Archive for the ‘Biopython’ Category
Tuesday, August 31st, 2010
The Biopython team is proud to announce Biopython 1.55, a new stable release, about three months after our last stable release (Biopyton 1.54) and the beta release earlier in August.
A lot of work has been towards Python 3 support (via the 2to3 script), but unless we broke something you shouldn't ...
Posted in Biopython, Code, Development, OBF, OBF Projects | No Comments »
Wednesday, August 18th, 2010
We've just released a beta of Biopython 1.55 for user testing.
Since Biopython 1.54 was released three months ago, we've made a good start on work for Python 3 support (via the 2to3 script), but as a side effect of this we've had to update quite a lot of the older ...
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Thursday, May 20th, 2010
The Biopython team is proud to announce Biopython 1.54, a new stable release of the Biopython library. Biopython 1.54 comes five months after our last release and brings new features, tweaks to some established functions and the usual collection of bug fixes.
This is the first stable release to feature ...
Posted in Biopython, Code, Community, Development, General, Google Summer of Code, OBF, OBF Projects | No Comments »
Sunday, May 2nd, 2010
I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors:
Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms
Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Development, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Friday, April 30th, 2010
In another quirk to the FASTQ story, recent Illumina FASTQ files don't actually use the full range of PHRED scores - and a score of 2 has a special meaning, The Read Segment Quality Control Indicator (RSQCI, encoded as 'B').
Hats off to Dr Torsten Seemann for raising awareness of this ...
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF, OBF Projects | No Comments »
Tuesday, April 27th, 2010
This is another blog post to highlight one of the neat tricks you'll be able to do with Biopython 1.54 (which you can help test with the Biopython 1.54 beta release).
It is often useful to be able to extract a few records from a larger sequence file - for example, ...
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Monday, April 5th, 2010
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also accept filenames.
This is a case of practicality beats purity ...
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Friday, April 2nd, 2010
A beta release for Biopython 1.54 is now available for download and testing.
Since Biopython 1.53 was released at the end of last year, several new features and more documentation have been added, plus the usual bug fixes. For full details see the NEWS file.
All the new features have been tested ...
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Sunday, March 21st, 2010
The Open Bioinformatics Foundation has been accepted as a mentoring organization for this summer's Google Summer of Code. Our list of project ideas and mentors is linked from the O|B|F GSoC page.
Student applications must be submitted to Google by April 9, 2010, see the official GSoC 2010 FAQ. That is ...
Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, BioRuby, Biopython, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | No Comments »
Thursday, December 17th, 2009
I'm delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects:
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto ...
Posted in BioJava, BioPerl, BioRuby, Biopython, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »