Making Biopython SeqIO and AlignIO…

[ April 5, 2010 ]

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 2, 2010 ]

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

O|B|F in Google Summer of…

[ March 21, 2010 ]

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

BOSC 2010 Call for Abstracts

[ March 2, 2010 ]

Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open. At-a-glance BOSC is an ISMB […]

OpenBio solution challenge: Project updates…

[ January 28, 2010 ]

The BOSC 2010 organizing committee is hard at work getting prepared for this July’s meeting in Boston: http://www.open-bio.org/wiki/BOSC_2010 One of […]

BioPerl at GMOD Meeting 2010

[ January 18, 2010 ]

BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were […]

BioRuby 1.4.0 released

[ December 29, 2009 ]

We are pleased to announce the release of BioRuby 1.4.0. This new release contains many new features, in addition to […]

BOSC 2010 Request for Input

[ December 18, 2009 ]

The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community. You may send your suggestions to the bosc@open-bio.org e-mail address or add suggestions to the BOSC 2010 talk/discussion wiki page at: http://www.open-bio.org/wiki/Talk:BOSC_2010. Please respond to the questions in this post by January 8, 2010.

Sanger FASTQ format and the…

[ December 17, 2009 ]

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 15, 2009 ]

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

2009 O|B|F Board of Directors…

[ December 14, 2009 ]

The official 2009 Board of Directors meeting is taking place today, Monday Dec 14, at 4pm EST (21:00 UTC) via […]

Interleaving paired FASTQ files with…

[ December 14, 2009 ]

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

Minutes:2009 ConfCall

[ December 14, 2009 ]

Agenda Old business 2008 BoD meeting minutes New business BOSC BOSC 2009 (Kam) Money spent/made attendee number, any other feedback […]

BioPerl interview in latest FLOSS…

[ November 22, 2009 ]

Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now […]

BioPerl core 1.6.1 PPM available

[ October 10, 2009 ]

BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. […]

First 1.6.1 alphas of BioPerl-Run,…

[ October 1, 2009 ]

Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network […]

BioPerl 1.6.1 released

[ September 29, 2009 ]

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can […]

Working with FASTQ files in…

[ September 25, 2009 ]

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.