Development

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]

Please forward as appropriate and forgive multiple postings. Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009 An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: /wiki/BOSC_2009 Abstract submission via EasyChair: https://www.easychair.org/login.cgi?conf=bosc2009 Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. [Read More]

Google is committed to run the Summer of Code program again this year. It will be for the 5th time. In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program apply during the organization application period (March 9-13 in 2009). Those accepted into the program provide project ideas and supply mentors that guide the work on those. [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]

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. [Read More]

We are pleased to announce the release of Biopython 1.49. There have been some significant changes since Biopython 1.48 was released a few months ago, which is why we initially released a beta for wider testing. Thank you to all those who tried this and reported the minor problems uncovered. As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library). [Read More]

We are pleased to announce a beta release of Biopython 1.49. There are been some significant changes since Biopython 1.48 was released two months ago, which is why we are initially releasing a beta for wider testing. As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library). As in the previous releases, Biopython 1.49 beta supports Python 2.3, 2. [Read More]

Many of you will be aware that Python 2.6 was released a month ago (October 1st, 2008). This supports a lot of new syntax and functionality, but also deprecates some old modules (e.g. the sets module). While Biopython 1.48 does mostly work with Python 2.6, we’ve been testing with Python 2.6 and have fixed a number of deprecations or breakages in our CVS repository. If using Biopython with Python 2.6 is important to you, please help out by testing the CVS code (which needs NumPy and not Numeric) and letting us know on the mailing list or bugzilla if we’ve missed anything. [Read More]