Posts

Bioperl developers are preparing a 1.5 release, you can grab the pre-release for testing at http://bioperl.org/DIST. We would greatly appreciate you downloading and testing this code before it is released by running ‘make test’.

See Aaron’s post announcing the RC1 candidate.

I’m happy to announce a new release of Biopython 1.30, available today from http://biopython.org. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we’ve bumped up to a brand new major number. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython at biopython.org or biopython-dev at biopython.org). For the full details about changes, please see: http://portal.open-bio.org/pipermail/biopython/2004-May/002078.html

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.