Welcome to our Google Summer of Code 2018 students

The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices.  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, as you will find out.

The Open Bioinformatics Foundation will host six student projects this year:

  • Hitesh Joshi will be working on a Bionode workflow engine for streamed data analysis
  • Synchon Mandal will be improving the constraint-based modeling in COBRApy
  • Sophia Mersmann will improve the posterior error probability estimation for OpenMS peptide search engine results
  • Edgar Garriga Nogales will implement support for Research Object specification into the Nextflow framework
  • Sarthak Sehgal will be rewriting the front-end code powering the BioJS websites
  • Megh Thakkar will be revamping the back-end of the BioJS websites

Please join me in welcoming all of them to the Open  Bioinformatics community and the respective subprojects. I’m sure we’ll have a great, productive summer together.

 

Kai Blin
OBF administrator for GSoC 2018

PS: We ask all our students to blog about their summer of code experience and will be updating this post with links to their respective blogs.

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BioJava 5.0.0 is out

BioJava 5.0.0 was released on the 23rd of March 2018. This represents a major milestone that brings more consolidation and reorganisation of modules. This is the first release to be based on Java 8, bring in your lambdas and stream API calls!

The release represents work done in the last 2 years, alpha releases were available for quite some time and now this makes all the changes officially public.

Some major refactoring occurred in the biojava-structure module. The data model to deal with macromolecular structures has been adapted to be closer to the mmCIF data model. Other improvements in biojava-structure are support for MMTF format and improved symmetry detection code.

See the full release notes or browse the official API documentation.

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

Biopython 1.71 released

Dear Biopythoneers,

Source distributions of Biopython 1.71 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI) including pre-compiled Wheel Packages for Linux, Mac OS X and Windows.

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy2.7 v5.10.0 and PyPy3.5 v5.10.1.

Python 3 is the primary development platform for Biopython. We will drop support for Python 2.7 no later than 2020, in line with the end-of-life or sunset date for Python 2.7 itself.

Setup changes:

We now explicitly recommend installation using “pip install biopython”, rather than the classic “python setup.py install” approach. In a related change, we depend on the Python package setuptools (rather than the older package distutils in the Python standard library) and have made the dependency on NumPy explicit and automatic.

License changes:

As of Biopython 1.69, we have started to dual-license Biopython under both our original liberal “Biopython License Agreement”, and the very similar but more commonly used “3-Clause BSD License”. A growing number of the Python files are explicitly available under either license, but most of the code remains under the “Biopython License Agreement” only. See the LICENSE file for more details.

Code changes:

Encoding issues have been fixed in several parsers when reading data files with non-ASCII characters, like accented letters in people’s names. This would raise UnicodeDecodeError: 'ascii' codec can't decode byte ... under some system locale settings.

Bio.KEGG can now parse Gene files.

The multiple-sequence-alignment object used by Bio.AlignIO etc now supports a per-column annotation dictionary, useful for richly annotated alignments in the Stockholm/PFAM format.

The SeqRecord object now has a translate method, following the approach used for its existing reverse_complement method etc.

The output of function format_alignment in Bio.pairwise2 for displaying a pairwise sequence alignment as text now indicates gaps and mis-matches.

Bio.SeqIO now supports reading and writing two-line-per-record FASTA files under the format name “fasta-2line”, useful if you wish to work without line-wrapped sequences.

Bio.PDB now contains a writer for the mmCIF file format, which has been the standard PDB archive format since 2014. This allows structural objects to be written out and facilitates conversion between the PDB and mmCIF file formats.

Bio.Emboss.Applications has been updated to fix a wrong parameter in fuzznuc wrapper and include a new wrapper for fuzzpro.

The restriction enzyme list in Bio.Restriction has been updated to the November 2017 release of REBASE.

New codon tables 27-31 from NCBI (NCBI genetic code table version 4.2) were added to Bio.Data.CodonTable. Note that tables 27, 28 and 31 contain no dedicated stop codons; the stop codons in these codes have a context dependent encoding as either STOP or as amino acid.

IO functions such as SeqIO.parse now accept any objects which can be passed to the builtin open function. Specifically, this allows using pathlib.Path objects under Python 3.6 and newer, as per PEP 519.

Bio.SearchIO can now parse InterProScan XML files.

For Python 3 compatibility, comparison operators for the entities within a Bio.PDB Structure object were implemented. These allow the comparison of models, chains, residues, and atoms with the common operators (==, !=, >, …) Comparisons are based on IDs and take the parents of the entity up to the model level into account. For consistent behaviour of all entities the operators for atoms were modified to also consider the parent IDs. NOTE: this represents a change in behaviour in respect to v1.70 for Atom comparisons. In order to mimic the behaviour of previous versions, comparison will have to be done for Atom IDs and alternative locations specifically.

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 PEP8PEP257 and best practice standard coding style.

Acknowledgements:

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

  • Adhemar Zerlotini
  • Ariel Aptekmann
  • Chris Rands
  • Christian Brueffer
  • Erik Cederstrand (first contribution)
  • Fei Qi (first contribution)
  • Francesco Gastaldello
  • James Jeffryes (first contribution)
  • Jerven Bolleman (first contribution)
  • Joe Greener (first contribution)
  • Joerg Schaarschmidt (first contribution)
  • João Rodrigues
  • Jeroen Van Goey
  • Jun Aruga (first contribution)
  • Kai Blin
  • Kozo Nishida
  • Lewis A. Marshall (first contribution)
  • Markus Piotrowski
  • Michiel de Hoon
  • Nicolas Fontrodona (first contribution)
  • Peter Cock
  • Philip Bergstrom (first contribution)
  • rht (first contribution)
  • Saket Choudhary
  • Shuichiro MAKIGAKI (first contribution)
  • Shyam Saladi (first contribution)
  • Siong Kong
  • Spencer Bliven
  • Stefans Mezulis
  • Steve Bond
  • Yasar L. Ahmed (first contribution)
  • Zachary Sailer (first contribution)
  • Zaid Ur-Rehman (first contribution)

Thank you all.

P.S. You can follow @Biopython on Twitter

Checksums:

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Welcome to our new board members!

As mentioned in our previous blog post, last Friday the OBF had a board of directors meeting. One of the notable meeting items this time was to elect more board members to help be involved with the community. We’re pleased to announce that both candidates, Bastian Greshake Tzovaras and Yo Yehudi, were unanimously voted in by the other board members!

Logically, one of their first moves as newly minted members was to draft this blog post! Some of the their possible ideas for the future include:

  • Applying to participate as a mentor organisation in Outreachy – a program similar to Google Summer of Code, but specifically dedicated to increasing diversity in open source.
  • Growing our network and connecting more closely with like-minded organizations in the open science-space

If any of these sound of interest and you’d like to be involved, please let us know by leaving a comment on this post, mailing the main OBF mailing group (membership required), or tweeting @obf_news. We’re especially keen to hear if any of you have other suggestions for things you’d like to see to help build the community!

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OBF Public Board Meeting to take place March 16, 2018 at 15:00 UTC

The OBF Board of Directors holds a public meeting about once a year, in accordance with our bylaws. The next such meeting will take place on March 16, 2018, at 15:00 UTC (11am EDT / 8am PDT / 16:00 CET). The meeting agenda can be found at https://www.open-bio.org/wiki/Minutes:2018_Mar_ConfCall.

At this public Board meeting, we will consider two new candidates running for Board seats: Bastian Greshake Tzovaras and Yo Yehudi. Both are known for their promotional and organizational involvement in open science, open data and open source bioinformatics.

Bastian has been active in the larger field of Open Science since 2010, when he helped to run a successful petition for the German legislative to overhaul their Open Access policies. He is the co-founder of openSNP and currently serves as the Director of Research at Open Humans. He mentors open science projects as part of the Mozilla Science Lab mentorship programs. Bastian recently earned a PhD in bioinformatics from the University of Frankfurt. He is on the BOSC organizing committee.

Yo works on software and community outreach for Intermine at the University of Cambridge. and is a passionate advocate of open* in research. She runs a project called Code is Science, dedicated to increasing the number of publications about scientific software that include Open Source code. Yo tweets about open science and open bioinformatics (for example, at BOSC 2017). She hopes to apply her scientific communication and outreach skills to help the OBF grow and deepen its community impact.

During the March 16 public Board meeting, the two candidates will introduce themselves, and the current board members will vote via secret (though verifiable) electronic ballots. Additionally, the minutes from the previous BoD meeting and the financial reports for previous years will be presented and approved.

All members of OBF are invited to join us for this meeting. Membership in OBF is free and open to anyone who is interested in and aligned with the objectives of the organization. If you would like to apply for membership, please visit https://www.open-bio.org/wiki/Membership.

Meeting time: March 16, 2018, 11.00am EDT (15:00 UTC, 16:00 CET, 8.00am PDT). Note that at the time of the meeting, the US will have switched already to DST, whereas Europe will not, so the time zone difference is an hour less than it would normally be.
Dial-in Information: +1-857-216-2939
PIN: 62534
http://www.uberconference.com/hlapp

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OBF accepted as a mentoring organisation for Google Summer of Code 2018

The Open Bioinformatics Foundation has been accepted as a mentoring organisation for the 2018 instance of the Google Summer of Code. OBF is acting as an umbrella for ten bioinformatics Open Source projects, making it possible to offer a very diverse set of student projects.

Are you a student and interested in applying for any of the projects? The student application period is open from March 12th through 27th from the official GSoC website. See the full timeline for details. Feel free to contact the mentors of projects you are interested in already, though.

Posted in Community, Development, Google Summer of Code, OBF, OBF Projects | Tagged | Leave a comment

GCCBOSC 2018: A Bioinformatics Community Conference – Call for Abstracts

Logo

We are pleased to announce that abstract submission and early registration for GCCBOSC2018 are now open. This event brings our annual Bioinformatics Open Source Conference and the Galaxy Community Conference together into a unified week-long event. If you work in open source life science or data-intensive biomedical research, then there is no better place than GCCBOSC 2018 to present your work and to learn from others.
Continue reading

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OBF Travel Fellowship – Coding in the Winter Wonderland: Galaxy Admin Training in Oslo, 2018

This blog post is syndicated from a post on Arun Decano’s blog, originally published Feb 1, 2018. Arun was supported by the ongoing OBF travel fellowship program to attend a Galaxy Admin Workshop held in Oslo, Norway Jan 7-14, 2018.

The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 April 2018. Continue reading

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Arun Decano awarded OBF Travel Fellowship

Arun Decano
Arun Decano is a PhD research fellow in the Infection Genomics Group at Dublin City University in Dublin, Ireland. Her research, with advisor Dr. Tim Downing, focuses on the phylogenomic study of a multidrug-resistant bacterial population and aims to develop novel infection control strategies using whole genome sequence data.

The Open Bioinformatics Foundation awarded Ms. Decano a travel fellowship to help defray the cost of attending the European Galaxy Administrator Workshop (https://www.elixir-europe.org/events/european-galaxy-administrator-workshop) in January 2018.

The OBF travel fellowship program was launched in 2016 to help increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The next application deadline will be April 15, 2018—see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for information and to apply.

Posted in OBF, Travel Fellowship | Tagged | 2 Comments

Mailing list consolidation

The OBF’s self-hosted mailman server is still struggling right now, so we are looking at migrating the active mailing lists to paid hosting, and as part of this consolidating down to ideally about a dozen mailing lists. Currently we have a lot of mailing lists, but many are dormant or redundant.
Continue reading

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blogroll, Community, Development, Essays, OBDA / BioSQL, OBF, OBF Projects | Leave a comment