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.
Biopython CVS to git migration [ September 24, 2009 ] Biopython has now moved from CVS to a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby project have been using github for some time, so we are in good company.
Biopython 1.52 released [ September 22, 2009 ] We are pleased to announce the availability of Biopython 1.52, a new stable release of the Biopython library. It may […]
Simpler, optimized format conversion with… [ September 22, 2009 ] In this post we’ll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions.
Indexing sequence files with Biopython [ September 21, 2009 ] The forthcoming release of Biopython 1.52 will include a couple of nice improvements to the Bio.SeqIO module, and here we’re going to introduce the new index function.
BioRuby 1.3.1 released [ September 2, 2009 ] We are pleased to announce the release of BioRuby 1.3.1. This new release fixes many bugs existed in 1.3.0. Here […]
Biopython 1.51 released [ August 17, 2009 ] We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by […]
Minutes:2009 BOSC Meeting [ June 27, 2009 ] Note: this is preliminary and needs some editing. OBF Business Meeting at BOSC 2009 Location: Rica Talk Hotel, Restaurant 2nd […]
Biopython 1.51 beta released [ June 23, 2009 ] A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 […]
Clever tricks with NCBI Entrez… [ June 21, 2009 ] Constructing complicated Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. This can tell you all the searchable fields available for each of the Entrez databases.
BOSC Schedule Posted [ June 1, 2009 ] The BOSC 2009 schedule of speakers with links to abstracts has been posted at http://www.open-bio.org/wiki/BOSC_2009_Schedule.
BOSC Update: Ruttenberg, Hanmer confirmed… [ May 13, 2009 ] Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC […]
Dropping Python 2.3 Support [ May 6, 2009 ] As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython […]
Introducing (and expanding) the Biopython… [ April 29, 2009 ] Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]