Archive for the ‘BioPerl’ Category
Monday, November 24th, 2003
Need to write a wrapper around sequence analysis service in a web form?
Richard Adams has written
a HOWTO document about his
Bio::Tools::Analysis modules. Available in CVS or in the latest developer release. See into BIOPERL/doc/howto/{sgml|html|pdf|txt}
for the SimpleWebAnalysis document in your favourite format.
Posted in BioPerl | Comments Off
Sunday, September 21st, 2003
I posted the slides for the Bioperl-db/BioSQL talk I gave at BOSC03.
-hilmar
Posted in BOSC/ISMB, BioPerl, OBDA / BioSQL | Comments Off
Friday, September 19th, 2003
The Bioperl developers are pleased to announce a 0.1 release of
bioperl-microarray, a Bioperl extension package dedicated to manipulation of microarray data.
The package is implemented using IO conventions Bioperl developers should already be familiar with. Data types currently supported are:
Affymetrix GeneChip CEL files (read and write)
Affymetrix GeneChip CDF files (read)
Affymetrix ...
Posted in BioPerl | No Comments »
Thursday, September 18th, 2003
Bioperl 1.2.3
On behalf of the Bioperl developers, we are pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile web-based sequence databases, Alignment parsing and manipulation, parsing ...
Posted in BioPerl | Comments Off
Saturday, August 30th, 2003
Hi Everyone,
Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers.
Simply put -- Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from ...
Posted in BioDAS, BioJava, BioMOBY, BioPerl, Biopython, General, OBDA / BioSQL | Comments Off
Thursday, August 14th, 2003
Jason has summarized a significant amount of work he has done on the CVS tree. Major work done on Bio::PopGen, Bio::Matrix and bug fixes to Bio::Tree and Bio::SeqIO.
All the juicy details can be read in his bioperl posting archived here:
http://bioperl.org/pipermail/bioperl-l/2003-August/013168.html
Posted in BioPerl | Comments Off
Tuesday, July 15th, 2003
Rob Edwards and Heikki Lehvaslaiho have been writing new restriction analysis classes. These will eventually replace the long serving Bio::Tools::RestrictionEnzyme by Steve Chervitz. The first working
versions are in CVS.
A UML graph shows the class relationships. A more verbose overview is below.
Posted in BioPerl | Comments Off
Tuesday, July 8th, 2003
This is a bug fix release from the stable branch.
The Bioperl release 1.2.2 is available at
http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz
and is propagating around CPAN now.
Bioperl-run is a collection of modules that wrap bioinformatics
applications to allow running them from bioperl. The release cycle of
bioperl-run follows the core. The latest bioperl-run release is
therefore at:
http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz
Posted in BioPerl | Comments Off
Wednesday, July 2nd, 2003
Our "Bioinformatics Open Source Conference" was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful --- 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.
Pictures are online here:
http://gallery.open-bio.org/
Posted in BOSC/ISMB, BioPerl, General | Comments Off
Wednesday, July 2nd, 2003
A possible release candidate for BioPerl 1.2.2 is now available for download:
http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz
Please download and give it a test. New aditions, features and fixes are in the "Changes" file.
Posted in BioPerl | Comments Off