Bioperl: Final pre release

[Jonathan Epstein]

I'm a bit afraid to ask this, but here goes.  Does this current prerelease
version interoperate with the current NCBI blast server?  Some previous
versions were incompatible after NCBI changed its Web submission format.

Have the bioperl developers consider using the blastcl3 client software as an
interface to NCBI blast?  This should be a much more stable interface.  If it
makes sense to do so, then I will take a look at it.  I will probably do this
sooner rather than later if the current blast bioperl software is broken ;-)

- Jonathan

At 01:22 PM 3/23/00 , Ewan Birney wrote:
>
>I have put in the 06 branch. This means that we have now decide on
>the feature set, functionality and general code to work for the new
>0.6 release of bioperl. 
>
>It is *very* important that people who use bioperl heavily that they
>try to pick this release up and test it, ideally in place of their
>exisiting bioperl. It *should* be backwardly compatible (you will
>get warnings when you use deprecated methods). There are so many
>new aspects to bioperl, including better performance and richer
>object definitions that it is undoubtedly worth upgrading.
>
>
>The release is at
>
>ftp://bio.perl.org/pub/birney/bioperl-06pre3.tar.gz
>
>It is a standard CPAN module, so installation should be trivial.
>
>
>
>I'd like to publically thank many people who contributed to this
>release and in particular the new comers. They include:
>
>  James   Gilbert
>  Heikki  Lehväslaiho
>  Jason   Stajich
>  Elia    Stupka
>  Lincoln Stein
>  Peter   Schattner
>  Michele Clamp
>  Kate    Linder
>  
>Please - I am not sure that I have everyone who has committed stuff over
>the last 6 months, so if you know you have contributed, whether in code,
>testing, documentation or design, please speak up. (yes - we need to start
>a contributor's list).
>
>Just to mention, bioperl is not possible without the continued work
>of 
>
>  Steve Chervitz
>
>and in particular, a big thank you to
>
>  Chris Dadigdan
>
>who provides system administration to the entire bio* set of sites
>
>
>
>
>Anyway - go get it - go test it! Expect the full release next week with a
>revamped web site.
>
>
>
>
>
>
>
>
>-----------------------------------------------------------------
>Ewan Birney. Mobile: +44 (0)7970 151230
><birney@ebi.ac.uk>
>-----------------------------------------------------------------
>
>
>
>
>
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Jonathan Epstein                                Jonathan_Epstein@nih.gov
Unit on Biologic Computation                    (301)402-4563
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