[DAS2] DAS and DAS2

[Brian Osborne]

Suzi,

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

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.

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, 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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