Bioruby

We are pleased to announce the release of BioRuby 1.5.1.

In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare NCBI website transitioning to HTTPS.

We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2),  improvement of codes, and bug fixes.

Here is a brief summary of changes.

• Ruby 2.0.0, 2.1, 2.2 support.
• Some features are removed because of remote service discontinuance or difficulty of code maintenance.
• Refactoring of code.
• Bio::SPTR is renamed as Bio::UniProtKB.
• Bug fixes.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

(This is a repost of a BLOG on Google Open Source news about Google’s open source student programs and software releases)

One of our goals with GSoC is to inspire young developers to participate in open source development, hopefully continuing well beyond the summer. Pjotr Prins from the Open Bioinformatics Foundation shared this story with us about a GSoC 2012 student who has continued leading the development of a software tool used in laboratories around the world. That tool, Sambamba, was recently featured in an Oxford University Press scientific journal. The Open Bioinformatics Foundation (OBF) participated in Google Summer of Code (GSoC) in 2012 and again in 2014. One of our projects,Sambamba, enables users to rapidly process large sequence alignment files in the SAM, BAM and CRAM formats using parallel processing. Sambamba, which means “parallel” in Swahili, was recently the subject of a paper published in Bioinformatics Journal by GSoC alumnus Artem Tarasov. Since the tool is now used in DNA sequencing centres around the world, Artem has become well known in the bioinformatics community as Sambamba’s creator.

Last year’s Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.

Google’s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the organisations accepted for GSoC 2015. For example, a Biopython project was included under NESCent for GSoC 2013.

In 2014, OBF had six students in the Google Summer of Code 2014™ (GSoC) program mentored under its umbrella of Bio* and related open-source bioinformatics community projects: Loris Cro (Bioruby) with mentors Francesco Strozzi and Raoul Bonnal; Evan Parker (Biopython) with mentors Wibowo Arindrarto and Peter Cock; Sarah Berkemer (BioHaskell) with mentors Christian Höner zu Siederdissen and Ketil Malde; and three students contributed to JSBML: Victor Kofia (mentors: Alex Thomas and Sarah Keating), Ibrahim Vazirabad (mentors: Andreas Dräger and Alex Thomas), and Leandro Watanabe (mentors: Nicolas Rodriguez and Chris Myers).

As a change from earlier years in which OBF participated in GSoC as a mentoring organization, in 2014 we purposefully defined our umbrella as much more inclusive of the wider bioinformatics open-source community, bringing it more in line with the annual Bioinformatics Open-Source Conference (BOSC).  In part this was also motivated by " paying it forward", a concept central to growing healthy open-source communities, after the larger domain-agnostic language projects such as SciRuby and PSF had extended an open hand to OBF mentors when OBF did not get admitted as a GSoC mentoring organization in 2013. In the end, four out of the six succeeding student applications were for projects outside of the traditional core Bio* projects, a result with which everyone won: We had a terrific crop of students, our community grew larger and stronger, and open-source bioinformatics was advanced in a more diverse way than would have been possible otherwise.

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

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 more information, see RELEASE_NOTES.rdoc and ChangeLog.

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 storing a graphics element.
• Many failures and errors running on JRuby and Rubinius are resolved.
• Strange behavior related with “circular require” is fixed.
• Fixed: Genomenet remote BLAST does not work.
• Fixed: Bio::NucleicAcid.to_re(“s”) typo.
• Fixed: Bio::EMBL#os raises RuntimeError.
• Fixed: bin/bioruby: Failed to save object with error message “can’t convert Symbol into String” on Ruby 1.9.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

Earlier this year BioRuby and then Biopython and BioPerl started 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:

• BioRuby
• Biopython
• BioPerl

The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.

Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing OBF BuildBot server which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.