O|B|F News

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:

tRNA genes in Arabidopsis thaliana

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.

Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF, OBF Projects | Tagged Biopython | Leave a 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. Continue reading →

Posted in BioRuby, Code, Development, OBF, OBF Projects | 1 Comment

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 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)

Posted in Biopython, Blogroll, Code, Community, Development, OBF, OBF Projects | Tagged Biopython, Development, news, open-source, release, releases | 1 Comment

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 their mentors (in alphabetical order):

Justinas Vygintas Daugmaudis
Michele dos Santos da Silva
(2 students!)
Mocapy++Biopython: from data to probabilistic models of biomolecules
mentored by Thomas Hamelryck and Eric Talevich

Chuan Hock Koh
BioJava – Amino acids physico-chemical properties calculation
mentored by Peter Troshin, Andreas Prlic, and Jay Vyas

Michał Koziarski
Representing bio-objects and related information with images
(BioRuby)
mentored by Raoul J.P. Bonnal and Francesco Strozzi

Sheena Scroggins
Major BioPerl Reorganization
mentored by Robert Buels and Chris Fields

Mikael Eric Trellet
Interface analysis module for BioPython
mentored by João Rodrigues and Eric Talevich

Once again this 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!

Posted in Google Summer of Code, OBF | Leave a comment

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:

Please report any bugs to our Redmine server.

Enjoy!

chris

Posted in BioPerl, Development, OBF | Leave a comment

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 various bug fixes, around 50

Just to note, this is the first release after we reworked the Build.PL system, so we will probably hit a few speed bumps along the way. This is in effort to simplify the process for further work this summer on modularizing BioPerl, but it also makes new releases much easier to make. In particular, this has only been tested on Ubuntu Linux and Mac OS X (no Windows testing has occurred yet). Please post if there are any problems.

Enjoy!

Posted in BioPerl, Development, General, OBF, OBF Projects | Leave a comment

Biopython 1.57 released

Posted on April 2, 2011 by Brad Chapman

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index.

Bio.SeqIO now includes an index_db() function which extends the existing
indexing functionality to allow indexing many files, and more importantly
this keeps the index on disk in a simple SQLite3 database rather than in
memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter
tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the
ability to run the BLAST tools and save the output as ASN.1 format, and then
convert this to any other supported BLAST ouput format (plain text, tabular,
XML, or HTML) with the blast_formatter tool. The wrappers were also updated
to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The SeqRecord object now has a reverse_complement method (similar to that of
the Seq object). This is most useful to reversing per-letter-annotation (such
as quality scores from FASTQ) or features (such as annotation from GenBank).

Bio.SeqIO.write’s QUAL output has been sped up, and Bio.SeqIO.convert now
uses an optimised routine for FASTQ to QUAL making this much faster.

Biopython can now be installed with pip. Thanks to David Koppstein and
James Casbon for reporting the problem.

Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and
IMGT output.

The Bio.PDB module received several fixes and improvements, including starting
to merge João’s work from GSoC 2010; consequently Atom objects now know
their element type and IUPAC mass. (The new features that use these
attributes won’t be included in Biopython until the next release, though, so
stay tuned.)

The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary
(previously it was a list of key,value tuples) to better match the standard.

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

Brad Chapman
Eric Talevich
Erick Matsen (first contribution)
Hongbo Zhu
Jeffrey Finkelstein (first contribution)
Joanna & Dominik Kasprzak (first contribution)
Joao Rodrigues
Kristian Rother
Leighton Pritchard
Michiel de Hoon
Peter Cock
Peter Thorpe (first contribution)
Phillip Garland
Walter Gillett (first contribution)

Feedback is most welcome on the mailing lists, or redmine.

Posted in Biopython, Code, Development, OBF, OBF Projects | Tagged Biopython, Development, release | Leave a comment

OBF and Google Summer of Code 2011

Posted on March 18, 2011 by Peter

Great news: Google announced today that the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for this summer’s 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 GSoC 2011 FAQ.

Student applications are due April 8, 2011 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 the OBF wiki page, 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 2011 Administrator

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blogroll, Code, Community, Development, Google Summer of Code, OBF, OBF Projects | Leave a comment

Introduction of OpenID logins for OBF wikis

Posted on March 17, 2011 by Chris Fields

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login system will be disabled and OpenID will be the default path for new accounts so users to make wiki changes. This currently appears to have cut the incidence of spam significantly. We will be adding information to the login pages to redirect new users to the new login page.

We also have one wiki (BioLib) that is testing out manual account approval via a wiki bureaucrat in case we have to take more extreme measures, though we would like to leave the barrier to community involvement with projects at the lowest possible level.

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Documentation, OBDA / BioSQL, OBF, OBF Projects, Website | Leave a comment