Posts

Agenda

Venue: to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC)  Dial-in Number: 1-605-475-5950 (US Midwest)  Participant Access Code: 279610

1. Old business
   • Apr 2013 BoD meeting minutes
2. New business
   1. Board elections (by secret electronic ballot):
      • Hilmar Lapp, running for a 2nd term as President
      • Peter Cock, running for office of Secretary
      • Nomi Harris, running for a 2nd term on the Board, as at-large member
   2. To the extent available, review of 2013 financials (Hilmar)
   3. BOSC 2014: update from and vote of confidence for the 2014 chairs (Nomi, Peter)
   4. Does OBF and/or BOSC want to be listed as an ISCB “Community of Special Interest” (COSI) along side other SIGs and communities? See NetBio and RegSys examples. (Peter)

Minutes

Attending:

Agenda

Venue: to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)  Dial-in Number: 1-605-475-5950 (Midwest)  Participant Access Code: 279610

1. Old business
   • Nov 2012 BoD meeting minutes
   • Treasurer’s 2012 report (Chris Dagdigian)
2. New business
   1. Administration of O|B|F’s 2013 Google Summer of Code participation (Pjotr Prins)

Minutes

Venue: held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)

Attending:

• Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Chris Fields, Peter Cock; Jason Stajich joined for the last 15 minutes.
• Guests: none

Minutes:

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5).

This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.

The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:

Note: I’m reposting here the original announcement from Florent Angly on the BioPerl mail list.

Dear all,

Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website.

This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5).

UPDATE:

As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March.

Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I’m packaging a new point release ( v1.6.920) that removes Bio::Biblio to prevent this.  That has now been uploaded to CPAN and should be available shortly.

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython is available for versions 2.5 and 2.7 and under PyPy for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013.

BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the ISMB/ECCB 2013 is in Berlin, Germany.

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.

• “gem install bio” failed with Ruby 2.0 or later versions.
• lib/bio/db/gff.rb script encoding issue
• Bio::Blast::Default::Report parse error when subject sequence contains spaces.

For more information, see RELEASE_NOTES.rdoc and ChangeLog.

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

The updated Biopython Tutorial and Cookbook is online ( PDF).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ‘beta’ installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows.