The day you’ve been waiting for is finally here. That’s right, it’s time for a brand new biopython.org website! Woo. Thanks to the hard work of Chris Dagdigian and your Biopython team, we’ve got our new website set up on a new up to date Linux server. Come check out all the excitement at biopython.org.
Heikki writes: Philip Lijnzaad has written a new sequence format module called ’tab’. It is in CVS.
Nigam Shah has created the necessary PPM/PPD distribution files for bioperl-1.2 .1 that will allow ActiveState perl users on Windows machines to easily install the bioperl suite and the most common bioperl external module dependencies. The PPD file is online at http://bioperl.org/ftp/DIST/Bioperl-1.2.1.ppd.
March 15-16, 2003 – About a dozen Moby developers gathered recently.
The release is available at http://www.bioperl.org/ftp/DIST/bioperl-1.2.1.tar.gz and is propagating around CPAN now. The main bug fixes in this release are: - inclusion of WrapperBase, making StandAloneBlast work from the release - fixes and cleanup of Bio::Coordinate - fixes to Bio::Index::EMBL and bpindex The 1.2.1 release does see some major additions in the Ontology area.
We need you! Please download and help test a potential 1.2.1 release candidate that is available at http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz If all goes well the official bioperl-1.2.1 will be released early next week.
GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are caveats for ambiguous names), an ontology file, and an annotation file, and determine the P_values for the observed frequency of annotation to those genes for each GO node.
In the March 2003 issue of Genome Technology, “Opposite Strand” contributor Gerald Barnett’s insightful article on “free choice for open source” is blighted by a gross misattribution.
A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at /mailman/listinfo/bioped-l This is intended to build off the initial work done in Perl for bioperl-pedigree but is applicable to all who want to contribute to the design or implementation in any language. Database persistence and pedigree rendering are initial areas that will be addressed.
A release candidate for an eventual Bioperl 1.2.1 release is online at: http://bioperl.org/ftp/birney/bioperl-1.2.1-rc1.tar.gz We need people to install and test this package on as many systems and architectures as possible.
Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is an analysis of the two LSID Resolution proposals. The document also includes brief descriptions of two use cases that seem appropriate to us. We would be very interested in any responses to this analysis.