Development

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.

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).

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.

Source distributions and Windows installers for Biopython 1.59 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy), and under PyPy (excluding our NumPy dependencies). We are now encouraging early adopters to help beta testing on these platforms.

We are pleased to announce the release of BioRuby 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance.

Here is a brief summary of changes.

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.

Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. See Schmitt et al (2011) in Briefings in Bioinformatics.

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index.

Bio.SeqIO now includes an index_db() function which extends the existing indexing functionality to allow indexing many files, and more importantly this keeps the index on disk in a simple SQLite3 database rather than in memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the ability to run the BLAST tools and save the output as ASN.1 format, and then convert this to any other supported BLAST ouput format (plain text, tabular, XML, or HTML) with the blast_formatter tool. The wrappers were also updated to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The Biopython team is pleased to release Biopython 1.56, almost exactly three months after our last stable release ( Biopython 1.55).

The Bio.SeqIO module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files (thanks to Andrea Pierleoni). Also the SeqFeature object gained some new methods, and the Bio.Seq translation function can now be used with an arbitrary genetic code.