[DAS2] DAS and DAS2

Steve Chervitz Steve_Chervitz at affymetrix.com
Thu Nov 30 22:59:22 UTC 2006

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.

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

> 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

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:

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.


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