[Bioperl-l] 1.0.1 preparing to release, 1.1 plans

Jason Stajich jason@cgt.mc.duke.edu
Mon, 10 Jun 2002 16:52:03 -0400 (EDT)

If anyone has any other changes that need to go into 1.01 - please speak
up now.  I'm going to tar and release this evening barring anyone speaking
up.  We'll push out to CPAN tomorrow.  I'll regenerate the Pdoc as well.

As for 1.1 developer release, I am planning to try and cleanup any
tests that are failing and release that before the end of the week.
Anyone wanting to help, I'm happy to have you.

For some simple things I would like us to do a better job cross
referencing return types with L<XXX> in the module documentation.
Additional mundane things include insuring that the skip() in tests
reports why they are skipped - so use
    skip('MESSAGE HERE', 1);
  instead of
    skip(1, 'MESSAGE HERE');

Insuring that POD is checked and that all modules have a runnable SYNOPSIS
is also a great service.

As for modules - if people have things in progress - a report would be in
order.  For me I have

* Bio::SeqFeature::Collection - bins features into Bins just like
  Bio::DB::GFF only with a pure DB_File implementation instead of in
  mysql. Use it to quickly find features that overlap/are containin in a range.

* Some new Bio::Graphics glyphs for splice site donators and acceptors.

I know that Andrew is going to fix UniGene parser to handle changes from
NCBI regarding the format.

While we're talking milestone goals, here are some I have 1.2

* Bio::DB::GenBank/GenPept needs to be ported to Eutils.
* Bio::SeqIO::game - am looking to do a rewrite for the latest GAME and
  handling Align and HSP objects as well.
* Novella integration (Martin Senger)
* Bio::SearchIO::Writer fixes and/or fixes to Bio::Search objects to work
  with psiblast and blast parser.  Probably try and remove the psiblast
  parser if we can ever migrate the functionality.
* Bio::SeqFeature::Mapper/Aggregator objects to map Generic Features that
  have the correct (or inferrable) sequence ontology designations into
  the appropriate Bio::SeqFeature object ( mostly for the
  Bio::SeqFeature::Gene objects, but Computation or even Similarity
  objects should be doable)

- There are proposals on the table to provide a new Bio::SeqIO
  implementation which is event driven.  Not clear who wants to help work
  with this - it would dovetail into the new GAME parser.

(pls add to the list if you have ideas or contributions)


Jason Stajich
Duke University
jason at cgt.mc.duke.edu