Biopython 1.65 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.65 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.

The most visible change is that the Biopython sequence objects now use string comparison, rather than Python’s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).

The Bio.KEGG and Bio.Graphics modules have been expanded with support for the online KEGG REST API, and parsing, representing and drawing KGML pathways.

The Pterobranchia Mitochondrial genetic code has been added to Bio.Data (and the translation functionality), which is the new NCBI genetic code table 24.

The Bio.SeqIO parser for the ABI capillary file format now exposes all the raw data in the SeqRecord’s annotation as a dictionary. This allows further in-depth analysis by advanced users.

Bio.SearchIO QueryResult objects now allow Hit retrieval using its alternative IDs (any IDs listed after the first one, for example as used with the NCBI BLAST NR database).

Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.

The new experimental module Bio.CodonAlign has been renamed Bio.codonalign (and similar lower case PEP8 style module names have been used for the sub-modules within this).

Bio.SeqIO.index_db(…) and Bio.SearchIO.index_db(…) now store any relative filenames relative to the index file, rather than (as before) relative to the current directory at the time the index was built. This makes the indexes less fragile, so that they can be used from other working directories. NOTE: This change is backward compatible (old index files work as before), however relative paths in new indexes will not work on older versions of Biopython!

Behind the scenes, we have done a lot of work applying PEP8 coding styles to Biopython, and improving the formatting of the source code documentation (PEP257 docstrings).

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

  • Alan Du (first contribution)
  • Carlos Pena (first contribution)
  • Colin Lappala (first contribution)
  • Christian Brueffer
  • David Bulger (first contribution)
  • Eric Talevich
  • Evan Parker (first contribution)
  • Hongbo Zhu
  • Kai Blin
  • Kevin Wu (first contribution)
  • Leighton Pritchard
  • Leszek Pryszcz (first contribution)
  • Markus Piotrowski
  • Matt Shirley (first contribution)
  • Mike Cariaso (first contribution)
  • Peter Cock
  • Seth Sims (first contribution)
  • Tiago Antao
  • Travis Wrightsman (first contribution)
  • Tyghe Vallard (first contribution)
  • Vincent Davis
  • Wibowo ‘Bow’ Arindrarto
  • Zheng Ruan

This is a longer list of contributors and changes than usual, but it was also a longer gap since our last release.

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

BOSC 2015 will be in Dublin with ISMB/ECCB 2015

We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland)..

Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. We would have been hosted by The Genome Analysis Centre (TGAC) just after and co-located with the Galaxy Community Conference 2015 (GCC 2015, hosted by The Sainsbury Laboratory). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.

Here is the summary of responses to the questions about the location of BOSC 2015:

BOSC2015_locations

BOSC2015_GCC

Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and welcome suggestions of people to invite.) You can reach us at bosc@open-bio.org

Nomi Harris and Peter Cock
Co-Chairs, BOSC 2015

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , , , | 9 Comments

BOSC 2014 video recording

We’re pleased to publicly announce that we aim to video record all the talks at BOSC 2014, and the panel discussion, to be made freely available online after the conference. This is on an opt-out basis, and thus far none of our speakers have declined to be filmed.YouTubeLast year we managed to record many of the talks – including both keynotes, which you can watch via the YouTube links on the BOSC 2013 Schedule. This year we are hiring a professional from Next Day Video (@NextDayVideo on Twitter).

Google LogoThis is thanks to very generous support from Google’s Open Source Programs Office (who also run the amazing Google Summer of Code program which the OBF and its member projects have regularly taken part in), a new sponsor for BOSC this year.

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OBF Mailing List Outage

This is a belated notice that the OBF mailing lists are down due to a server failure. Posting a tweet is easier than writing a blog post, please follow @OBF_news for updates.

We have a complete back up and running as a virtual machine hosted on Amazon Web Services (AWS), which should become live by Monday pending DNS updates etc.

Back in later 2012 we previously migrated the OBF websites AWS, and this has proved very reliable and saves us worrying about looking after physical hardware.

Update (Monday 16 June 2014): The replacement mailman server is now live, but our apologies for the inconvenience. Some delayed emails should now be delivered, but unfortunately older emails where you received a failure message will have to be resent.

Posted in OBF | 4 Comments

Biopython 1.64 released

Source distributions and Windows installers for Biopython 1.64 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2.

The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan.

Bio.Phylo now has tree construction and consensus modules, from on the GSoC work by Yanbo Ye.

Bio.Entrez will now automatically download and cache new NCBI DTD files for XML parsing under the user’s home directory (using ~/.biopython on Unix like systems, and $APPDATA/biopython on Windows).

Bio.Sequencing.Applications now includes a wrapper for the samtools command line tool.

Bio.PopGen.SimCoal now also supports fastsimcoal.

SearchIO hmmer3-text, hmmer3-tab, and hmmer3-domtab now support output from hmmer3.1b1.

BioSQL can now use the mysql-connector package (available for Python 2, 3 and PyPy) as an alternative to MySQLdb (Python 2 only) to connect to a MySQL database.

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

  • Chunlei Wu (first contribution)
  • Edward Liaw (first contribution)
  • Eric Talevich
  • Leighton Pritchard
  • Manlio Calvi (first contribution)
  • Markus Piotrowski (first contribution)
  • Melissa Gymrek (first contribution)
  • Michiel de Hoon
  • Nigel Delaney (first contribution)
  • Peter Cock
  • Saket Choudhary
  • Tiago Antao
  • Vincent Davis (first contribution)
  • Wibowo ‘Bow’ Arindrarto
  • Yanbo Ye (first contribution)
  • Zheng Ruan (first contribution)
Posted in Biopython, Code, Community, Development, OBF Projects | Tagged , , , , , | 18 Comments

OBF Google Summer of Code students 2014

Hi all, I’m pleased to announce the acceptance of OBF’s Google Summer of Code 2014 (GSoC) students:[GSoC 2014 Logo]

  • Sarah Berkemer – “Open source high-performance BioHaskell” (Mentors: Christian Höner zu Siederdissen, Ketil Malde) (blog)
  • Loris Cro – “An ultra-fast scalable RESTful API to query large numbers of VCF datapoints” (Mentors: Francesco Strozzi, Raoul Bonnal & the BioRuby team) (blog)
  • Victor Kofia – “JSBML: Redesign the implementation of mathematical formulas” (Mentors: Alex Thomas, Sarah Keating & the JSBML team) (blog)
  • Evan Parker – “Addition of a lazy loading sequence parser to Biopython’s SeqIO package” (Mentors: Wibowo Arindrarto, Peter Cock & the Biopython team) (blog)
  • Ibrahim Vazirabad – “Improving the Plug-in interface for CellDesigner” (Mentors: Andreas Dräger, Alex Thomas & the JSBML team) (blog)
  • Leandro Watanabe – “Dynamic Modeling of Cellular Populations within JSBML” (Mentors: Nicolas Rodriguez, Chris Myers & the JSBML team) (blog)

Congratulations to our accepted students!

Thanks very much to all the students who applied, we very much appreciate your hard work.

We are now in the GSoC Community Bonding Period. Official work starts on May 23rd, and until then, students should prepare for their projects: get on the project mailing lists, solidify your plans, figure out where all the version control repositories are and which branch or fork you’ll be working on, and start doing preparatory work.

Here’s to a great 2014 Summer of Code,

Eric & Raoul

OBF GSoC 2014 Organization Administrators

Posted in Biopython, Blogroll, Code, Community, Development, Google Summer of Code, OBF, OBF Projects | Tagged , , , , , | 9 Comments

Catering at BOSC CodeFest 2014

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc.

Thanks to this sponsorship, this year the organisers will able to include catering for the participants – I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

If you are wondering what happens exactly at a CodeFest, I suggest Brad’s blog post from the BOSC Codefest 2013, or Möller et al (2013). Basically these meeting are a chance for developers of open source bioinformatics (not just the OBF’s Bio* projects) to get together and work on common interests. Things work best with some pre-meeting planning on the usual project development mailing lists or IRC, but are also a great way to meet other scientists and developers in person with more time to chat than during a conference coffee break.

Please note that while there is no registration fee for the BOSC Codefest 2014, please do fill in the registration form to help with the planning/catering.

We’re hoping all the Codefest participants will stay for the BOSC meeting itself, which requires formal paid registration as one of the big ISCB 2014 conference’s SIG satellite meetings. Note that we’re offering a BOSC fee waiver for student speakers, this year. If you are going to BOSC, please remember to submit your BOSC abstracts this week!

Peter

Posted in Blogroll, BOSC/ISMB, Code, Community, Development, General, OBF, OBF Projects | Tagged , , , , , , , , , | 4 Comments

Free registration to student presenters at BOSC 2014

To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we’re waiving the registration fee for accepted student presenters. When you submit your abstract (BOSC abstract call open until 4th April), you must tick the student box:

Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.

Please note that because BOSC registration is via the ISCB as one of the ISCM SIG meetings, eligible students must contact us before filling in their ISCB registration to ensure the BOSC SIG fee is waived.

Furthermore, as in previous years, BOSC Student Travel Awards sponsored by Eagle Genomics will be awarded to the top student presentations to help with your travel and accommodation costs.

Update (2 May 2014): We’ve just sent out the accepted talk invitations, and are offering a registration fee waiver to four student speakers.

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , | 15 Comments

OBF GSoC 2014: Call for student applications

Google Summer of Code 2014Are you a university student and interested in spending the summer developing open-source bioinformatics software?

(Good! Keep reading.)

On Monday, March 10, Google Summer of Code 2014 (GSoC) will begin accepting student applications to work with mentoring organizations like OBF.

Here are the steps for you to prepare an application and apply for GSOC 2014 with OBF:

  1. Check the OBF ideas page for potential projects you’d like to work on, and identify one or a few that you’re most interested in doing.
  2. Read our guide for prospective GSoC students on the OBF wiki. Also see Google’s GSoC FAQ and GSoC student guide, if you’re with us so far.
  3. Introduce yourself on the OBF GSoC mailing list. Tell us which project(s) you like, any modifications to them you’d like to make, or propose your own idea.
  4. Once you’ve settled on a project or two and contacted your potential mentors, begin preparing a detailed project timeline for the summer. This timeline should cover each week of the summer, as far as you can plan it, describing the week’s specific goals, coding tasks, anticipated problems and open questions. (Example 1, Example 2)
  5. Submit your application to Google early. You can keep revising it on the Melange website until the deadline on March 21, but once you’ve submitted your basic information we can begin giving you feedback and suggestions to improve your application. In addition to your weekly timeline, you can link to examples of code you’ve written (e.g. on GitHub); a small contribution of code (e.g. a bug fix) to the project you’re applying to work with would really impress us.

Feel free to contact us on the mailing list or Google Plus if you have any questions.

Posted in OBF | 5 Comments

BOSC 2014 call for abstracts

Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.

[BOSC Logo]

Important Dates:

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. This year’s session topics are:

[Eagle Genomics Logo]
  • Open Science and Reproducible Research
  • Software Interoperability
  • Genome-scale Data and Beyond
  • Visualization
  • Translational Bioinformatics
  • Bioinformatics Open Source Libraries and Projects
GigaScience Journal Logo

Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel Awards, and welcome the open access journal GigaScience as a new sponsor for BOSC 2014.

BOSC 2014 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , | 24 Comments