[DAS2] DAS and DAS2

[Steve Chervitz]

Brian,

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

I'm targetting mid-late January for completing the transition to the wiki
site. But as for making an appearance, you can check it out now at:

http://biodas.org/wiki/Main_Page

There's literally nothing there yet, except for a new BioDAS icon I threw
together in a few minutes.

If anyone is interested in helping with the migration, let me know. Anyone
who has suggestions for how to organize the site, just post them to this
list.

Steve
 
> 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 
>>>> 
>>> 
>>> 
>> 
> 
>