[Bioperl-l] Status 0.7

Hilmar Lapp hlapp@gmx.net
Tue, 16 Jan 2001 11:53:58 -0800

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

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?

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.

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.

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.

Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757