Posts

Agenda

• Old Business
  1. Approval of minutes from 2007
• New Business
  1. Current Board
     • Confirm past term expirations of those who did not run again for the Board.
     • What to do about the Secretary seat?
     • Some of the items on the agenda here need a legitimate vote by the Board (with prior notification and quorum satisfied). Should plan for a (presumably virtual) voting Board meeting soon afterwards.
     • How can we better ensure quorum?
  2. Voting on the board appointments
     • Kam Dalhquist has already served as a major organizer for BOSC and is interested in helping lead the OBF to achieve more outreach and education.
     • Darin London has served as BOSC chair for the past 4 years
     • Strengthen connection with O|B|J
     • Procedure for appointment of additional BOD members
  3. Financial report (Treasurer)
     • Account standing, reserves
     • 501(c)3 accounting and filing status
     • Sponsorship accounting
  4. BOSC
     • Short 2007 report (attendance, talk highlights)
     • BOSC 2008 summary (attendance, talk hightlights)
     • Should BOSC 2009 to be held in conjuction with ISMB2009?
     • Possibilities for including submitted papers for a publication.
  5. OBF Membership accounting and drive to register more members
     • Membership forms physical records
     • Members who are citizens of trade-restricted countries - legal advice, file for exemption?
     • Form doesn’t give date, need to amend
  6. OBF future directions
  7. Review of By-Laws (Parliamentarian)
     • 10-days prior notice of Board meeting requirement: need to change or have a standing Board meeting (BoF) on day 1 or 2 of BOSC
     • Not clear who elects officers - members may, but not a requirement, Directors can elect officers too. Leave as is or change?

Minutes

Location: Radisson Harbourfront, 5th floor poolside, July 18, 2008

The OBF board meeting will be held via conference call on Nov 19, from 12:30PM to 2PM PST.  Agenda items and information about participating is available on the agenda webpage. We anticipate this call primarily to manage administrative tasks for the foundation. We welcome input on including more members in the OBF leadership and helping set the direction for the foundation.

We are pleased to announce a beta release of Biopython 1.49. There are been some significant changes since Biopython 1.48 was released two months ago, which is why we are initially releasing a beta for wider testing.

As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).

As in the previous releases, Biopython 1.49 beta supports Python 2.3, 2.4 and 2.5 but should now also work fine on Python 2.6. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see previous news article).

Many of you will be aware that Python 2.6 was released a month ago (October 1st, 2008). This supports a lot of new syntax and functionality, but also deprecates some old modules (e.g. the sets module).

While Biopython 1.48 does mostly work with Python 2.6, we’ve been testing with Python 2.6 and have fixed a number of deprecations or breakages in our CVS repository. If using Biopython with Python 2.6 is important to you, please help out by testing the CVS code (which needs NumPy and not Numeric) and letting us know on the mailing list or bugzilla if we’ve missed anything.

To date, Biopython releases have relied on the original numerical python library, Numeric (used in python with “import Numeric”).  In the next release we will at last be moving to its successor, NumPy (used in python with “import numpy”).

This transition is already under way in the Biopython source code repository.  For further details, or to voice your opinion or enthusiasm, please join the Biopython Mailing List(s).

Finally, for anyone interested in the background story, the SciPy project has a page describing the history of the numerical python libraries.

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