[DAS2] DAS and DAS2

Brian Osborne bosborne11 at verizon.net
Thu Dec 7 18:56:52 UTC 2006


Perfect, thank you.

You mentioned a DAS Wiki - do you know when this will make its first

Brian O.

On 12/7/06 1:41 PM, "Steve Chervitz" <Steve_Chervitz at affymetrix.com> wrote:

> DAS applications generally take the form of graphical genome browsers,
> protein feature/structure browsers, and even gene information browsers.
> I don't necessarily have a comprehensive list of DAS clients in current use
> today, but here are a few of the major ones I know of (anyone else: feel
> free to chime in here):
> IGB: http://genoviz.sourceforge.net
> Gbrowse: http://www.gmod.org/gbrowse_installation
> Ensembl: http://www.ensembl.org/info/data/external_data/das/ensembl_das.html
> Spice: http://www.efamily.org.uk/software/dasclients/spice/
> Dasty: http://www.ebi.ac.uk/das-srv/uniprot/dasty/content?ID=:dis=BioSapiens
> Dasty2: http://www.ebi.ac.uk/~rafael/pre_dasty2/
> For an example of how Ensembl acts as a DAS client for gene information
> browsing, see the "Gene DAS Report" section of this page:
> http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000165029
> Here's an insteresting review of EBI DAS clients:
> http://www.ebi.ac.uk/~rafael/das/index.php?display=clients
> When the wiki version of biodas.org gets set up, a page devoted to various
> clients and their DAS/1 vs DAS/2 support status would be a good idea.
> Steve
>> From: Brian Osborne <bosborne11 at verizon.net>
>> Date: Wed, 06 Dec 2006 09:58:47 -0500
>> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>, DAS/2 Discussion
>> <das2 at lists.open-bio.org>
>> Cc: GMOD Helpdesk <wg-emod at nescent.org>
>> Conversation: [DAS2] DAS and DAS2
>> Subject: Re: [DAS2] DAS and DAS2
>> Steve,
>> Thank you for your thorough response. One more question: what applications
>> are the actual "DAS clients" these days?
>> Thanks again,
>> Brian O.
>> On 11/30/06 5:59 PM, "Steve Chervitz" <Steve_Chervitz at affymetrix.com> wrote:
>>> Hi Brian,
>>> Brian Osborne wrote on Mon, 27 Nov 2006:
>>>> My name is Brian Osborne, I¹m working on documentation for GMOD and
>>>> GMOD-related packages as part of the newly created GMOD Help Desk position.
>>> Great. Looking forward to more quality documentation for GMOD, a la your
>>> excellent contributions to Bioperl documentation.
>>>> Some of my colleagues here in the GMOD community are recommending that we
>>>> consider DAS, 1 or 2, as important GMOD-related software so I¹m joining
>>>> your
>>>> list in order to learn more about DAS.
>>> DAS is definitely appropriate for GMOD. Providing a DAS-compatible interface
>>> to MOD data would help write software tools and perform data analyses that
>>> integrate data from different sources.
>>> In fact, a DAS/2 server reference implementation is being developed within
>>> the GMOD sourceforge CVS, though it's not officially been released as part
>>> of GMOD. Here are the CVS commit logs for it.
>>> http://sourceforge.net/mailarchive/forum.php?forum_id=42210
>>> Other DAS/2 software is also being developed under open source licenses. See
>>> links on http://biodas.org in the About section, look for "The DAS/2 code
>>> base".
>>>> I have some initial questions, I was
>>>> wondering if someone could help me out with them (I did read the DAS
>>>> Overview and browsed most of the specs at biodas.org).
>>>> 1. Are DAS1 and DAS2 designed to inter-operate? For example, will I be able
>>>> to use a DAS2 client and a DAS1 server?
>>> DAS/2 is a complete redesign of the spec, so direct interoperation is not
>>> possible. However, DAS/2 has all of the capabilities of the DAS/1 spec (and
>>> more!).
>>> As proof of this, Andrew Dalke is developing a proxy adapter that will allow
>>> you to put a DAS/2 interface around an existing DAS/1 server, allowing DAS/2
>>> clients to interact with existing DAS/1 servers:
>>> http://lists.open-bio.org/pipermail/das2/2006-October/000867.html
>>> To fully realize 1 <-> 2 interoperation, one would also need to write a
>>> DAS/1 proxy adapter for DAS/2 servers, to permit DAS/1 clients to interact
>>> with DAS/2 servers. I don't know of any plans for that yet.
>>>> 2. Do you think DAS2 is going to replace DAS1 or co-exist with it? Yes,
>>>> this
>>>> may not be easy to answer.
>>> The proxy adapter approach should enable some degree of peaceful
>>> co-existence between DAS/1 and DAS/2 systems, and should facilitate the
>>> transition to DAS/2, which has many niceties not present in DAS/1. As far as
>>> replacing DAS/1, the proof will be in the pudding.
>>>> 3. Is there a DAS2 release date?
>>> The DAS/2 schema for retrieval of genomic annotations has been officially
>>> frozen since mid-November (das2_schemas.rnc and das2_schemas.xsd in the
>>> biodas/das/das2 CVS repository).
>>> The corresponding html version of this spec, viewable from biodas.org, is
>>> soon to be finalized as well (probably by end of next week). When that
>>> happens, DAS/2 for genome retrieval will be considered released. Stay tuned
>>> to this list for an announcement.
>>> The DAS/2 writeback spec is still under development and I don't believe a
>>> timeframe for it's release has been set.
>>> Steve 

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