Category Archives: BioPerl

Travis-CI for Testing

Posted on July 30, 2012 by Peter

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

Posted on April 21, 2011 by Chris Fields

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

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BioPerl 1.6.9 released

Posted on April 14, 2011 by Chris Fields

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 →

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OBF and Google Summer of Code 2011

Posted on March 18, 2011 by Peter

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

Posted on March 17, 2011 by Chris Fields

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

Posted on March 17, 2011 by Chris Fields

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

Posted on May 14, 2010 by Chris Fields

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

O|B|F Google Summer of Code Accepted Students

Posted on May 2, 2010 by Robert Buels

I’m pleased to announce the acceptance of OBF’s 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) – Improvements to BioJava including Implementation of Multiple Sequence Alignment … Continue reading →

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

O|B|F in Google Summer of Code

Posted on March 21, 2010 by Robert Buels

O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010. Continue reading →

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

BioPerl at GMOD Meeting 2010

Posted on January 18, 2010 by Chris Fields

BioPerl developers and users attended the BioPerl satellite meeting on January 13th, just prior to the GMOD Meeting.  Several items were covered on the agenda: In order to start addressing whole genome data with more lightweight objects, we are planning on … Continue reading →

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