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

[Lincoln S. <ls...@cs...>]

The caveat, of course, is that this hasn't been tested yet, so it will al=
most=20
certainly fail the first time we try it.  However, once the hidden=20
assumptions in the GMOD browser are shaken out, subsequent ports should b=
e=20
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::D=
asI
> > interface from bioperl-live on top of BioSQL, Ensembl and whatever el=
se
> > 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 outguessin=
g
> > > the process (which I think should be fairly straightforward) can yo=
u
> > > 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 Ensem=
bl?)
> > > 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