Posts

Bioperl 1.2.3

On behalf of the Bioperl developers, we are pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile web-based sequence databases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many more features.

This release constitutes several major bugfixes from the 1.2.2 release earlier this summer and provides some new minor functionality improvements. This release is intended to be compatible with code which has been programmed using the API in the 1.2.x series of releases.

The release is available as always from http://bioperl.org/DIST/.

Hi Everyone,

Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.

Simply put – Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.

Jason has summarized a significant amount of work he has done on the CVS tree. Major work done on Bio::PopGen, Bio::Matrix and bug fixes to Bio::Tree and Bio::SeqIO.

All the juicy details can be read in his bioperl posting archived here: http://bioperl.org/pipermail/bioperl-l/2003-August/013168.html

Available now at http://biopython.org/download/

Changes include: added Andrew Dalke’s EUtils library added Michiel de Hoon’s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman’s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler’s NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman’s fixes to Genbank code – now parses whole database Kayte Lindner’s LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich’s patch to read T_Coffee files Larry Heisler’s fix for primer3 output Bio.Medline now uses proper iterator objects copen now handles SIGTERM correctly small bugfixes and updates in Thomas Hamelryck’s PDB package bugfixes and updates to SeqIO.FASTA reader updates to Registry system, conforms to 2003 hackathon OBDA spec Yu Huang patch to support tblastn in wublast expression

The “Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry” posted online at http://www.biojava.org/docs/bj_in_anger/index.htm has been translated into French and Japanese

Rob Edwards and Heikki Lehvaslaiho have been writing new restriction analysis classes. These will eventually replace the long serving Bio::Tools::RestrictionEnzyme by Steve Chervitz. The first working versions are in CVS.

A UML graph shows the class relationships. A more verbose overview is below.

This is a bug fix release from the stable branch.

The Bioperl release 1.2.2 is available at http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz and is propagating around CPAN now.

Bioperl-run is a collection of modules that wrap bioinformatics applications to allow running them from bioperl. The release cycle of bioperl-run follows the core. The latest bioperl-run release is therefore at: http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz

Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.

Pictures are online here: http://gallery.open-bio.org/

A possible release candidate for BioPerl 1.2.2 is now available for download: http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz

Please download and give it a test. New aditions, features and fixes are in the “Changes” file.