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:

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.

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.

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.

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

The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN:

• BioPerl-Run
• BioPerl-DB
• BioPerl-Network

Please report any bugs to our Redmine server.

Enjoy!

chris

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.

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.

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.

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.

The OBF now has a sparkly new Redmine instance running on Amazon EC2, thanks to efforts from Chris Dagdigian and Jason Stajich (with some admin help from yours truly).  Bugs and user names (along with email contacts) from our old Bugzilla v2 server have been migrated over, though some links need to be fixed.

Redmine is a project management web application that has several nice features over other systems, including issue tracking, multiple project management, wikis, forums, and calendaring.