[DAS2] DAS and DAS2

[Steve Chervitz]

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