[DAS] Fugu and mouse das servers

Ewan Birney birney@ebi.ac.uk
Sat, 22 Dec 2001 11:34:34 +0000 (GMT)

On Fri, 21 Dec 2001, Cheung, Foo wrote:

> 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?

I know that Elia Stupka's group in Singapore has an internal Ensembl style
system running - the question is when they will go public, which I believe
is "soon" - but have no other timeline than that.

I've cc'd in Elia so he can let us know what is up or remain mysterious
as he chooses ;)

> (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
> Foo
> -----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
> and
> > 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
> translation
> > 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
> servers)?
> 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?
>    Thomas.
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