Tony writes: I have just checked in to the Bio::Das perl beta CVS repository (“Bio-Das2”) a collection of modules that creates a minimal DAS reference server from a single AGP file (or a directory of one or more files). There is also a sample server script in the “eg” directory.
Jason writes: I’ve added a parser for the ab initio gene predictor GlimmerM in Bio::Tools::Glimmer. Tests are added to t/Genpred.t now. It follows the Bio::Tools::AnalysisParser interface which support the next_prediction call and returns a Bio::Tools::Prediction::Gene object in the same way as Genscan. I also have some scripts for building the training set file so you can run Glimmer on other species.
Hilmar writes: I got the Oracle version of the biosql schema fully migrated, at least as far as I can tell from here. I’m going to commit the new version some time today. There will also be a sql*plus migration script from pre-Singapore to the current version that supposedly keeps your data intact (be sure to read the disclaimer though). This means we’re getting ready to release Biosql 1.0, possibly as early as next week.
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.