[DAS] Fugu and mouse das servers

Cheung, Foo FCheung@tigr.org
Fri, 21 Dec 2001 14:26:30 -0500

Thanks Thomas
Glad to hear that about the transformation coordinate system!
I look forward to seeing the mouse reference server!

Does anybody know when Fugu is coming to DAS?

(The more reference servers that are up, the more I can help doing TC/Genome
alignments and the more I can play with DAS.)

Keep the reference servers rolling!

Happy Holidays

-----Original Message-----
From: Thomas Down
To: Cheung, Foo
Cc: das@biodas.org
Sent: 12/21/01 1:44 PM
Subject: Re: [DAS] Fugu and mouse das servers

On Fri, Dec 21, 2001 at 01:06:51PM -0500, Cheung, Foo wrote:
> Does anyone know when is there going to be reference servers for Mouse
> Fugu?
>  and what format will this be in? scaffolds? cosmids?

I'm potentially interested in getting a mouse server running,
if nobody else jumps on this first.  Maybe when the next Ensembl
mouse release comes out.

If I set this up, I'd guess it will probably mirror the data
model of the ensembl database, just as my human reference server
implementation does at the moment.

I'm open to suggestions, though.

> Does this mean there would be another requirement for a separate
> system for each? :(

What do you mean by this?  Are you refering to the
coorinate transformations required when fetching data
from a server with `assembled' annotation (like the Ensembl

This really shouldn't require separate code per reference
server.  Assembly handling is documented in the DAS spec.
I can't speak for other client writers, but the BioJava client
library should be able to assemble annotation from any reasonably
spec-compliant server.  If it can't, please could you point me
at an example, and I'll take a look ASAP.

Or am I missing the point here?