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.

For the accepted students: congratulations! You have risen to the top of a very competitive application process. Now it’s time to “put your money where your mouth is”, as the saying goes. Let’s get out there and write some great code this summer!

Best regards,

Robert Buels
OBF GSoC 2012 Organization Administrator

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.

The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from sequence search I/O in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a next-generation BioRuby interface to Ensembl to developing cloud-optimized versions of BioJava modules. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also particularly welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 26 through Friday, April 6th, 2012.

INQUIRIES:

We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details.

2012 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs

Rob Buels
OBF GSoC 2012 Admin

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.

Student applications are due April 6, 2012 at 19:00 UTC. Students who are interested in participating should look at the OBF’s GSoC page, which lists project ideas, and whom to contact about applying.

For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project’s GSoC wiki page.

Thanks to all who helped make OBF’s application to GSoC a success, and let’s have a great, productive summer of code!

Rob Buels
OBF GSoC 2012 Administrator

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 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.

We invite you to submit one-page abstracts for talks and posters. This year’s session topics are:

• Cloud and Parallel Computing
• Linked Data
• Genome-scale Data Management
• Data Visualization and Imaging
• Translational Bioinformatics
• Software Interoperability (possibly a joint session with BSI-SIG, the Bioinformatics Software Interoperability SIG)
• Bioinformatics Open Source Project Updates
• Interfacing with Industry (panel)

Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards. Each winner will be awarded $250 to defray the costs of travel to BOSC 2012.

For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts

BOSC 2012 Organizing Committee:
Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice

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.

Note while this example is in the Tutorial HTML and PDF online, it was not in the zip/tarball for Biopython 1.59, and nor was the Proux_et_al_2002_Figure_6.py script. It will be in future releases.

Another motivating use case for this functionality was to produce vector images of whole genome alignments in the style of the Artemis Comparison Tool (ACT) or Mauve. We’ve got a poster printer in the building just crying out to be used for showing whole genome comparison of a dozen bacteria strains!

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.

The installation setup.py now supports ‘install_requires’ when setuptools is installed. This avoids the manual dialog when installing Biopython via easy_install or pip and numpy is not installed. It also allows user libraries that require Biopython to include it in their install_requires and get automatic installation of dependencies.

Features

New module Bio.TogoWS offers a wrapper for the TogoWS REST API, a web service based in Japan offering access to KEGG, DDBJ, PDBj, CBRC plus access to some NCBI and EBI resources including PubMed, GenBank and UniProt. This is much easier to use than the NCBI Entrez API, but should be especially useful for Biopython users based in Asia.

The NCBI Entrez Fetch function Bio.Entrez.efetch has been updated to handle the NCBI’s stricter handling of multiple ID arguments in EFetch 2.0 (released February 2012, see this announcement), however the NCBI have also changed the retmode default argument so you may need to make this explicit. e.g. add retmode="text" to your EFetch calls (see this announcement).

The position objects used in Bio.SeqFeature now act almost like integers, making dealing with fuzzy locations in EMBL/GenBank files much easier. Also the SeqFeature‘s strand and any database reference are now properties of the FeatureLocation object (a more logical placement), with proxy methods for backwards compatibility.

Bio.Graphics.BasicChromosome has been extended to allow simple sub-features to be drawn on chromosome segments, suitable to show the position of genes, SNPs or other loci.

Bio.Graphics.GenomeDiagram has been extended to allow cross-links between tracks, and track specific start/end positions for showing regions. This can be used to imitate the output from the Artemis Comparison Tool (ACT). Also, a new attribute circle_core makes it easier to have an empty space in the middle of a circular diagram (see tutorial).

Note Bio.Graphics requires the ReportLab library.

Bio.Align.Applications now includes a wrapper for command line tool Clustal Omega for protein multiple sequence alignment.

Bio.AlignIO now supports sequential PHYLIP files (as well as interlaced PHYLIP files) as a separate format variant.

Additionally there have been other minor bug fixes and more unit tests, and updates to the documentation including the Biopython Tutorial (PDF).

Contributors

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Andreas Wilm (first contribution)
• Alessio Papini (first contribution)
• Brad Chapman
• Brandon Invergo
• Connor McCoy
• Eric Talevich
• João Rodrigues
• Konrad Förstner (first contribution)
• Michiel de Hoon
• Matej Repič (first contribution)
• Leighton Pritchard
• Peter Cock

The meeting will on Tuesday 8 November 2011, at 11am EST, 8am PST, 16:00 UTC/GMT, 17:00 CET, or Wednesday 9 November 1am JST. Note for translating into other time zones that by then both Europe and the US have gone off DST.

Note that this meeting, like all O|B|F Board meetings, is public; every member may call in at their leisure. Please see the agenda of the meeting (including dial-in information), see also the current board.

Here’s a PDF version too. This example just parses the Arabidopsis thaliana GenBank files to get the chromosome lengths and the tRNA gene placements. There are so many tRNA on the forward strand of Chr I that their labels are forced to overlap. Here the figure just uses a different color for each chromosome, but you can color each feature individually.

This kind of diagram is often used for showing the placement of SNPs or other loci of interest (e.g. disease or breeding markers).

P.S. Biopython produces these and other graphics using ReportLab, an open source Python library capable of outputting PDF, SVG, PNG, etc. Very handy.

Here is a brief summary of changes.

Speed-up of Bio::RestrictionEnzyme::Analysis.cut: The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.

New classes Bio::DDBJ::REST, REST interface for DDBJ Web API for Biology (WABI) web service in additon to SOAP. Currently, only selected APIs are implemented.

Bio::Blast with remote DDBJ server uses REST instead of SOAP because Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9. We can now use remote DDBJ BLAST server with Ruby 1.9.

The Tutorial.rd is updated by Pjotr Prins and Michael O’Keefe.

Many unit tests are added for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. Most of them are developed by Kazuhiro Hayashi during the Google Summer of Code 2010.
New methods: Bio::Fastq#to_s, Bio::NCBI::REST::EFetch.nucleotide, Bio::NCBI::REST::EFetch.protein.

Bug fixes:

• Bio::Blast: Failure of remote BLAST execution is fixed, due to the changes in GenomeNet and DDBJ.
• Bio::Blast: When executing remote BLAST with “genomenet” server, options “-b” and “-v” are now correctly used to limit the number of hits to be reported.
• Bio::SPTR (Bio::UniProt): Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines were not correctly parsed.
• Bio::Reference#pubmed_url: Updated to follow recent NCBI changes.
• Bio::Newick#reparse failure.
• Bio::MEDLINE#reference: doi field should be filled.
• Bio::Reference#endnote fails when url is not set.
• Bio::FastaFormat#query passes nil to the given factory object.
• BioRuby Shell: efetch(), getent(), and demo() fail.

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

The archive is available at: http://bioruby.org/archive/bioruby-1.4.2.tar.gz

Gem file is also available at:  http://bioruby.org/archive/gems/bio-1.4.2.gem

We also put RubyGems pacakge at RubyForge and RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command:
% gem search –remote bio
and find “bio (1.4.2)” in the list. Then,
% sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches. In addition, thanks to NDBC / DBCLS BioHackathon2011 participants and organizers who try BioRuby during the BioHackathon2011.

Hope you enjoy.

A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.

Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. See Schmitt et al (2011) in Briefings in Bioinformatics.

Bio.SeqIO now includes read support for ABI files (“Sanger” capillary sequencing trace files, containing called sequence with PHRED qualities).

The Bio.AlignIO “fasta-m10″ parser was updated to cope with the marker lines as used in Bill Pearson’s FASTA version 3.36, without this fix the parser would only return alignments for the first query sequence.

The Bio.AlignIO “phylip” parser and writer now treat a dot/period in the sequence as an error, in line with the official PHYLIP specification. Older verions of our code didn’t do anything special with this character. Also, support for “phylip-relaxed” has been added which allows longer record names as used in RAxML and PHYML.

Of potential interest to anyone subclassing Biopython objects, any remaining “old syle” Python classes have been switched to “new style” classes. This allows things like defining properties.

Bio.HMM’s Viterbi algorithm now expects the initial probabilities explicitly.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Aaron Gallagher (first contribution)
• Bartek Wilczynski
• Bogdan T. (first contribution)
• Brandon Invergo (first contribution)
• Connor McCoy (first contribution)
• David Cain (first contribution)
• Eric Talevich
• Fábio Madeira (first contribution)
• Hongbo Zhu
• Joao Rodrigues
• Michiel de Hoon
• Peter Cock
• Thomas Schmitt (first contribution)
• Tiago Antao
• Walter Gillett
• Wibowo Arindrarto (first contribution)