[DAS2] DAS and DAS2

Thu Dec 7 20:38:21 UTC 2006

On Dec 7, 2006, at 11:59 AM, Brian Osborne wrote:

> Suzi,
>
> That's good to know - do you mean one could both read and write  
> through DAS
> if the code was updated?

Reading was working, but not writing. Nomi would know if any progress  
was made on writing or not (but I'm guessing the answer is no).

>
> By the way I don't think this is mentioned in the Apollo user  
> documentation,
> the HTML files in Apollo/doc/html, though the Chado adaptor is  
> mentioned.

That's an oversight. Probably because it never got driven to  
completion by a group of users who needed it at the time.

>
> Brian O.
>
>
> On 12/7/06 2:27 PM, "Suzanna Lewis" <suzi at berkeleybop.org> wrote:
>
>> Might add apollo to the list. I'm sure it's das client is in need of
>> an update, but it is there in a basic form that would give a leg up
>> to a developer who was interested.
>>
>>
>> On Dec 7, 2006, at 10:41 AM, 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/
>>>
>>> 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, I’m 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 I’m
>>>>>> 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
>>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> DAS2 mailing list
>>> DAS2 at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das2
>>>
>>
>
>
>
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