Archive for the ‘Development’ Category
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 ...
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Tuesday, September 22nd, 2009
We are pleased to announce the availability of Biopython 1.52, a new stable release of the Biopython library.
It may only have been one month since the last release, but in that time we've added enough useful features to warrant a new release. In particular, Biopython 1.52 includes more substantial support ...
Posted in Biopython, Code, Development, OBF Projects | 2 Comments »
Tuesday, September 22nd, 2009
As per Peter's recent post we are using this space to show of a couple of the new features in Biopython 1.52 before it is released. In this post we'll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52.
No one has ever complained ...
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Monday, September 21st, 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. This will of course be covered in the Biopython Tutorial & Cookbook (PDF) once this code is released.
Suppose you have a large sequence ...
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Wednesday, September 2nd, 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 is a brief summary of changes.
Refactoring of BioSQL support.
Bio::PubMed bug fixes.
Bio::NCBI::REST bug fixes.
Bio::GCG::Msf bug fixes.
Bio::Fasta::Report bug fixes and added support for multiple query sequences.
Bio::Sim4::Report bug fixes.
Added unit tests for Bio::GCG::Msf and ...
Posted in BioRuby, Code, Community, Development, OBF Projects | No Comments »
Monday, August 17th, 2009
We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number of minor bugs.
In particular, the SeqIO module ...
Posted in Biopython, Code, Community, Development, OBF, OBF Projects | 1 Comment »
Tuesday, June 23rd, 2009
A beta release for Biopython 1.51 is now available for download and testing.
In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO's support for the FASTQ format to include files created by Illumina 1.3+, and added a ...
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Sunday, June 21st, 2009
Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help.
For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the Entrez web interface, for use in a script with ...
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Wednesday, May 6th, 2009
As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython must be posted to the main Biopython mailing list no later than Friday, May 8.
Posted in Biopython, Code, Community, Development, OBF | 2 Comments »
Wednesday, April 29th, 2009
Hi all,
You may have noticed we're trying out using the wiki for Biopython cookbook entries. It's a new idea so at the moment there are only a few 'recipes' on offer. If you have some tricks you find yourself using time and again to solve a problem why not ...
Posted in Biopython, Code, Community, Documentation, HOWTO, OBF, Website | No Comments »