Bioperl

Todd Harris has released GD::SVG in CPAN. This module implements support for most features of GD that are used by Bio::Graphics (together with the SVG module).

Try out the publication publication quality graphics directly from CVS and help to squash the last bugs before stable bioperl release. See all_glyphs.pl and dynamic_glyphs.pl in examples/biographics directory.

I posted the slides for the Bioperl-db/BioSQL talk I gave at BOSC03.

-hilmar

The Bioperl developers are pleased to announce a 0.1 release of bioperl-microarray, a Bioperl extension package dedicated to manipulation of microarray data.

The package is implemented using IO conventions Bioperl developers should already be familiar with. Data types currently supported are:

Affymetrix GeneChip CEL files (read and write) Affymetrix GeneChip CDF files (read) Affymetrix GeneChip Microarray Suite 5.0 normalized files (read) Affymetrix GeneChip dChip normalized files (read)

Data types for which support is planned in a 0.2 release include:

Bio::MAGE objects and MAGE-ML (read and write) Affymetrix SNPChip genotype files (read) GenePix GPR files (read)

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

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/