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!

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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.

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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

OBF Redmine server now available

Posted on March 17, 2011 by Chris Fields

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.

Previous Bugzilla users will need to either reset their password using their original Bugzilla login (an email address) or contact the OBF Helpdesk to get their password.

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

Bioinformatics Open Source Conference (BOSC 2011) Call for Abstracts

Posted on March 4, 2011 by Peter

[BOSC Logo]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: http://www.open-bio.org/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.

We invite you to submit abstracts for talks and posters. Sessions include:

  • Approaches to parallel processing
  • Cloud-based approaches to improving software and data accessibility
  • The Semantic Web in open source bioinformatics
  • Data visualization
  • Tools for next-generation sequencing
  • Other Open Source software

In addition to the above sessions, there will be a panel discussion about “Meeting the challenges of inter-institutional collaboration”. We are also working to arrange a joint session with one of the other ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011.

For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee:
Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor

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BOSC 2010 Proceedings published today in BMC Bioinformatics

Posted on December 21, 2010 by Kam Dahlquist

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.

Posted in BOSC/ISMB, Community, OBF | Leave a comment

Biopython 1.56 released

Posted on November 26, 2010 by Peter

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.

Bio.Entrez will now try to download any missing NCBI DTD files and cache them in the user’s home directory, and includes the latest current DTD files.

The provisional BioSQL SQLite Schema we’ve been using since Biopython 1.53 is now official, and has been updated slightly.

For population genetics, Bio.PopGen.FDist now supports the DFDist command line tool as well as FDist2.

Note that as previously announced, this is expected to be our last release to support Python 2.4. We also support Python 2.5, 2.6 and 2.7, while work is on going for Python 3.

(At least) 13 people have contributed to this release, including 6 new people – thank you all:

  • Andrea Pierleoni (first contribution)
  • Bart de Koning (first contribution)
  • Bartek Wilczynski
  • Bartosz Telenczuk (first contribution)
  • Cymon Cox
  • Eric Talevich
  • Frank Kauff
  • Michiel de Hoon
  • Peter Cock
  • Phillip Garland (first contribution)
  • Siong Kong (first contribution)
  • Tiago Antao
  • Uri Laserson (first contribution)

Source distributions and Windows installers are available from the downloads page on the Biopython website (biopython.org).

As usual, feedback is most welcome on the mailing lists (or bugzilla).

Posted in Biopython, Code, Development, OBDA / BioSQL, OBF Projects | Tagged , , | 1 Comment

Biopython dropping Python 2.4 Support?

Posted on November 18, 2010 by Peter

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.

Most operating systems which come with Python now ship with Python 2.5 or later, with the notable exception of CentOS where Python 2.4 is still used. Also, those of you running a Linux server may still be running an old but still supported OS – for example the Ubuntu 6.06 LTS (Dapper Drake) server edition is maintained until June 2011, and comes with Python 2.4.

If you would be negatively affected by Biopython dropping support for Python 2.4, please let us know as soon as possible, ideally via the mailing list.

Thank you.

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BioRuby 1.4.1 released

Posted on October 22, 2010 by Naohisa Goto

We are pleased to announce the release of BioRuby 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added.

Here is a brief summary of changes.

Continue reading →

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