Category Archives: OBF

General Open Bioinformatics News

Call for abstracts for BOSC 2012

Posted on March 5, 2012 by Peter

Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012. Dates: July 13-14, 2012 Location: Long Beach, California Web site: http://www.open-bio.org/wiki/BOSC_2012 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important … Continue reading →

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Cross-links in GenomeDiagram

Posted on March 2, 2012 by Peter

I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. You can now control the start and end points of individual tracks, and you can add cross-links between regions of … Continue reading →

Posted in Biopython, Blogroll, Code, Community, Development, HOWTO, OBF, OBF Projects | Tagged | 1 Comment

Biopython 1.59 released

Posted on February 24, 2012 by Peter

Source distributions and Windows installers for Biopython 1.59 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Continue reading →

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OBF Annual Meeting 2011

Posted on October 28, 2011 by Peter

The annual Board of Directors Meeting of the Open Bioinformatics Foundation will take place on November 8, 2011. As in previous years, it will be held by conference call, estimated to be about 2 hrs long. Continue reading →

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Chromosome Diagrams in Biopython

Posted on October 28, 2011 by Peter

One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. I’ve just been updating the Biopython Tutorial (current version here, PDF) to include an example drawing this: Here’s a PDF … Continue reading →

Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF, OBF Projects | Tagged | 1 Comment

BioRuby 1.4.2 released

Posted on August 26, 2011 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.2. This new release fixes bugs existed in 1.4.1 and adds new features and improvement of performance. Here is a brief summary of changes.

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Biopython 1.58 released

Posted on August 18, 2011 by Peter

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI). A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of … Continue reading →

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Announcing OBF Google Summer of Code Accepted Students

Posted on April 26, 2011 by Robert Buels

I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 6 very capable students to work on OBF projects this summer as part of the Google Summer of Code program. The accepted students, their projects, and … Continue reading →

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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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