We are pleased to announce the release of Biopython 1.45.

This release includes numerous code improvements and fixes, including in Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.PopGen, Bio.SwissProt, Bio.Cluster, Bio.SCOP, Bio.InterPro, Bio.GenBank, Bio.ExPASy, BioSQL, and the Biopython documentation. Too many to list them all here!

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

–Michiel on behalf of the Biopython developers

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.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

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.
• Show-and-tell was received positively, but didn’t play as big a role anymore
• Want to continue running the conference
• Venue:
  • Seems much favorable to associate with an existing major event
  • One model could be to associate with different events on an alternating basis, such as IMSB every other year and a different conference every other year
• Need a new Organizing Committee, several people volunteered to help organizing
  • Committee should decide on sessions, timetable, outreach venues
  • Session chairs who are also charged to identify the most desirable speakers
  • Should have budget to reimburse travel for key speakers who otherwise wouldn’t be able to come
  • Need to look into venue and procedure for publishing the talks
  • Include a hackathon?

Action items:

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.

http://bioperl.org/wiki/BOSC2007_Meetup

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.

Two things that have been discussed on the mailing list lately are:

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.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.