Bioperl

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here:

Via CPAN:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/

Via the BioPerl website:

http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip

The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).

Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution.

All,

I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000).

FIXED:

1. Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names
2. Bio::Tools::Run::Vista tests now pass if Vista.jar is installed.
3. bug fix in bioperl-network

What remains for the 1.6 release series:

\* Documentation, Documentation, and Documentation. I haven’t had much time unfortunately to work on documentation, primarily for BUGS/ INSTALL/README etc within db/run/network (the latter has been mainly updated by Brian O.) I will attempt to update these for the next point release, tentatively scheduled for mid-April.

Release Pumpkin Chris Fields has announced the release of BioPerl 1.6 - the first stable release in a several years containing many significant improvements and bug fixes.

I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available.  This is the first BioPerl core release in the 1.6 series and is considered a ‘stable’ (non-developer) release.  The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours.  A direct CPAN link is here:

[Read More]

RC4 is up, we are days away from final release…

BioPerl has branched for 1.6 and the RC1 is up for testing as Chris announced.

BioPerl is preparing for version 1.6 release in the coming months. As part of this some restructuring and simplification of the packaging is occurring.

• Bio-Graphics has been split off into its own package back on Sourceforge to allow for a separate release schedule. It will be uploaded to CPAN as a separate package. In the future other small groups of modules will also be split off from the Core.  Eventually the Core will constitute components that will be the main parsers and data objects while less-common use cases or tightly related modules (like bioperl-network) will be released to CPAN on their own.
• Tests have been split off into smaller chunks.
• Anyone who has contributed to the code and feels their name should be included in the authors’ list needs to either add it or email the mailing list or Chris Fields.
• S endu has moved ModuleBuildBioperl and BioperlTest into Bio::Root
• Bugs are being triaged at bugzilla so if you have any opinions you can vote on the bugs in the queue.

I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2

I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.

I am pleased to announce the 1.5.1 developer release of Bioperl.

Essential links here Core http://bioperl.org/DIST/bioperl-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-1.5.1.zip http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2

Run http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.1.zip http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2

Ext http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-ext-1.5.1.zip http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2

MD5 sum http://bioperl.org/DIST/SIGNATURES.md5

Please see my mailing list post for more information.

Release Candidate 4 for bioperl 1.5.1 (Developer release) core, run, and ext packages is available.

Several bug fixes went in last week so I’ve made what I hope to be the last release candidate before 1.5.1 goes out.

More Info: http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019904.html