[Biojava-l] Preparation for a 1.1 release?

[uwe.plikat@pharma.Novartis.com]

Hi Thomas,

reading "Blast parsers" and hearing Matthews presentation last week at EBI,
I just want to make one comment:
Matthew mentioned a Blast2XML parser. Since Blast by itself can produce XML
output (option -m7) it would be a good idea, if this parser (kind of
obsolete...) produces the XML format identical to the original one from
NCBI. The DTD is available at NCBI's ftp site.

I apologize for my ignorance if this is already the case.

Greetings,

Uwe





Thomas Down <td2@sanger.ac.uk>@biojava.org on 12/07/2000 04:40:43 PM

Sent by:  biojava-l-admin@biojava.org


To:   biojava-l@biojava.org
cc:
Subject:  [Biojava-l] Preparation for a 1.1 release?


Hi...

It's not about four months since the BioJava 1.0 release.  In
that time, we've seen a fair number of core changes:

  - Change events and listener support throughout the core APIs
  - Improved I/O interfaces (newio).
  - Matthew's Symbol changes

We're still in a `dust settling' period for the latter two, but
so far they seem to be holding up quite well.

There are also some functionality additions:

  - Blast and PDB parsers
  - Revamp of the dynamic programming code
  - DAS client functionality

(plus plenty of other changes).  I'd therefore suggest that
we are now reaching the point where it is worth taking some
time out to build a stable release with these features in.
As well as being useful for people who want a copy of BioJava
which isn''t going to change overnight, the stabilization
effort before 1.0 helped the overall code quality along.

Does anyone have any problems with the tentative target of
getting a 1.10 release out sometime early in the new year?

Otherwise, let's start a list of things which should be
done before we cut the relase branch.  Please add additions /
comments / offers of code as appropriate:

BioCorba:

   Can we move all the `CORBA packages' (both the interfaces
   and the bridges) out to their own package (biojava-corba?).
   They can then take on their own release cycle (matching
   the biocorba.org people).  Right now the packages could
   do with a little bit of love to get them upgraded to the
   latest IDL.  In any case, moving to another module should
   be easy.

I/O:

   - We're currently without a working GENBANK parser (our
     only major regression since 1.0).  I guess this is my
     responsibility, but if there is anyone out there who
     uses GENBANK files more than I do, please have a go
     at this.

   - GAME

Sequence searching:

   - It would be good to have some tests for this.  Does anyone
     feel like glueing the current BLAST parser to Gerald's
     org.biojava.bio.search interfaces?

Toolchain:

   - The idea of using programs in the demos directory as test
     cases doesn't really seem to be working out -- I'd like
     to see a proper test harness, and a java equivalent of
     `make test'.

Documentation: <insert horror movie theme tune here...>

   - The web-site tutorials are out of date.  I'll volunteer
     to update the `symbols and symbollists' tutorial to include
     the recent changes, and to write a new chapter on the newio
     interfaces.

   - Does anyone have any comments about the current set of
     tutorials?

   - More tutorials would be great.  In particular:

      + SequenceDBs
      + The search packages (if we get this hooked up to BLAST and/or
        FASTA).
      + Distribution objects
      + The dynamic programming toolkit.

    Anyone feel like honing their writing skills?

   - Review to source code and check that javadoc is complete
     and up-to-date.

Any thoughts?

   Thomas.
--
``If I was going to carry a large axe on my back to a diplomatic
function I think I'd want it glittery too.''
           -- Terry Pratchett
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