Archive for the ‘BioPerl’ Category
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.
(more...)
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
Friday, June 27th, 2003
Heikki has converted some Bioperl workshop materials to a web slide show that is available here:
http://www.ebi.ac.uk/~lehvasla/bioperl/
Posted in BioPerl | Comments Off
Thursday, June 12th, 2003
Do you need to access sequences from multiple places? Would you like
to easily retrieve your own local sequences from indexed flat files,
all other sequences on species X from department wide raletional
database and the rest from global internet servers?
The Open Biological Database Access (OBDA) System was designed so that
one could use ...
Posted in BioJava, BioPerl, BioPython, OBDA / BioSQL | No Comments »
Thursday, May 29th, 2003
Shawn Hoon announces the release of bioperl-run-1.2.0 which is an extention to the bioperl framework that contains modules that act as wrappers for common informatics applications.
The full release announcement can be read here:
http://bioperl.org/pipermail/bioperl-l/2003-May/012308.html
Posted in BioPerl | Comments Off
Wednesday, May 28th, 2003
Jonathan Epstein has a simple script and directions for browsing bioperl list traffic offline via a mobile device.
The full post can be read online at:
http://bioperl.org/pipermail/bioperl-l/2003-May/012287.html
Posted in BioPerl | Comments Off
Friday, May 23rd, 2003
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.
Briefly, the server is started ...
Posted in BioDAS, BioPerl | Comments Off