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We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete).

The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO:

• reading and writing “tab” format (simple tab separated)
• writing “nexus” files
• reading “pir” files (NBRF/PIR)
• basic support for writing “genbank” files (GenBank plain text)

This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers.

This is a belated news entry announcing the second BioSQL v1.0 (code-named Tokyo) release, v1.0.1, which was made on August 2, 2008. It is available from the BioSQL downloads page.

This version of the schema should be fully backwards compatible with the v1.0.0 schema for nearly all software and queries. The only change is relaxing a column width constraint. Migration scripts are for those who want to simply upgrade their existing database.

We are pleased to announce the release of Biopython 1.47.

This release includes a new Bio.AlignIO module, updates to Bio.Blast, parsers for NCBI’s Entrez E-Utilities, numerous other code improvements and fixes, and an extended and updated documentation. In particular if you use Biopython to access NCBI’s E-Utilities, we encourage you to download and install this release to ensure full compliance with NCBI’s access rules.

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

The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative multi-user online applications and virtual worlds.

For further information about Dr. Lombardi, see the Wikipedia entry about him, his blog, and the OpenCroquet website.

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