Posts

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.

Call for Abstracts for the 12th Annual Bioinformatics Open Source Conference ( BOSC 2011), an ISMB 2011 Special Interest Group (SIG).

Dates: July 15-16, 2011 Location: Vienna, Austria Web site: /wiki/BOSC_2011 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:

• April 18, 2011: Deadline for submitting abstracts to BOSC 2011
• May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
• July 13-14, 2011: Codefest 2011 programming session
• July 15-16, 2011: BOSC 2011
• July 17-19, 2011: ISMB 2011

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.

On behalf of the BOSC 2010 Organizing Committee, I am pleased to announce that the BOSC 2010 Proceedings has been published today in BMC Bioinformatics.  Special thanks go to the abstract and proceedings reviewers who helped make this possible.

The Biopython team is pleased to release Biopython 1.56, almost exactly three months after our last stable release ( Biopython 1.55).

The Bio.SeqIO module has been updated to support protein EMBL files (used for the patents database), IMGT files (a variant of the EMBL file format, with help from Uri Laserson), and UniProt XML files (thanks to Andrea Pierleoni). Also the SeqFeature object gained some new methods, and the Bio.Seq translation function can now be used with an arbitrary genetic code.

This is a reminder that the forthcoming Biopython 1.56 release is planned to be our last release to support Python 2.4.

Looking back, we supported Python 2.3 for about six years - it was released July 2003, and Biopython 1.50 released in April 2009 was the last to support it. Similarly, Python 2.4 was released six years ago (November 2004).

Dropping Python 2.4 support will allow use to assume standard library modules like the ElementTree XML parser and SQLite 3 support will be available. There are also several new language features in Python 2.5+ which will be useful, and it should make supporting Python 3 a little easier as well.