Archive for the ‘Documentation’ Category

Clever tricks with NCBI Entrez EInfo (& Biopython)

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 ...

Introducing (and expanding) the Biopython Cookbook

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 ...

Biopython paper published

Sunday, March 22nd, 2009

An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of the Open Access article is available online: P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de ...

Google Summer of Code: Project ideas page

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

Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network

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 ...

BioRuby 1.3.0 is released

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 ...

Updated PDoc software

Monday, June 26th, 2006

Raphaël Leplae has updated the Pdoc software to have an improved stylesheet and fix several bugs including problems rendering Bio::DB::Fasta. Thanks a lot Raphaël and Patrick Meidl for getting the bugs reported and fixed for this nice POD to HTML converter. You can see the Pdoc for Bioperl packages in ...

Deobfuscator interface now available

Sunday, May 14th, 2006

I'm glad to announce the availability of the Deobfuscator interface at the BioPerl website. You can use it at the following URL: http://bioperl.org/cgi-bin/deob_interface.cgi Many thanks to Laura Kavanaugh and David Messina for this great contribution to the BioPerl project!

BioPerl-run in FreeBSD

Tuesday, May 2nd, 2006

It's my great pleasure to announce the availability of the BioPerl-run packages (stable & developer releases) for the FreeBSD operating system. For instructions on how to install BioPerl ports in FreeBSD, please take a look into the Getting Bioperl section of the BioPerl Wiki.

Bioperl ListSummaries for April 12-25

Tuesday, April 25th, 2006

The newest summary of the BioPerl mailing lists has been posted to the wiki: April 12-25 Post gripes, harrassments, and faint praises at the regular places.