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Category Archives: BioPerl
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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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
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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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O|B|F Google Summer of Code Accepted Students
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
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O|B|F in Google Summer of Code
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 gsoc, news, twitter
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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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Sanger FASTQ format and the Solexa/Illumina variants
I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading
Posted in BioJava, BioPerl, Biopython, BioRuby, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects
Tagged BioJava, BioPerl, Biopython, BioRuby, EMBOSS, FASTQ
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