Posts

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.

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 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a ‘beta’ installer for Python 3.2 under 32-bit Windows.

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 new feature: SCOP data can now be accessed from either the
original SCOP site in the UK (v. 1.75) or from Berkeley (v. 1.75A) .

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, their projects, and their mentors (in alphabetical order):

• Wibowo Arindrarto:
  SearchIO Implementation in Biopython
  mentored by Peter Cock
• Lenna Peterson:
  Diff My DNA: Development of a Genomic Variant Toolkit for Biopython
  mentored by Brad Chapman, Reece Hart, James Casbon
• Marjan Povolni:
  The worlds fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby
  mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
• Artem Tarasov:
  Fast parallelized GFF3/GTF parser in C++, with Ruby FFI bindings
  mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal
• Clayton Wheeler:
  Multiple Alignment Format parser for BioRuby
  mentored by Francesco Strozzi and Raoul Bonnal

As in every year, we received many great applications and ideas. However, funding and mentor resources are limited, and we were not able to accept as many as we would have liked. Our deepest thanks to all the students who applied: we sincerely appreciate the time and effort you put into your applications, and hope you will still consider being a part of the OBF’s open source projects, even without Google funding. I speak for myself and all of the mentors who read and scored applications when I say that we were truly honored by the number and quality of the applications we received.

Applications due 19:00 UTC, April 6, 2012. /wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation (OBF) Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code (GSoC).

Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.

Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for Google Summer of Code 2012!

Google Summer of Code (GSoC) is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the GSoC 2012 FAQ.

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: /wiki/BOSC_2012 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

• April 13, 2012: Deadline for submitting abstracts
• May 7, 2012: Notification of accepted talk abstracts emailed to authors
• July 11-12, 2012: Codefest 2012 programming session
• July 13-14, 2012: BOSC 2012
• July 15-17, 2012: ISMB 2012

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

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 different tracks, as shown here:

This example attempts a simplified reproduction of Figure 6 in Proux et al. (2002), and shows three related phage genomes one above the other. Different classes of genes have been given different colors, while the strength of the red shaded cross-links indicates the percentage identity of the linked genes. Note there are some minor differences in the GenBank annotation we’ve used and the genes shown in the original figure.

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).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy), and under PyPy (excluding our NumPy dependencies). We are now encouraging early adopters to help beta testing on these platforms.