Archive for the ‘Code’ Category
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 ...
Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF Projects | Comments Off
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 »
Thursday, March 26th, 2009
Those of you doing next generation sequencing may be pleased to know that the next release of Biopython is expected to include support for reading and writing FASTQ and QUAL files within our Bio.SeqIO interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche ...
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Tuesday, March 17th, 2009
Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems ...
Posted in Biopython, Code, Community, Development, OBF | 1 Comment »
Tuesday, March 10th, 2009
A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:
http://open-bio.org/wiki/Google_Summer_Code_2009
Posted in Code, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »