[DAS2] DAS and DAS2

[Rafael C. Jimenez]

Hi there,

I just wanted to make a remark ...

On 07 Dec 2006, at 6:41 PM, Steve Chervitz 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/

The EBI is currently developing Dasty2. It is simply a protein feature 
viewer. This version is not the final version and is continuously 
changing hence it might not work 100%. We expect the first release at 
the end of December. The content in my folder is just a testing 
version: http://www.ebi.ac.uk/~rafael/javascript/

If you want more information about it please don't hesitate to contact 
me.

Cheers,
Rafael.

>
> 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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