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

BOSC 2013

Hello from Berlin, where the pre-BOSC informal CodeFest 2013 meeting is already underway. We’re looking forward to seeing even more of you on Friday and Saturday for BOSC 2013.

BOSC 2013 will be the 14th annual Bioinformatics Open Source Conference, and is organised by the Open Bioinformatics Foundation (OBF). It is held as a Special Interest Group (SIG) meeting in conjunction with the ISMB conference, which itself is held jointly with the ECCB meeting every second year. This year the ISMB/ECCB 2013 is in Berlin, Germany.

You can follow BOSC on Twitter @OBF_BOSC, and we’ll be using the Twitter Hashtag #BOSC2013.

We also have a low-volume BOSC announcements mailing list, please sign up if you’d consider attending or submitting a talk or poster for next year – BOSC 2014 and the ISMB 2014 will be in Boston, USA in July 2014.

Posted in Blogroll, BOSC/ISMB, Community, OBF, OBF Projects | Tagged , | 2 Comments

BioRuby 1.4.3.0001 Released

We are pleased to announce the release of BioRuby 1.4.3.0001. This new release fixes the following bugs.

  • “gem install bio” failed with Ruby 2.0 or later versions.
  • lib/bio/db/gff.rb script encoding issue
  • Bio::Blast::Default::Report parse error when subject sequence contains spaces.

For more information, see RELEASE_NOTES.rdoc and ChangeLog.

Continue reading

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

Biopython 1.61 released

Source distributions and Windows installers for Biopython 1.61 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

The updated Biopython Tutorial and Cookbook is online (PDF).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython 2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C extensions). We are still encouraging early adopters to help test on these platforms, and have included a ‘beta’ installer for Python 3.2 (and Python 3.3 to follow soon) under 32-bit Windows.

Please note we are phasing out support for Python 2.5. We will continue support for at least one further release (Biopython 1.62). This could be extended given feedback from our users. Focusing on Python 2.6 and 2.7 only will make writing Python 3 compatible code easier.

Features

GenomeDiagram has three new sigils (shapes to illustrate features). OCTO shows an octagonal shape, like the existing BOX sigil but with the corners cut off. JAGGY shows a box with jagged edges at the start and end, intended for things like NNNNN regions in draft genomes. Finally BIGARROW is like the existing ARROW sigil but is drawn straddling the axis. This is useful for drawing vertically compact figures where you do not have overlapping genes.

New module Bio.Graphics.ColorSpiral can generate colors along a spiral path through HSV color space. This can be used to make arbitrary ‘rainbow’ scales, for example to color features or cross-links on a GenomeDiagram figure.

The Bio.SeqIO module now supports reading sequences from PDB files in two different ways. The “pdb-atom” format determines the sequence as it appears in the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this). Alternatively, you can use the “pdb-seqres” format to read the complete protein sequence as it is listed in the PDB header, if available.

The Bio.SeqUtils module how has a seq1 function to turn a sequence using three letter amino acid codes into one using the more common one letter codes. This acts as the inverse of the existing seq3 function.

The multiple-sequence-alignment object used by Bio.AlignIO etc now supports an annotation dictionary. Additional support for per-column annotation is planned, with addition and splicing to work like that for the SeqRecord per-letter annotation.

The Bio.Motif module has been updated and reorganized. To allow for a clean deprecation of the old code, the new motif code is stored in a new module Bio.motifs, and a PendingDeprecationWarning was added to Bio.Motif.

Experimental Code – SearchIO

This release also includes Bow’s Google Summer of Code work writing a unified parsing framework for NCBI BLAST (assorted formats including tabular and XML), HMMER, BLAT, and other sequence searching tools. This is currently available with the new BiopythonExperimentalWarning to indicate that this is still somewhat experimental. We’re bundling it with the main release to get more public feedback, but with the big warning that the API is likely to change. In fact, even the current name of Bio.SearchIO may change since unless you are familiar with BioPerl its purpose isn’t immediately clear.

Contributors

  • Brandon Invergo
  • Bryan Lunt (first contribution)
  • Christian Brueffer (first contribution)
  • David Cain
  • Eric Talevich
  • Grace Yeo (first contribution)
  • Jeffrey Chang
  • Jingping Li (first contribution)
  • Kai Blin (first contribution)
  • Leighton Pritchard
  • Lenna Peterson
  • Lucas Sinclair (first contribution)
  • Michiel de Hoon
  • Nick Semenkovich (first contribution)
  • Peter Cock
  • Robert Ernst (first contribution)
  • Tiago Antao
  • Wibowo ‘Bow’ Arindrarto
Posted in Biopython, Blogroll, Code, Community, Development, OBF, OBF Projects | Tagged | Comments Off

OBF Board meeting 13 Nov

The Open Bioinformatics Foundation (OBF) will be holding a public Board of Directors meeting on Tuesday, 13 Nov, 2012, at 11.30am EST (8.30am PST, 17:30 CET, 16:30 UTC/GMT).

The meeting will be held online or over conference call. We will post details about how to dial in or connect closer to the date (here).

On the agenda Richard Holland and Chris Fields are running for election to the Board, and some other items primarily up for discussion, including how to keep our membership roll up-to-date and increasing with the least barriers. We will post a more detailed agenda in advance of the meeting (here).

OBF members should have already received notice of this meeting via the OBF member’s mailing list.

Posted in Blogroll, Community, General, Mailing lists, OBF, OBF Projects, Website | Tagged , , , , , , | Leave a comment

Server transition process to AWS servers

Our aging server which has run for 5+ years the OBF sites has finally reached end of its lifespan. We are currently migrating sites to AWS volumes and sites for a temporary period while we decide about how to continue to support these services in the future.  There will be some downtime while the all-volunteer OBF admin team makes time to fix this.

Nearly all projects use public source code repositories such as github or sourceforge so no problems with access to the code should be limiting. Mailing lists are still using the old server but will be moved to the AWS site in the next few days and we are working to have little downtime for the lists.  Mediawiki sites are moving in stages and so far Bioperl, Biopython, and the OBF wikis have been migrated.  This news site has also been migrated to AWS and this is the 1st post from it (will it work!?)

Posted in OBF, OBF Projects, Website | 3 Comments

OBF is now an SPI-associated project

I am very pleased to announce that the Open Bioinformatics Foundation (O|B|F) is now a Software in the Public Interest (SPI) associated project, rather than its own not-for-profit incorporation.

An electronic vote of O|B|F members on whether or not to provisionally approve the invitation from SPI closed yesterday at 19:00 UTC. We had a participation of 39 out of 105 eligible, or 37%, which is far above the quorum of 10%. The tally is 38 for provisionally accepting and 1 against. The tally can be seen (and audited) here:
https://vote.heliosvoting.org/helios/e/OBFjoiningSPI

The SPI Board vote on resolution 2012-09-28.jb.1 (“Open Bioinformatics Foundation as associated project”) resulted in 8 yes, 0 no, 0 abstain. Given the result of our election, I accepted the invitation right away.

Thanks to everyone who voted. On behalf of the Board, I am thrilled about the turnout!

This terminates O|B|F’s status as its own corporation, which over the years has been more trouble than gain. As an SPI-associated project, we can now accept donations that are 501(c)3 tax-exempt in the US, aside from other benefits. In the coming weeks and months we will be articulating what kind of objectives, platforms, and activities we can or should pursue, given our new status. I’ll communicate separately about that once it gets off the ground.

Finally, please join me in thanking Josh Berkus (SPI & PostgreSQL) for shepherding our joining SPI all the way through. And please also join me in saying hi to the SPI community – as I have done earlier I’d like to encourage everyone to consider joining the SPI as well. It’s a friendly community, and I like to think we can enrich it.

This is a historic day for our organization. Have a drink tonight :-)

Cheers,

-hilmar

Note: This post is based on an email sent yesterday to the OBF member’s mailing list.

Posted in Blogroll, Community, General, OBF, OBF Projects | Leave a comment

BioRuby 1.4.3 released

We are pleased to announce the release of BioRuby 1.4.3. This new release fixes bugs existed in 1.4.2 and improves portability on JRuby and Rubinius.

Here is a brief summary of changes.

  • Bio::KEGG::KGML bug fixes and new class Bio::KEGG::KGML::Graphics for storing a graphics element.
  • Many failures and errors running on JRuby and Rubinius are resolved.
  • Strange behavior related with “circular require” is fixed.
  • Fixed: Genomenet remote BLAST does not work.
  • Fixed: Bio::NucleicAcid.to_re(“s”) typo.
  • Fixed: Bio::EMBL#os raises RuntimeError.
  • Fixed: bin/bioruby: Failed to save object with error message “can’t convert Symbol into String” on Ruby 1.9.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

The archive is available at: http://bioruby.org/archive/bioruby-1.4.3.tar.gz
Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.3.gem

We also put RubyGems pacakge at RubyGems.org and RubyForge. You can easily install by using RubyGems. First, check the version number by using search command:
% gem search –remote bio
and find “bio (1.4.3)” in the list. Then,
% sudo gem install bio

Acknowledgments: Thanks to all persons reporting issues and/or submitting patches.

Hope you enjoy.

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

Travis-CI for Testing

Earlier this year BioRuby and then Biopython and BioPerl started using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated:

The BioRuby team are also using Travis-CI for automated testing of their new ‘plugin’ ecosystem, BioRuby Gems, or BioGems.

Travis-CI gives us continuous testing, but for the moment only covers one operating system (currently 32 bit Ubuntu Linux using Virtual Machines). This automated testing is therefore complementary to our existing OBF BuildBot server which aims to run nightly tests on volunteer developer machines setup to cover a broad range of operating systems and configurations.

However, Travis-CI are working on a new feature – automatic testing of pull requests, currently only available on a donation basis – which the OBF was happy to support.

What this means is that when a contributor has some code ready for integration, they can issue a GitHub pull request, and then Travis-CI will automatically run the unit tests with those proposed changes. This is something that currently the core-developers would normally do manually as part of evaluating proposed changes, so having this happen automatically should be a big help.

We’re excited about making more use of Travis-CI for other OBF projects. Thus far we’ve been really impressed with Travis-CI.

Posted in BioPerl, Biopython, BioRuby, Blogroll, Code, Community, Development, OBF, OBF Projects | Leave a comment