[Bioperl-l] Status 0.7

Jason Stajich jason@chg.mc.duke.edu
Tue, 16 Jan 2001 21:34:11 -0500 (EST)

On Tue, 16 Jan 2001, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > 
> > A couple of days I updated the task list for 0.7
> > 
> > http://bio.perl.org/wiki/html/BioPerl/TaskList.html
> > 
> > which is getting much more "green". Hilmar - I think we drop some of the
> > more unlikely things to make it into 0.7 (NetIO class for example?) and
> > concentrate on the last important features ...
> > 
> I think we should stick to our goal of finalizing the 0.7 release
> by the end of January. The situation actually doesn't look bad.
> Major things remaining to be addressed as I see it basically
> comprise of the following.
> 1) Fuzzy locations coverage. This is probably the most significant
> hurdle. Jason's already elaborating an interface outline. If
> anyone has suggestions/views/experience, feel encouraged to post.
> You may also want to check out Ewan's proposal
> (http://bioperl.org/pipermail/bioperl-l/2000-November/001724.html).

Hopefully will have something by the end of the week or early next week.
> 2) With the preceding being addressed, a review of SeqFeatureI and
> BioCorba interoperability may go hand in hand. Jason, Brad, is
> BioCorba 0.2 interoperability still within sight?

I haven't played with this much, I was planning on doing it after the
SeqFeatureI - LocationI stuff was settled.

> 3) BPlite update. Lorenz seems to have abandoned the list, or is
> too busy with other things. It's priority 2, but I think at the
> same time as we are phasing out support for Blast.pm we need to
> increase support for BPlite. Anyone out there who would volunteer
> to assume responsibility?
> 4) SeqAnalysisParserI needs more elaboration, according to a
> discussion we (Jason, Ewan, I) had in December. It'll probably be
> the three of us who thrash this out.
 Hmm, we need to determine what the future of SeqFeatureProducerI is as
 well in this context.
> 5) Bio::SeqFeature::Transcript object. This will be related to
> GeneStructure and the concept has been worked out between Ewan and
> myself. Still, I'll need to put it into Perl code :)
> 6) Bugs reported on Incoming. (!) (These tend to be forgotten, but
> I'm sure they won't be fixed in a matter of minutes.)
> 7) The rest I think (I hope :) is smaller fixups, some of which I
> need to address myself.
> We'll probably have to drop Root::StreamIO (priority 3), and
> probably also fixing Blast.pm bugs, unless SteveC finds the time
> to fix them. It seems that almost all priority 2 tasks will make
> it into 0.7, BioCorba 0.2 being the only one not started yet.

I wanted to wait until code was stable before working on BioCorba stuff
since it is entirely dependant on the bioperl modules api.

> Since more or less all of us can do BioPerl work only on weekends,
> I suggest that we freeze the code on a Monday. I'll be off to San
> Jose (is anyone else going to attend the Microarray Meeting at
> BiOS?) the next weekend, so I propose to schedule the 0.7 code
> freeze for Feb. 5th (one week earlier would be Jan 29th). Note
> that once this is agreed upon, it will be a firm deadline.

Yes.  Feb 5 is reasonable.  Let's see how close we are the week before and
take stock.  Thanks for being the lead on this!

> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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Jason Stajich
Center for Human Genetics
Duke University Medical Center