After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at http://biosql.org/DIST/ as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The full release announcement can be found in the BioSQL mailing list archives, and in the distribution itself.
Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada. For the first time this year, the second conference day will overlap with the ISMB tutorial day, in an attempt to make the overall stay shorter for those who want to attend both BOSC and ISMB.
We are pleased to announce the release of Biopython 1.44. This release includes lots of code improvements and fixes in the Blast interface and parsers, sequence input/output, the SwissProt parser, the clustering routines, as well as a brand new module for population genetics. For reasons of compatibility, some radical changes were necessary in some parts of the code; please let us know if you find some functionality missing.
Venue: Cafe Prückl, Vienna Date: 7/21/2007, 5.30pm Attending: Jason Stajich (OBF President), Hilmar Lapp (OBF Parliamentarian), Darin London, Kam Dahlquist BOSC Had 94 attendees registered specifically for BOSC as of July 9th Do we have an audience? Is there a niche that BOSC continues to fill? The numbers seem to speak a clear voice.
If you’ll be at BOSC or ISMB - please see this page and sign your name if you would like to try and meet up. We’ll do a developer’s dinner as well as have a BoF.
So Mailing list summaries have stopped because we need someone else to help post these summaries. Not a light job unfortunately. If you are interested, please post to the mailing list or contact Jason, Sendu, or Chris for more details. This is one way you can help BioPerl without contributing code if you aren’t comfortable with that type of commitment.
I updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree files. This uses the Bio::Tree::Draw::Cladogram module that will draw Phylograms or Cladograms. With a few unix tools ( eps2png and epstopdf [part of TeX]) you can generate png and pdf files automatically making this an easy addition to phylogenetic pipelines that generate webpages as well as stand alone applications.
Updated mediawiki to 1.10 Did a bulk creation of a number of modules wiki pages for modules that had been previously created but not added to the wiki. Added them with default module templates.
We are pleased to announce the release of Biopython 1.43. This release includes a brand-new set of parsers in Bio.SeqIO by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new UniGene flat-file parser by Sean Davis, and numerous improvements and bug fixes in Bio.PDB, Bio.SwissProt, Bio.Nexus, BioSQL, and others. Believe it or not, even the documentation was updated.
I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2
I’m proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2