Archive for the ‘Code’ Category
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 ...
Posted in Biopython, Code, Community, Development, OBF Projects | No Comments »
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 ...
Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF | No Comments »
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 | 1 Comment »
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 ...
Posted in Biopython, Code, Development, OBF | Comments Off
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 »
Thursday, February 26th, 2009
All,
I am proud to announce that the 1.6 release for BioPerl-run, BioPerl-
db, and BioPerl-network are now available by direct download and via
CPAN. These are designated as 1.006000, with a requirement for
BioPerl 1.6 and higher (1.006000).
FIXED:
1) Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as
executable ...
Posted in BioPerl, Code, Development, Documentation | No Comments »
Wednesday, February 25th, 2009
Hi all,
We are pleased to announce the release of BioRuby 1.3.0.
The archive is available at:
http://bioruby.org/archive/bioruby-1.3.0.tar.gz
Web page:
http://bioruby.org/
http://bioruby.open-bio.org/
API documentation:
http://bioruby.org/rdoc/
Bug report:
http://rubyforge.org/projects/bioruby/
(Updating of http://bioruby.rubyforge.org/ is still
in progress. Please wait for a moment.)
We also put RubyGems pacakge at RubyForge as always.
You can easily install by ...
Posted in BioRuby, Code, Development, Documentation | No Comments »
Tuesday, February 24th, 2009
Please forward as appropriate and forgive multiple postings.
Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009
An ISMB 2009 Special Interest Group (SIG)
Date: June 27-28, 2009
Location: Stockholm, Sweden
URL: http://www.open-bio.org/wiki/BOSC_2009
Abstract submission via EasyChair:
https://www.easychair.org/login.cgi?conf=bosc2009
Important Dates
Monday, April 13: Abstract deadline
May 1, 2009: Notification of accepted abstracts
May 15, 2009: Early Registration ...
Posted in BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects | No Comments »