[DAS2] [DAS] DAS workshop presentations
Ann Loraine
aloraine at gmail.com
Wed Apr 2 03:16:29 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.
> >>>> _______________________________________________
> >>>> DAS mailing list
> >>>> DAS at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/das
> >>>>
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> >> Affymetrix, Inc.
> >
> > -----------------------------------------------------------------------
> >
> > 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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>
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