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

[Lincoln Stein]

The caveat, of course, is that this hasn't been tested yet, so it will almost 
certainly fail the first time we try it.  However, once the hidden 
assumptions in the GMOD browser are shaken out, subsequent ports should be 
straightforward!

Lincoln

On Friday 14 June 2002 10:55 pm, Elia Stupka wrote:
> > 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 twith it.
>
> Great, all I needed to know, just a pointer, thanks, I imagined it had to
> be extremely simple.
>
> Elia
>
> > 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