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The Mailing list post

Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004.

The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl:

Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs)

Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience.

Bioperl version 1.4 for Windows is available. Thanks once again to Nigam Shah for creating and testing the PPM and PPD files.

BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!

I’m happy to announce the 1.24 release of Biopython. As normal Biopython is available from http://biopython.org.

The major changes in this release, in addition to the usual bug fixes, are:

New parsers for Phred and Ace format files – thanks to Frank Kauff New Code for dealing with NMR data – thanks to Bob Bussell New SeqUtils modules for codon usage, isoelectric points and other protein properties – thanks to Yair Benita New code for dealing with Wise contributed by Michael EZ-Retrieve sequence retrieval now supported thanks to Jeff Bio.Cluster updated along with documentation by Michiel BioSQL fixed so it now works with the current SQL schema – thanks to Yves Bastide for patches

The stable Bioperl release 1.4 is available for immediate use at: http://bioperl.org/DIST.

We are releasing simultaneously three modules:

• bioperl-core - core bioperl modules ( gz b2z)

• bioperl-ext - C compiled extensions ( gz b2z)

• bioperl-run - wrappers for external programs ( gz b2z)

They will also appear shortly at the IUBIO mirror (later today) and in CPAN.

Remember, all the external modules needed by bioperl-core can be installed from CPAN under name Bundle-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.

Jeff announces a new release of Biopython:

Biopython 1.23 is now available from the website at: http://www.biopython.org/

This is mostly a maintenance release, which fixes some problems in the installation. You do not need to update from 1.22 unless you are using the Bio.Cluster, Bio.KDTree, or Bio.PDB.mmCIF packages. The changes made in this release are: Fixed distribution of files in Bio/Cluster Now distributing Bio/KDTree/_KDTree.swig.C minor updates in installation code added mmCIF support for PDB files

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)