[DAS] [DAS2] DAS workshop presentations

Ann Loraine aloraine at gmail.com
Wed Apr 2 03:16:44 UTC 2008


A compare/contrast document on DAS1/2 would be great.

On a different note ---

Does anyone know if the Gbrowse/GMOD system includes a DAS service?

-Ann


On Tue, Apr 1, 2008 at 9:03 PM, Steve Chervitz
<Steve_Chervitz at affymetrix.com> 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.
>
>  [ 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.
>  >>>>  _______________________________________________
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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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