BioPerl release 1.6.923

The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve Bio::Location (among other bits and pieces).

Contributing to the release:

  • Francisco Ossandón
  • Brian Osborne
  • Dave Messina
  • Carnë Draug
  • Chris Fields
  • Benjamin Warren

Enjoy!

chris

Posted in BioPerl, Code, Community | 5 Comments

BOSC 2014 Keynote Competition

We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference (BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently:

Titus Brown (@ctitusbrown):
C. Titus BrownExcited to be a keynote speaker at BOSC 2014! My title: “A History of Bioinformatics (in the year 2039)” – plenty of room for mischief ;)
https://twitter.com/ctitusbrown/status/410934403565490176

In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we’re announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.

To enter, please tweet using hashtag #bosc2014 and include us via @OBF_BOSC, e.g.

I think @OBF_BOSC should invite “Professor X” to be a keynote speaker at #BOSC2014 because …

The first correct entry (within one week) will be awarded one complementary BOSC 2014 registration fee for themselves, or a nominated group member. This does not cover travel or accommodation, and there is no cash substitute if you cannot attend BOSC 2014. Members of the OBF board, BOSC organizing committee, and ISMB SIG committee are not eligible, nor are the keynote speakers themselves.

We intend to announce the mystery keynote speaker and any Twitter competition winner in one week’s time, but reserve the right to cut short, modify, or cancel the competition.

Our ulterior motive is to crowd source ideas for future keynote speakers in BOSC 2015, so some serious suggestions please ;)

Further details about BOSC 2014 will be posted here:
http://www.open-bio.org/wiki/BOSC_2014

Thank you,

Peter Cock & Nomi Harris, BOSC 2014 co-chairs.

Posted in Blogroll, BOSC/ISMB, Community, General, Humor, OBF | Tagged , , , , , , | 10 Comments

Biopython 1.63 released

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and (soon) from the Python Package Index (PyPI).

The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5).

This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.

The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:

from __future__ import print_function

Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators’ .next() method. This language feature is also available under Python 2.6 and 2.7.

The restriction enzyme list in Bio.Restriction has been updated to the December 2013 release of REBASE.

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

  • Chris Mitchell (first contribution)
  • Christian Brueffer
  • Eric Talevich
  • Gokcen Eraslan (first contribution)
  • Josha Inglis (first contribution)
  • Konstantin Tretyakov (first contribution)
  • Lenna Peterson
  • Martin Mokrejs
  • Nigel Delaney (first contribution)
  • Peter Cock
  • Sergei Lebedev (first contribution)
  • Tiago Antao
  • Wayne Decatur (first contribution)
  • Wibowo ‘Bow’ Arindrarto
Posted in Biopython, Code, Community, Development, OBF Projects | Tagged , , , , , | 22 Comments

Initial release of BioPerl Bio::Community distribution

Note: I’m reposting here the original announcement from Florent Angly on the BioPerl mail list.


Dear all,

Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.

Today, I am happy to announce the release of the first version of these modules, which can be obtained from CPAN:

http://search.cpan.org/search?query=Bio-Community&mode=dist

Obviously, this is just the beginning for these modules and I hope that interested developers will join me to expand them.

Best,

Florent

Posted in OBF | 7 Comments

Biopython 1.63 beta released

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website.

This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5).

This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.

The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:

    from __future__ import print_function

Similarly we now use the Python 3 style built-in next function in place of the Python 2 style iterators’ .next() method. This language feature is also available under Python 2.6 and 2.7.

Contributors

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

  • Chris Mitchell (first contribution)
  • Christian Brueffer
  • Eric Talevich
  • Josha Inglis (first contribution)
  • Konstantin Tretyakov (first contribution)
  • Lenna Peterson
  • Martin Mokrejs
  • Nigel Delaney (first contribution)
  • Peter Cock
  • Sergei Lebedev (first contribution)
  • Tiago Antao
  • Wayne Decatur (first contribution)
  • Wibowo ‘Bow’ Arindrarto
Posted in Biopython, Code, Community, Development, OBF, OBF Projects | Tagged , , , , , | 15 Comments

BioPerl v.1.6.910 released

UPDATE:

As a bit of time has passed since we originally intended to make a new release, I forgot that (in that time period) Carnë Draug had released a split-out version of Bio::Biblio to CPAN this past March.

Unfortunately that release (v1.7) appears to have version collisions with this one (v.1.6.910); therefore I’m packaging a new point release (v1.6.920) that removes Bio::Biblio to prevent this.  That has now been uploaded to CPAN and should be available shortly.

ORIGINAL POST:

All,

I would like to announce that BioPerl v. 1.6.910 has been released to CPAN and should be showing up imminently.  This is primarily a bug fix release.  Two key items of note:

  1. Beyond minor fixes to address problems on other distributions, this will be the last of the BioPerl 1.6 series.  We will be repackaging code into separate repositories and likewise releasing them as separate distributions on CPAN during the next (1.7.x) releases.
  2. Two distributions have already been split out:
  • Bio::FeatureIO has been moved into a separate distribution.  The code for Bio::FeatureIO is undergoing revision and will be released at a future point.  If you need access to it, it is available on GitHub.
  • Bio::DB::EUtilities and it’s related modules have also been into a separate distribution and are now available on CPAN.  I will be updating the release on that code as well.

The first 1.7 release is scheduled for sometime in late fall-early winter, with the primary focus (as mentioned above) being repackaging of core code.

Thanks all!

chris

Posted in BioPerl, Code, Development, OBF Projects | 10 Comments

Biopython 1.62 released

Source distributions and Windows installers for Biopython 1.62 are now available from the downloads page on the official Biopython website and (soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports Python 3. Specifically, this is supported under Python 3.3. Older versions of Python 3 may still work albeit with some issues, but are not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython is available for versions 2.5 and 2.7 and under PyPy for versions 1.9 and 2.0. However, unlike CPython, Jython and PyPy support is partial: NumPy and our C extensions are not covered.

Please note that this release marks our last official for support Python 2.5. Beginning from Biopython 1.63, the minimum supported Python version will be 2.6.

Highlights

  • The translation functions will give a warning on any partial codons (and this will probably become an error in a future release). If you know you are dealing with partial sequences, either pad with “N” to extend the sequence length to a multiple of three, or explicitly trim the sequence.
  • The handling of joins and related complex features in Genbank/EMBL files has been changed with the introduction of a CompoundLocation object. Previously a SeqFeature for something like a multi-exon CDS would have a child SeqFeature (under the sub_features attribute) for each exon. The sub_features property will still be populated for now, but is deprecated and will in future be removed. Please consult the examples in the help (docstrings) and Tutorial.
  • Thanks to the efforts of Ben Morris, the Phylo module now supports the file formats NeXML and CDAO. The Newick parser is also significantly faster, and can now optionally extract bootstrap values from the Newick comment field (like Molphy and Archaeopteryx do). Nate Sutton added a wrapper for FastTree to Bio.Phylo.Applications.
  • New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats from UniProt-GOA.
  • The BioSQL module is now supported in Jython. MySQL and PostgreSQL databases can be used. The relevant JDBC driver should be available in the CLASSPATH.
  • Feature labels on circular GenomeDiagram figures now support the label_position argument (start, middle or end) in addition to the current default placement, and in a change to prior releases these labels are outside the features which is now consistent with the linear diagrams.
  • The code for parsing 3D structures in mmCIF files was updated to use the Python standard library’s shlex module instead of C code using flex.
  • The Bio.Sequencing.Applications module now includes a BWA command line wrapper.
  • Bio.motifs supports JASPAR format files with multiple position-frequence matrices.

Additionally there have been other minor bug fixes and more unit tests.

Contributors

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

  • Alexander Campbell (first contribution)
  • Andrea Rizzi (first contribution)
  • Anthony Mathelier (first contribution)
  • Ben Morris (first contribution)
  • Brad Chapman
  • Christian Brueffer
  • David Arenillas (first contribution)
  • David Martin (first contribution)
  • Eric Talevich
  • Iddo Friedberg
  • Jian-Long Huang (first contribution)
  • Joao Rodrigues
  • Kai Blin
  • Lenna Peterson
  • Michiel de Hoon
  • Matsuyuki Shirota (first contribution)
  • Nate Sutton (first contribution)
  • Peter Cock
  • Petra Kubincová (first contribution)
  • Phillip Garland
  • Saket Choudhary (first contribution)
  • Tiago Antao
  • Wibowo ‘Bow’ Arindrarto
  • Xabier Bello (first contribution)
Posted in Biopython, BOSC/ISMB, Code, Community, Development, OBF, OBF Projects | Tagged , , , , , , , | 6 Comments