Bioperl

We are happy to announce the long-awaited release of BioPerl v1.7.0. The release is now available on CPAN and Github. During this release series, we will move some extraneous code to separate repositories and CPAN releases, primarily to reduce the number of dependencies required for BioPerl installation (in many cases for modules that are never used) and also reduce maintenance overhead. This may only impact you if your code incorrectly list the immediate downstream dependencies that you utilize. [Read More]

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants Peter J. A. Cock ( Biopython), Christopher J. Fields ( BioPerl), Naohisa Goto ( BioRuby), Michael L. Heuer ( BioJava) and Peter M. Rice ( EMBOSS). Nucleic Acids Research, doi:10. [Read More]

Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is the first run where we’ve switched to a regular Module::Build installation, so expect some initial bumps! There are a few initial problems that I plan on addressing soon, the main one being none of the modules are assigned version numbers (this may be a consequence of not pulling the version from a specific module). [Read More]

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. [Read More]

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: Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names Bio::Tools::Run::Vista tests now pass if Vista.jar is installed. bug fix in bioperl-network What remains for the 1.6 release series: \* Documentation, Documentation, and Documentation. [Read More]

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. [Read More]