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. If anyone sees any problems with the current schema that he/she thinks should be corrected before this release, please speak up now. I guess I should make an effort and generate an updated ERD before release; the dated ones are confusing wrt the current schema. If there is consensus I’ll put out a release candidate early next week.

Heikki writes:

Philip Lijnzaad has written a new sequence format module called ’tab’. It is in CVS. Here is the blurb he wrote:

It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine that you have a format converter ‘seqconvert’ along the following lines:

my $in  = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to);
print $out $_ while <$in>;

then you can very easily filter sequence files for duplicates as:

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. The actual PPD file is at http://bioperl.org/DIST/bioperl-1.2.1-ppm.tar.gz

More information on bioperl Windows installations can be read online at http://www.bioperl.org/Core/Latest/INSTALL.WIN

March 15-16, 2003 – About a dozen Moby developers gathered recently. Minutes from the meeting are online at http://www.biomoby.org/twiki/bin/view/TWiki/CarnegieTAIR and pictures are online at http://biomoby.org/MOBY-DIC-III/MOBYDICIII.html

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. There are currently some differences between how the P-values are

The full announcement can be read here: http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html

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. He writes that Open Bioinformatics Foundation has proposed that “all federally funded bioinformatics software should be released as open source.” In fact, the O|B|F has explicitly rejected this extreme and inflexible view, as specified in our January 2002 statement on public funding & open source, which states:

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.