Category Archives: BioPerl

Call for Organization Admins for OBF’s 2014 Google Summer of Code participation

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of … Continue reading

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | 7 Comments

BioPerl release 1.6.923

The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve … Continue reading

Posted in BioPerl, Code, Community | 5 Comments

BioPerl v.1.6.910 released

UPDATE: As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March. Unfortunately that … Continue reading

Posted in BioPerl, Code, Development, OBF Projects | 10 Comments

Travis-CI for Testing

BioRuby, Biopython and BioPerl are now using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated. Continue reading

Posted in BioPerl, Biopython, BioRuby, Blogroll, Code, Community, Development, OBF, OBF Projects | Leave a comment

BioPerl-DB, BioPerl-Run, BioPerl-Network 1.6.9 released

The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network Please report any bugs to our Redmine server. Enjoy! chris

Posted in BioPerl, Development, OBF | Leave a comment

BioPerl 1.6.9 released

BioPerl 1.6.9 is now available in CPAN.  In this release: Refactored Bio::Species/Bio::Tree New SeqIO modules (gbxml, msout, mbsout) Updates for perl 5.12 Bio::Assembly support for SAM/BAM, Newbler, ace output Bio::DB::SeqFeature updates PAML updated to work with v. 4.4d lots of … Continue reading

Posted in BioPerl, Development, General, OBF, OBF Projects | Leave a comment

OBF and Google Summer of Code 2011

Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code! Continue reading

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blogroll, Code, Community, Development, Google Summer of Code, OBF, OBF Projects | Leave a comment

Introduction of OpenID logins for OBF wikis

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Documentation, OBDA / BioSQL, OBF, OBF Projects, Website | Leave a comment

OBF Redmine server now available

The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly).  Bugs and user names (along with email contacts) from our old Bugzilla … Continue reading

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Code, Community, Development, OBDA / BioSQL, OBF, OBF Projects | Leave a comment

BioPerl has moved to GitHub

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 … Continue reading

Posted in BioPerl, Blogroll, Code, Community, Development, Documentation, General, OBF, OBF Projects | 1 Comment