[DAS2] DAS and DAS2

[Brian Osborne]

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 
>