OBF and Google Summer of Code 2011

March 18th, 2011 by

Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code!

Introduction of OpenID logins for OBF wikis

March 17th, 2011 by

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new […]

OBF Redmine server now available

March 17th, 2011 by

The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason […]

Biopython 1.56 released

November 26th, 2010 by

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

Biopython dropping Python 2.4 Support?

November 18th, 2010 by

The forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4. If you would be negatively affected us dropping support for Python 2.4, please let us know as soon as possible.

Biopython 1.55 released

August 31st, 2010 by

The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable […]

Biopython 1.55 beta released

August 18th, 2010 by

We’ve just released a beta of Biopython 1.55 for user testing. Since Biopython 1.54 was released three months ago, we’ve […]

Biopython 1.54 released

May 20th, 2010 by

The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes […]

O|B|F Google Summer of Code Accepted Students

May 2nd, 2010 by

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their […]

Illumina FASTQ files – Read Segment Quality Control Indicator

April 30th, 2010 by

In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]

Partial sequence files with Biopython

April 27th, 2010 by

This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 […]

Making Biopython SeqIO and AlignIO easier

April 5th, 2010 by

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) […]

Biopython 1.54 beta released

April 2nd, 2010 by

A beta release for Biopython 1.54 is now available for download and testing.

O|B|F in Google Summer of Code

March 21st, 2010 by

O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010.

Sanger FASTQ format and the Solexa/Illumina variants

December 17th, 2009 by

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the […]

Biopython 1.53 released

December 15th, 2009 by

We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months […]

Interleaving paired FASTQ files with Biopython

December 14th, 2009 by

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]

Working with FASTQ files in Biopython when speed matters

September 25th, 2009 by

Biopython’s SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster.