Posts

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.

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.