Category Archives: OBF Projects

Open Bioinformatics Projects

BioRuby 1.4.3.0001 Released

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs. “gem install bio” failed with Ruby 2.0 or later versions. lib/bio/db/gff.rb script encoding issue Bio::Blast::Default::Report parse error when subject sequence contains spaces. For … Continue reading

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Biopython 1.61 released

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). The updated Biopython Tutorial and Cookbook is online (PDF). Platforms/Deployment We currently support Python … Continue reading

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OBF Board meeting 13 Nov

The Open Bioinformatics Foundation (OBF) will be holding a public Board of Directors meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT). The meeting will be held online or over conference call. We will … Continue reading

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Server transition process to AWS servers

Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue … Continue reading

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OBF is now an SPI-associated project

I am very pleased to announce that as of the SPI’s Board meeting that took place yesterday, O|B|F is now an SPI-associated project. Continue reading

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BioRuby 1.4.3 released

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius. Here is a brief summary of changes. Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for … Continue reading

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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

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Biopython 1.60 released

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI). Platforms/Deployment We currently support Python 2.5, 2.6 and 2.7 and also test under Jython … Continue reading

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BioJava 3.0.4 released

BioJava 3.0.4 has been released and is available from http://www.biojava.org/wiki/BioJava:Download as well as from the BioJava maven repository at http://www.biojava.org/download/maven/ . – This is mainly a bug fix release addressing issues with the protein structure and disorder modules – One … Continue reading

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Students selected for GSoC

Hello all, I’m very pleased and excited to announce that the Open Bioinformatics Foundation has selected 5 very capable students to work on OBF projects this summer as part of the Google Summer of Code (GSoC) program. The accepted students, … Continue reading

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