Archive for the ‘Documentation’ Category
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 »
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 ...
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF, OBF Projects | No Comments »
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 ...
Posted in Biopython, Blogroll, Code, Development, Documentation, 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 »
Monday, December 14th, 2009
This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython's Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ).
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF Projects | No Comments »
Saturday, October 10th, 2009
BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be greatly appreciated.
Posted in BioPerl, Development, Documentation, OBF, OBF Projects | No Comments »
Tuesday, September 29th, 2009
We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl's core code. You can grab it here:
Via CPAN:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/
Via the BioPerl website:
http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2
http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
http://bioperl.org/DIST/BioPerl-1.6.1.zip
The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it ...
Posted in BioPerl, Community, Development, Documentation, General, OBF, OBF Projects | 1 Comment »
Friday, September 25th, 2009
Biopython 1.51 onward includes support for Sanger, Solexa and Illumina 1.3+ FASTQ files in Bio.SeqIO, which allows a lot of neat tricks very concisely. For example, the tutorial (PDF) has examples finding and removing primer or adaptor sequences.
However, because the Bio.SeqIO interface revolves around SeqRecord objects there is often a ...
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Thursday, September 24th, 2009
The release of Biopython 1.52 earlier this week marked the end of an era, it was our last release using CVS for source code control.
As of now, Biopython is using a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby ...
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, OBF, OBF Projects | Comments Off