[Open-bio-l] Re: [Bioperl-l] -db and -gui?

[Brian Osborne]

Jason et al,

Sounds good, I await. In fact, I've been sitting on the fence a bit, waiting
for "the dust to clear" with OBDA, Biosql, "bioperl-db", etc. before working
on bptutorial or biodatabase.pod sections.

For those of you in this group who have joined more recently please realize
that the growth of bioperl could be characterized as a succession of good
ideas regarding sequence representation, database access, sequence analysis,
and so on, each implementation a bit better and a bit more sophisticated
than the previous. It's also true that some parts of bioperl have been
through enough of these transformations that they're stable and mature, but
other sections are more youthful and unformed.  The bioperl authors know
this, and they know precisely where work is needed. So, instead of telling
the authors what they already know, that such-and-such a section needs work,
I suggest you join them and help make it happen.

Brian O.


----- Original Message -----
From: "Jason Stajich" <jason@cgt.mc.duke.edu>
To: <open-bio-l@open-bio.org>
Cc: "Bioperl" <bioperl-l@bioperl.org>; "Brian Osborne"
<brian_osborne@cognia.com>
Sent: Sunday, April 21, 2002 10:39 AM
Subject: Re: [Bioperl-l] -db and -gui?


> Good point Brian - They are available through the ftp site -
> ftp://bioperl.org/pub/DIST
> The bioperl-db is going through a transition with the new OBDA/BioSQL
> schema being implemented.  I would say it is 90% finished with some more
> testing and roundtripping needed at least on the perl end.
>
> It is hard to coordinate the release of associated packages with a bioperl
> core release considering the amount of work it takes to just try a release
> the core - however I think when the Biosql work is stable and ready
> for a release we are going to want to display it prominently.
>
> Chris M and others, do you think we can set a timeframe when you think we
> can put a stable release out there for the current version of the schema
> (With the ontology tables I assume?).  Would be nice if this could be a
> coordinated release with biopython and biojava so we can proclaim all
> toolkits supporting the schema but I'm not sure how far that is away?
>
> I would really like to push for all toolkits supporting the biosql schema
> before BOSC in August so that we can move the OBDA work along - is that a
> reasonable request for everyone?  Perhaps if the devs are having trouble
> finding time to work on things they could report where they are and
> what needs to get done so other potential volunteers can know where they
> can help?  Not sure who the biopython rep is - but I assume Thomas was
> still biojava-biosql pointman and Chris M was the bioperl-biosql lead.
> Can you guys chime in on where things are and where they need to go for a
> stable or alpha release?
>
> -jason
> On Sat, 20 Apr 2002, Brian Osborne wrote:
>
> > bioperl-l,
> >
> > Neither the bioperl-db nor the bioperl-gui packages are available
through
> > the Download or the Download Latest Stable release (1.0) links at
> > http://wwww.bioperl.org. How does one download these packages now?
Shouldn't
> > we feature these packages a bit more?
> >
> > Thanks again,
> >
> > Brian O.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
>
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