Obf-Projects

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.65 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.

The most visible change is that the Biopython sequence objects now use string comparison, rather than Python’s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).

Source distributions and Windows installers for Biopython 1.64 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2.

The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan.

Hi all, I’m pleased to announce the acceptance of OBF’s Google Summer of Code 2014 (GSoC) students:

• Sarah Berkemer - " Open source high-performance BioHaskell" (Mentors: Christian Höner zu Siederdissen, Ketil Malde) ( blog)
• Loris Cro - " An ultra-fast scalable RESTful API to query large numbers of VCF datapoints" (Mentors: Francesco Strozzi, Raoul Bonnal & the BioRuby team) ( blog)
• Victor Kofia - " JSBML: Redesign the implementation of mathematical formulas" (Mentors: Alex Thomas, Sarah Keating & the JSBML team) ( blog)
• Evan Parker - " Addition of a lazy loading sequence parser to Biopython’s SeqIO package" (Mentors: Wibowo Arindrarto, Peter Cock & the Biopython team) ( blog)
• Ibrahim Vazirabad - " Improving the Plug-in interface for CellDesigner" (Mentors: Andreas Dräger, Alex Thomas & the JSBML team) ( blog)
• Leandro Watanabe - " Dynamic Modeling of Cellular Populations within JSBML" (Mentors: Nicolas Rodriguez, Chris Myers & the JSBML team) ( blog)

Congratulations to our accepted students!

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc. Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

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:

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.