BioPerl v1.7.0 released

We are happy to announce the long-awaited release of BioPerl v1.7.0.  The release is now available on CPAN and Github.

During this release series, we will move some extraneous code to separate repositories and CPAN releases, primarily to reduce the number of dependencies required for BioPerl installation (in many cases for modules that are never used) and also reduce maintenance overhead.

This may only impact you if your code incorrectly list the immediate downstream dependencies that you utilize.  For example, we have now moved Bio::Coordinate code to a separate repo and will release it as a separate distribution on CPAN.  If your tools require Bio::Coordinate::Result and list this module as a dependency, you should be fine: a separate Bio::Coordinate release should pull in the latest BioPerl, until then it would pull in the last BioPerl release with that module.  However, if you list Bio::Root::Root or Bio::Perl as a dependency to pull in Bio::Coordinate::Result, your installation will not work correctly (as Bio::Root::Root is not the proper code dependency).  We can work with distributions affected to help with this transition and will be more consistently evaluating reverse dependencies on CPAN for upcoming releases as we split out code.  Please post issues on Github if you see problems with your code and the latest release.

In addition to the above, modules relying on a remote web services that are no longer active or pose a security issue will be deprecated for use and (in some cases) immediately removed.  Normally these don’t affect normal tests, but we have noticed some remote services out of our control causing problems with network-requiring or release testing.

In addition, the following changes have been made since the last release:

  • NCBI HTTPS support [Mark Johnson (aka mjohnson) and others]
  • We have migrated to Github Pages. This was actually planned, but the
    recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!!
  • Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!)
  • Previously deprecated modules have been removed
    • Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
    • Bio::DB::SeqHound has been removed due to the service no longer being available
    • Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert
    • Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
    • Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be released independently on CPAN
  • Docker instances of tagged releases are available! [hlapp]
  • Bio::SearchIO::infernal
    • Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
    • Bio::Search::HSP::ModelHSP: Added a ‘noncanonical_string’ method to retrieve the NC line from CMSEARCH reports [pcantalupo]
    • Bio::Search::Result::INFERNALResult – Added new module to represent features of Infernal reports [pcantalupo]
  • SQLite support for Bio::DB::Taxonomy – [cjfields]
  • WrapperBase quoted option values [majensen]
  • Various documentation fixes and updates [bosborne]

And many many bug fixes.  Please see the Changes file with the distribution.

Thanks, and enjoy!

chris

Posted in BioPerl, OBF, Uncategorized | 10 Comments

BioRuby 1.5.1 released

We are pleased to announce the release of BioRuby 1.5.1.

In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare NCBI website transitioning to HTTPS.

Continue reading

Posted in BioRuby, Code, Development, OBF, OBF Projects | Tagged | 2 Comments

Biopython 1.68 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.68 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but this will be our final release to run on Python 2.6. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Bio.PDB has been extended to parse the RSSB’s new binary Macromolecular Transmission Format (MMTF, see http://mmtf.rcsb.org), in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the mmtf-python library.

Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski). It is now faster, addresses some problems with local alignments, and also now allows gap insertions after deletions, and vice versa, inspired by the preprint from Flouri et al.

The two sample graphical tools SeqGui (Sequence Graphical User Interface) and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide transcription, back-transcription and translation into amino acids using Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython. xbbtools is able to open Fasta formatted files, does simple nucleotide operations and translations in any reading frame using one of the NCBI genetic codes. In addition, it supports standalone Blast installations to do local Blast searches.

New NCBI genetic code table 26 (Pachysolen tannophilus Nuclear Code) has been added to Bio.Data (and the translation functionality), and table 11 is now also available under the alias Archaeal.

In line with NCBI website HTTPS changes, Biopython now uses HTTPS rather than HTTP to connect to the NCBI Entrez and QBLAST API.

Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 and best practice standard coding style.

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

  • Anthony Bradley (first contribution)
  • Ben Fulton
  • Carlos Pena
  • Connor T. Skennerton
  • Iddo Friedberg
  • Kai Blin
  • Kristian Davidsen (first contribution)
  • Markus Piotrowski
  • Olivier Morelle (first contribution)
  • Peter Cock
  • Tiago Antao
  • Travis Wrightsman
  • Uwe Schmitt (first contribution)
  • Xiaoyu Zhuo (first contribution)

Thank you all.

P.S. You can follow @Biopython on Twitter

Checksums:

$ md5sum biopython-1.68.*
078e915185485a5327937029b7577ddc biopython-1.68.tar.gz
362e964543a424a2f7585ea4008ea834 biopython-1.68.win32-py2.6.exe
772d07d9a6490d674688d00ede2bdfe9 biopython-1.68.win32-py2.7.exe
fda2d1c8d4a7862f6af85122c86fcd0f biopython-1.68.win32-py2.7.msi
8de95a90704f15f4c22d5359dbc54b75 biopython-1.68.win32-py3.3.exe
92f40105761520daeeb9128254a8bc94 biopython-1.68.win32-py3.3.msi
b1cd3f6b4ad1096347d5019c68128dac biopython-1.68.win32-py3.4.exe
9403b9b0d01c22b49edb34e2164c31de biopython-1.68.win32-py3.4.msi
72202792fc387376c07e28997ece181f biopython-1.68.win32-py3.5.exe
ff0cfc6c835ddf890b69ba872fb46b39 biopython-1.68.win32-py3.5.msi
adb3e8ce60b02b3b46330bbca68f9732 biopython-1.68.zip
$ shasum -a 256 biopython-1.68.*
d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f  biopython-1.68.tar.gz
09449d7204c65e6010545092f2bc1dc662a0b5f6a873e52a08e19392f935fdb7  biopython-1.68.win32-py2.6.exe
a7c2fe52ce8dcf503a492e4ee006dd8bc62faa77078d04c92abdbf7713bf2166  biopython-1.68.win32-py2.7.exe
f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41  biopython-1.68.win32-py2.7.msi
bce6a4cece7b75650d6a478f4ed9d7d1a5351df42a1820866a0cbd74c254565d  biopython-1.68.win32-py3.3.exe
85bd5d499400e594f77d297966f56c139499711513b9cd24b87fece5a0463fbe  biopython-1.68.win32-py3.3.msi
05c1f59933ef35ecb838649f6fabacb823f2a48c2498ed57ac59a6b3629b5369  biopython-1.68.win32-py3.4.exe
10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef  biopython-1.68.win32-py3.4.msi
5d08e4de11f920ec5207e10d264fceb837e2000843a56fd684e0ee2dfb948fe5  biopython-1.68.win32-py3.5.exe
299888c32b36f32542775952e7b863bd9c3d362f61a69b7d8a136a63aeabec36  biopython-1.68.win32-py3.5.msi
986a0fa6919d2b51959259011dd0674b115383237e109c5a55c37cb18eef999b  biopython-1.68.zip

Updated 29 August 2016 to include the Python 3.5 installer checksums.

Posted in Biopython, Blogroll, Code, Development, OBF, OBF Projects | Tagged | 30 Comments

BOSC 2016 in Disney World with Donald Docker!

First I would like to congratulate OBF that supports diversity in the community with its travel awards initiative. I was very pleased to be one of the three travel fellowship awardees. Thank you OBF! Ιt was great to attend BOSC 2016 and meet remarkable people and know their work.

It was one of the most welcoming meetings I have attended and Ι liked that is was active on the social media and the conference materials and speaker presentations were available online. It made it fun and useful and we could focus less on our notebooks and more on the speakers. Τhis also attracted a lot of positive comments from the other Special Interest Groups. So “Bravo” to the organizers!

On the scientific part, it was nice to see Docker making an impression on the bioinformatics community. Everyone was talking about it. It is an awesome way to package bioinformatics applications and the fact that it received so much attention got me pretty excited. I am planning to use it to package CollOS, an open source web application I presented at the conference, that tracks, annotates and barcodes biological samples to facilitate wet lab scientists to locate and identify biological samples.

Last but definitely not least, I would like to congratulate Mónica Muñoz-Torres and the organizers for their reference to the recent tragic shooting incident in Orlando.

Hope to see you next year in Prague!

Dimitra

Posted in BOSC/ISMB, Community, OBF | Tagged , , , | 7 Comments

New BioJava Logo Design Competition

BioJava is organizing a design competition to come up with a new logo.
Anybody can participate:

  • The logo should look modern and be better than the current one (yellow
    circle)

  • The logo should be able to be rendered as a favicon, as well as large
    (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.

  • Logos shall not look similar in any way to the trademarked Java
    programming language logo. This means no coffee cups in any way.

Deadline:
Deadline for submissions is July 4th.

Announcement of Winner:
The winner of the new logo competition will be announced during BOSC 2016.

Prize:
We will print t-shirts with the new logo and the designer will get a free
t-shirt.

If the designer of the winning new logo will be attending ISMB 2016, the
attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

Details:
For full details of the competition and how to make a submission please
view here:

https://github.com/biojava/logo

Result Update:

As announced via the mailing list and at BOSC 2016, the winning logo was by Aleix Latifa:

Posted in BioJava, Blogroll, BOSC/ISMB, Community, Development, OBF, OBF Projects, Website | Tagged , , , , , , | 7 Comments

Biopython 1.67 released

This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.

Source distributions and Windows installers for Biopython 1.66 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Comparison of SeqRecord objects until now has used the default Python object comparison (are they the same instance in memory?). This can be surprising, but comparing all of the attributes would be too complex. As of this release attempting to compare SeqRecord objects should raise an exception instead. If you want the old behaviour, use id(record1) == id(record2) instead.

New experimental module Bio.phenotype is for working with Phenotype Microarray plates in JSON and the machine vendor’s CSV format (contributed by Marco Galardini).

Following the convention used elsewhere in Biopython, there is a new function Bio.KEGG.read(…) for parsing KEGG files expected to contain a single record only – the existing function Bio.KEGG.parse(…) is intended to be used to iterate over multi-record files.

When a gap character is defined, Bio.Seq will now translate gap codons (e.g. “—“) into a single gap (“-“) in the protein sequence. The gap character is inferred from the Seq object’s alphabet, but it can also be passed as an argument to the translate method.

The new NCBI genetic code table 25, covering Candidate Division SR1 and Gracilibacteria, has been added to Bio.Data (and the translation functionality).

The Bio.Entrez interface will automatically use an HTTP POST rather than HTTP GET if the URL would exceed 1000 characters. This is based on NCBI guidelines and the fact that very long queries like complex searches can otherwise trigger an HTTP Error 414 Request URI too long.

Foreign keys are now used when creating BioSQL databases with SQLite3 (this was not possible until SQLite version 3.6.19). The BioSQL taxonomy code now updates the taxon table left/right keys when updating the taxonomy.

There have been some fixes to the MMCIF structure parser which now uses identifiers which better match results from the PDB structure parse.

The restriction enzyme list in Bio.Restriction has been updated to the May 2016 release of REBASE.

The mmCIF parser in Bio.PDB.MMCIFParser has been joined by a second version which only looks at the ATOM and HETATM lines and can be much faster.

The Bio.KEGG.REST will now return unicode text-based handles, except for images which remain as binary bytes-based handles, making it easier to use with the mostly text-based parsers in Biopython.

Note that the BioSQL test configuration information is now in a new file Tests/biosql.ini rather than directly in Tests/test_BioSQL_*.py as before. You can make a copy of the provided example file Tests/biosql.ini.sample as Tests/biosql.ini and edit this if you wish to run the BioSQL tests.

Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 standard coding style, and in converting our docstring documentation to use the reStructuredText markup style.

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

  • Aaron Rosenfeld (first contribution)
  • Anders Pitman (first contribution)
  • Barbara Mühlemann (first contribution)
  • Ben Fulton
  • Ben Woodcroft (first contribution)
  • Brandon Invergo
  • Brian Osborne (first contribution)
  • Carlos Pena
  • Chaitanya Gupta (first contribution)
  • Chris Warth (first contribution)
  • Christiam Camacho (first contribution)
  • Connor T. Skennerton
  • David Koppstein (first contribution)
  • Eric Talevich
  • Jacek Śmietański (first contribution)
  • João D Ferreira (first contribution)
  • João Rodrigues
  • Joe Cora (first contribution)
  • Kai Blin
  • Leighton Pritchard
  • Lenna Peterson
  • Marco Galardini (first contribution)
  • Markus Piotrowski
  • Matt Ruffalo (first contribution)
  • Matteo Sticco (first contribution)
  • Nader Morshed (first contribution)
  • Owen Solberg (first contribution)
  • Peter Cock
  • Steve Bond (first contribution)
  • Terry Jones (first contribution)
  • Vincent Davis
  • Zheng Ruan

Again this list of contributors is longer than usual, which is good, but partly reflects the delay since our last release. My apologies.

Posted in Biopython, Blogroll, Code, Development, OBF, OBF Projects | Tagged , , , , | 39 Comments

BOSC 2016 Panel: Growing and Sustaining Open Source Communities

Every year, BOSC includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. BOSC is all about community, so this year’s panel topic–Growing and Sustaining Open Source Communities–is right at the heart of what we do. Since the first BOSC in 2000, we have focused on bringing together open source bioinformatics developers and users to form and expand collaborations and grow the communities that use and improve their tools and resources.

Community projects have resulted in some of the most popular bioinformatics resources. However, there are many challenges that may be encountered as a community effort develops and evolves. For example:

  • How can an open source community integrate a diverse set of participants, including people with different levels of experience, different interests, and different demographic characteristics?
  • How can non-developers (for example, people who primarily write documentation, or who are users of the software) contribute to these projects?
  • What funding approaches have successfully sustained open source communities after any core funding has run out?
  • What technologies have helped open source communities coordinate efficient communication and planning across multiple locations?
  • What organizational models have some of these communities followed?

This panel brings together six people (five panelists plus a moderator) who have worked to sustain open source communities. They will join audience members in an open dialog about challenges encountered during the life cycle of these communities and approaches to addressing them.

Panel chair Mónica Muñoz-Torres is the biocuration lead for Berkeley Bioinformatics Open-Source Projects (BBOP) at Lawrence Berkeley National Laboratory.

Abigail Cabunoc Mayes is the Lead Developer of the Mozilla Science Lab.

Bastian Greshake co-founded openSNP, a crowdsourced/citizen science open data project.

Jamie Whitacre is the technical project manager for Project Jupyter, which grew out of the widely used IPython Notebook.

John Chilton of Penn State is a software developer on the Galaxy project, and one of the co-founders of the Common Workflow Language.

Natasha Wood of the University of Cape Town is the co-founder of the Cape Unseminars in Bioinformatics.

Please see https://www.open-bio.org/wiki/BOSC_2016_Panel for more information about the panelists.

Posted in BOSC/ISMB, Community | 16 Comments

First three OBF travel fellowships awarded

The first round of the Open Bioinformatics Foundation travel fellowship program has granted funds to three open source bioinformatics software developers to help them attend the Bioinformatics Open Source Conference (BOSC) 2016 in Orlando, Florida, this July. The travel fellowship program (announced 1 May 2016) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.

Out of more than a dozen applicants from four different continents, the OBF Board chose the following three recipients:

  • Dimitra Sarantopoulou of the University of Pennsylvania is an open source bioinformatics developer who focuses on web applications for proteomic analysis.
  • Michael R. Crusoe (@biocrusoe) is the Co-founder & Community Engineer for the Common Workflow Language (CWL), and previously was the lead developer of khmer.
  • Anurag Priyam is a self-taught bioinformaticst who has created several successful open source tools, including  SequenceServer and oswitch, a Docker-based virtual environment switcher.

The OBF Board congratulates the three winners!

This first round has also shown several points of improvement, both for the program description and the application form. We are in the process of making small adjustments to both, and expect to reopen the application form for the next round of funding at the latest by the time BOSC 2016 rolls around (July 8). We encourage others for whom travel costs are a barrier to participating in open source bioinformatics events to apply for this next round (due date is August 15, 2016).

Posted in Blogroll, BOSC/ISMB, Community, OBF, Website | Tagged , , , , , | 6 Comments

Welcome to our Google Summer of Code 2016 students

The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one after all.

The Open Bioinformatics Foundation gets to host eight student projects this year:

  • Alisha Mechtley will work with the ETE toolkit on tree searching using regular-expression-like queries.
  • Anton Khodak will work on the Common Workflow Language, creating an automated tool wrapper/converter for CWL
  • Christian Fischer will work on the GeneNetwork Genome Browser
  • Graham Dyer will work on openSNP, extending the quantified-self support
  • Julian Mazzitelli will work on a workflow engine for streamed data analysis in Bionode
  • Mariana Nave will improve the prediction for RiPP clusters in antiSMASH
  • Mateus Jabor will work on improving the user experience in openSNP
  • Vivek Rai will work on linking phenotypes to SNPs in openSNP

Please join me in welcoming all of them in the Open Bioinformatics Foundation community and the respective subprojects. It looks like this will be a great summer.

Kai Blin

OBF administrator for GSoC 2016

Posted in Blogroll, Community, Development, Google Summer of Code, OBF, OBF Projects | Tagged , , | 26 Comments

Phyloinformatics Summer of Code supports OBF Travel Fellowship Program

The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the OBF travel fellowship program. The program, announced earlier this year on March 1, aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The program includes but is not limited to the annual Bioinformatics Open Source Conference (BOSC), OBF’s flagship event.

The funds for this gift are a legacy of the seven years during which the National Evolutionary Synthesis Center (NESCent) served as a mentoring organization in the Google Summer of Code™. Over the years, NESCent’s program, the Phyloinformatics Summer of Code, supported dozens of students for three-month paid internships developing open source software for evolutionary and biodiversity informatics.  Each year, Google made a small award to Duke University, NESCent’s administrative home, to support the program, and when NESCent ceased operations in 2015, the funds for this gift remained.

Todd Vision, former Associate Director of Informatics at NESCent, says “With this gift, OBF will carry on the legacy of the Phyloinformatics Summer of Code in building a diverse and collaborative open source bioinformatics community.”

OBF has only been able to underwrite the Travel Fellowship program for an initial 3 years, for at most a handful of awards each year. As Hilmar Lapp, President of OBF’s Board, and former Assistant Director of Informatics at NESCent, explains, “This program is a signature part of our commitment to inclusivity and growing our community, and we are keen to make it a sustained effort. This gift is a key step in that direction, and I hope that we can convince other donors to follow.”

The gift is specifically earmarked for awards to increase diversity at bioinformatics community events. “By targeting travel costs, we hope to remove one barrier to participation. Meeting face to face can be a critical step to becoming part of an existing community.”, says Karen Cranston, OBF Board Member, who ran the Phyloinformatics Summer of Code program for several years while at NESCent.

There have been long-standing ties between the Phyloinformatics Summer of Code and OBF. They have shared project ideas and mentors, and some graduates from the summer program have subsequently taken on prominent roles in OBF’s projects and community. A student from the 2011 summer program, Sarah Hird, even served as the Outreach Coordinator for BOSC 2015, the theme of which was Increasing Diversity.

About OBF: The Open Bioinformatics Foundation (OBF) is a nonprofit volunteer run organization founded in 2001 with a mission to promote the practice and philosophy of open-source software development and open science within the biological research community. OBF is incorporated as an affiliate project of Software in the Public Interest, Inc., a 501(c)(3) fiscal sponsorship organization.

About NESCent: The National Evolutionary Synthesis Center (NESCent) was a science center dedicated to cross-disciplinary research in evolution, jointly operated by Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University from 2004-2015, with support largely from the National Science Foundation. In 2015, it transitioned to the Triangle Center for Evolutionary Medicine (TriCEM).

Posted in Community, Google Summer of Code, OBF | Tagged , , | 4 Comments