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Author Archives: Chris Fields
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
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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
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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
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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
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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
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BioPerl at GMOD Meeting 2010
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
Posted in BioPerl, Code, Community, Development, OBF, OBF Projects
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BioPerl interview in latest FLOSS Weekly
Two of the core BioPerl developers, Jason Stajich and Chris Fields, were interviewed by FLOSS Weekly. The interview is now available as an MP3 on the FLOSS Weekly website; several streaming versions (including podcast) are also available.
Posted in BioPerl, BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects
Tagged BioPerl
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BioPerl core 1.6.1 PPM available
BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. This has been tested only for ActivePerl 5.10 and above, so any feedback with older versions of BioPerl would be … Continue reading
First 1.6.1 alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network
Running a bit late on this, so just a quick note that the first alphas for BioPerl-Run, BioPerl-DB, and BioPerl-Network have been uploaded to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network They can also be downloaded from the BioPerl website: http://bioperl.org/DIST/RC/ This is … Continue reading
BioPerl 1.6.1 released
We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally … Continue reading
Posted in BioPerl, Community, Development, Documentation, General, OBF, OBF Projects
Tagged BioPerl, FASTQ
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