Call for Ideas for OBF’s 2014 Google Summer of Code

Google Summer of Code is on again for 2014, and OBF is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors.

Since OBF is an umbrella organization covering several member projects, most of these GSoC ideas will likely be associated with a specific Bio* community. For our GSoC application, and for the convenience of students, we aggregate each Bio* project’s ideas on the GSoC page of the OBF wiki, but the details of each idea are posted on the specific Bio* project’s own wiki. So, if you have an idea for a Summer of Code project, please post your idea on your Bio* project mailing list for discussion and start an outline on the corresponding wiki page. Feel free to reuse or adapt ideas from 2013 or previous years that were not taken on by a student already, if you feel the idea is still viable.

We also welcome ideas that fit with OBF’s mission but are not part of a single Bio* project, or span multiple projects — these ideas can be posted on the OBF wiki page and discussed on the OBF mailing list.

Potential students, we’re interested in your ideas, too! This is a good occasion to introduce yourself to the OBF community.  If you have an idea for something you’d particularly like to work on during GSoC 2014, please ask us on the mailing list and we’ll try to find a suitable mentor.

Here’s to another fun and productive Summer of Code!

Posted in Code, Community, Development, Google Summer of Code, OBF | 7 Comments

Call for Organization Admins for OBF’s 2014 Google Summer of Code participation

Update: The deadline for responding has been extended to January 25.

GoogleSummer_2014logo The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve.

An org admin’s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to “keep it together.” Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org’s mentors. The org admin’s responsibilities include:

  • Representing our online face to GSoC, in particular to GSoC students
  • Shepherding our mentoring organization application, and submitting it.
  • Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.
  • Knowing GSoC rules and processes, and making sure ours are consistent with them.
  • Reminding participants of rules, and enforcing them in the event it is necessary.
  • Mediating, and sometimes arbitrating between students and mentors when needed.
  • Ensuring that GSoC timelines are met by everyone.

The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.

If you are interested in helping us out in this role, please email us (by Jan 25, 2014) a statement at board@open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project’s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.

We are looking forward to hearing from you!

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | 7 Comments

BOSC 2014 Keynote Speakers

Thanks to those who participated in the BOSC 2014 Keynote Competition! Our winner is Manuel Corpas, who correctly surmised Philip Bourne:

(In fact, we had already confirmed Philip Bourne as our second keynote speaker before his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to BOSC 2014!

Dr. Bourne’s keynote talk will be entitled “Biomedical Research as an Open Digital Enterprise”:

The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.

Our other keynote speaker at BOSC 2014, as already announced, will be Titus Brown, whose topic is “A History of Bioinformatics (in the Year 2039)”.

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

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