Archive for the ‘Code’ 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 »
Thursday, August 26th, 2010
After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal. The article is open access, so please take a look.
BioRuby: Bioinformatics software for the Ruby programming language
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq475
Posted in BioRuby, Code, Community, Development, Documentation, 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 »
Friday, May 14th, 2010
BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the great public git hosting site repo.or.cz.
If you are a current BioPerl developer (had a previous account for direct access to our prior Subversion repository), please sign up for a GitHub ...
Posted in BioPerl, Blogroll, Code, Community, Development, Documentation, General, OBF, OBF Projects | 1 Comment »
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 ...
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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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Monday, January 18th, 2010
BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting. Several items were covered on the agenda:
In order to start addressing whole genome data with more lightweight objects, we are planning on setting up a lightweight Bio::SeqI object that has a flexible DB ...
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