>> spec. A given DAS server would be compliant with the core and
>>>> either the genome or protein specific extensions of the spec.
>>>>
>>>> Cheers,
>>>> Steve
>>>>
>>>>
>>>>> From: Ann Loraine <aloraine at gmail.com>
>>>>> Date: Thu, 27 Mar 2008 10:04:21 -0400
>>>>> To: Andreas Prlic <ap3 at sanger.ac.uk>
>>>>> Cc: Steve Chervitz <Steve_Chervitz at affymetrix.com>, DAS/2
>>>>> Discussion
>>>>> <das2 at lists.open-bio.org>, <das at biodas.org>
>>>>> Subject: Re: [DAS] DAS workshop presentations
>>>>>
>>>>> Regarding the funding issue:
>>>>>
>>>>> NSF is awarding me some funds that will support developing a
>>>>> Distributed Annotation Server to use for Arabidopsis data. (It is
>>>>> through the 2010 program.)
>>>>>
>>>>> DAS is not the main focus of the grant, but will play a big part
>>>> in what we
>>>>> do.
>>>>>
>>>>> I am also working on arranging a number we could use to carry on
>>>>> the
>>>>> DAS conference calls.
>>>>>
>>>>> Previously they were hosted by Affymetrix, but I think we can
>>>> probably
>>>>> do this for the group here at Charlotte. (I'm at University of
>>>>> North
>>>>> Carolina Charlotte.)
>>>>>
>>>>> All the best,
>>>>>
>>>>> Ann
>>>>>
>>>>> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic <ap3 at sanger.ac.uk>
>>>> wrote:
>>>>>> Hi Steve,
>>>>>>
>>>>>> We did not have an "official" slot for DAS/2, partially
>>>>>> because we
>>>>>> did not have any DAS/2 related speakers. In the informal
>>>> discussions
>>>>>> some concern re DAS/2 was raised,
>>>>>> particularly about backwards compatibility issues and regarding
>>>>>> whether DAS/2 is still active and funded.
>>>>>>
>>>>>> Cheers,
>>>>>> Andreas
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 27 Mar 2008, at 01:24, Steve Chervitz wrote:
>>>>>>
>>>>>>> Thanks Andreas. Looks like you had a good workshop.
>>>>>>> Was there any discussion pertaining to DAS/2?
>>>>>>>
>>>>>>> Steve
>>>>>>>
>>>>>>>> From: Andreas Prlic <ap3 at sanger.ac.uk>
>>>>>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000
>>>>>>>> To: <das at biodas.org>
>>>>>>>> Subject: [DAS] DAS workshop presentations
>>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> We recently were hosting a DAS workshop at the Genome Campus in
>>>>>>>> Hinxton, U.K..
>>>>>>>>
>>>>>>>> In case you are interested, the presentations of the first day
>>>> (DAS -
>>>>>>>> client developers day) are available from:
>>>>>>>> http://www..dasregistry.org/course.jsp
>>>>>>>>
>>>>>>>> The slides used for the second day (hands-on) are available
>>>>>>>> from:
>>>>>>>> http://www.biodas.org/wiki/DASworkshop200802
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Andreas
>>>>>>>>
>>>>>>>>
>>>> --------------------------------------------------------------------
>>>> -
>>>>>>>> --
>>>>>>>>
>>>>>>>> Andreas Prlic Wellcome Trust Sanger Institute
>>>>>>>> Hinxton, Cambridge CB10 1SA, UK
>>>>>>>> +44 (0) 1223 49 6891
>>>>>>>>
>>>>>>>>
>>>> --------------------------------------------------------------------
>>>> -
>>>>>>>> --
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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.
>>>>>>>> _______________________________________________
>>>>>>>> DAS mailing list
>>>>>>>> DAS at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>>>
>>>>>>
>>>>>>
>>>> --------------------------------------------------------------------
>>>> --
>>>> -
>>>>>>
>>>>>> Andreas Prlic Wellcome Trust Sanger Institute
>>>>>> Hinxton, Cambridge CB10 1SA, UK
>>>>>> +44 (0) 1223 49 6891
>>>>>>
>>>>>>
>>>> --------------------------------------------------------------------
>>>> --
>>>> -
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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.
>>>>>> _______________________________________________
>>>>>> DAS mailing list
>>>>>> DAS at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>>
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>>>
>>> ---------------------------------------------------------------------
>>> --
>>>
>>> Andreas Prlic Wellcome Trust Sanger Institute
>>> Hinxton, Cambridge CB10 1SA, UK
>>> +44 (0) 1223 49 6891
>>>
>>> ---------------------------------------------------------------------
>>> --
>>>
>>>
>>>
>>>
>>> --
>>> 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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