[DAS2] DAS and DAS2

[Steve Chervitz]

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 
>> 
> 
>