[Bioperl-l] Re: [GMOD-devel] GMOD on top of biosql

[Lincoln Stein]

Hi Elia,

For the GMOD browser, it is really simple.  Just implement the Bio::DasI 
interface from bioperl-live on top of BioSQL, Ensembl and whatever else you 
like, and the GMOD browser will work with it.

I'm running in and out, so I'm sorry to have taken so long to respond, but 
I'll write a more detailed message over the weekend.

Lincoln

On Wednesday 12 June 2002 22:44, Elia Stupka wrote:
> Hi Lincoln,
>
> we want to get GMOD to work with biosql, and rather than outguessing the
> process (which I think should be fairly straightforward) can you give us a
> roadmap of how you think we should do it? As far as I see it already
> relies on bioperl sequence and feature objects, so all that is needed is
> to write adaptors that rather than talking to DB:GFF talk to bioperl-db,
> right? If that is correct, how do you want us to do it? Would you like us
> to be GMOD developers and create directories and namespaces for each type
> of adaptor (GFF, bioperl-db, why not Ensembl?) within the GMOD codebase?
>
> Let me know:
>
> a)if you have already done steps in this direction
>
> b)how best to focus our efforts not to waste time, and to do it in
> whichever way GMOD would prefer it to work
>
> Thanks,
>
> Elia

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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