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.

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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

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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
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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.

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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.

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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.

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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

Biopython 1.60 released

Source distributions and Windows installers for Biopython 1.60 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 and PyPy 1.9 (which does not cover NumPy or our C extensions). Please note that Python 2.4 or earlier is not supported.

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy). We are now encouraging early adopters to help beta testing on these platforms, and have included a ‘beta’ installer for Python 3.2 under 32-bit Windows.

Features

New module Bio.bgzf supports reading and writing BGZF files (Blocked GNU Zip Format), a variant of GZIP with efficient random access, most commonly used as part of the BAM file format and in tabix. This uses Python’s zlib library internally, and provides a simple interface like Python’s gzip library. Using this the Bio.SeqIO indexing functions now support BGZF compressed sequence files. See this blog post for more background on BGZF and SeqIO.

The GenBank/EMBL parser will now give a warning on unrecognized feature locations and continue parsing (leaving the feature’s location as None). Previously it would abort with an exception, which was often unhelpful.

The Bio.PDB.MMCIFParser is now compiled by default (but is still not available under Jython, PyPy or Python 3).

The SFF parser in Bio.SeqIO now decodes Roche 454 ‘universal accession number’ 14 character read names, which encode the timestamp of the run, the region the read came from, and the location of the well.

In the Phylo module, the “draw” function for plotting tree objects has become much more flexible, with improved support for matplotlib conventions and new parameters for specifying branch and taxon labels. Writing in the PhyloXML format has been updated to more closely match the output of other programs. A wrapper for the program RAxML has been added under Bio.Phylo.Applications, alongside the existing wrapper for PhyML.

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:

  • Brandon Invergo
  • Eric Talevich
  • Jeff Hussmann (first contribution)
  • John Comeau (first contribution)
  • Kamil Slowikowski (first contribution)
  • Kevin Jacobs
  • Lenna Peterson (first contribution)
  • Matt Fenwick (first contribution)
  • Peter Cock
  • Paul T. Bathen
  • Wibowo Arindrarto
Posted in Biopython, Code, Development, OBF, OBF Projects | Tagged | 2 Comments

BioJava 3.0.4 released

BioJava 3.0.4 has been released and is available from
http://www.biojava.org/wiki/BioJava:Download as well as from the
BioJava maven repository at http://www.biojava.org/download/maven/ .

- This is mainly a bug fix release addressing issues with the protein
structure and disorder modules

- One new feature: SCOP data can now be accessed from either the
original SCOP site in the UK (v. 1.75) or from Berkeley (v. 1.75A) .

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