Mailing list outage, and public board meeting update

This time of year we’d normally be having a public board meeting as part of our commitment to communication with our member projects and the wider OBF community. As per our bylaws we notify the community at least 10 days in advance, and we’d also handle election of new board members and leadership changes where appropriate. For a couple of reasons, we’re going to postpone that until early 2018.

Our mailing list server (which hosts many of our member project lists) has been overwhelmed in the past few days, leading to delayed or blocked communication not just to our members but for our member projects who rely on it. We’re looking into options for solving this problem, which might include migrating to a hosted solution.

This comes at the same time that the OBF board has been taking a look at how best to direct the organisation as we move forward. We’d like to have that conversation with our members after we’ve crystallised our thoughts a bit, and we’re still in the process of doing that.

As we’re sorting this out, we decided to push the public meeting back to early 2018 so everyone involved can get the most out of it. We hope you understand, and we’re looking forward to hearing from as many of you as we can at that meeting.

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BOSC 2017 report

BOSC 2017 (https://www.open-bio.org/wiki/BOSC_2017) was held in Prague in July 2017 as part of the annual ISMB conference. Nearly 250 people, half of whom were first-time attendees, participated in the meeting. Over 50 talks and a similar number of posters covered topics ranging from workflow tools to a crowd-funded “tree of beers.” This year’s Open Data theme was reflected in the keynote talks by Madeleine Ball and Nick Loman and the panel discussion about the opportunities and challenges of open data.

A report about BOSC 2017 is now available on F1000 (https://f1000research.com/articles/6-1858/v1), and most of the talk and poster abstracts and talk videos are linked from the schedule page (https://www.open-bio.org/wiki/BOSC_2017_Schedule).

In 2018, BOSC will be partnering with the Galaxy Community Conference (GCC) as an experiment in broadening the BOSC community. We invite anyone who has an interest in open source bioinformatics or open science to join us in Portland, Oregon, June 25-30–see https://gccbosc2018.sched.com/ for more information.

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Biopython on Podcast.__init__

Podcast.__init__ describes itself as “The Podcast About Python and the People Who Make It Great”, and the most recent episode is “Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão (Episode 125)“.

Listening to the finished podcast, interviewer Tobias Macey did a great job. There are things I would have liked to have said – but it turned out pretty well. I hope you’ll agree:

Its worth looking back over the podcast archives, here are a few that caught my eye:

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OBF Travel Fellowship – BOSC session of the ECCB/ISMB 2017

This blog post is syndicated from a post on Jonathan Sobel’s blog, originally published July 27, 2017. Jonathan was supported by the ongoing OBF travel fellowship program to attend the 2017 Bioinformatics Open Source Conference (BOSC), held as part of the 2017 ISMB/ECCB meeting in Prague, Czech Republic, in July 2017.

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 December 2017. Continue reading

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OBF Travel Fellowship – IGC Bioinformatics Training

This blog post is syndicated from a post on Vitalina Kirgizova’s blog, originally published June 6, 2017. Vitalina was supported by the ongoing OBF travel fellowship program to attend bioinformatics training course held at the Instituto Gulbenkian de Ciência, Oeiras, Portugal, in November 2016.

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 December 2017. Continue reading

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Travel fellowships: deadline August 15

The next deadline for the OBF travel fellowship is coming up soon on August 15, 2017. If you are attending any event that develops / promotes open source software or open science, and you are willing to write a blog post about the event, we welcome your application. See the travel fellowship page for more details and link to the application form.

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Biopython 1.70 released

Dear Biopythoneers,

Source distributions of Biopython 1.70 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI). Windows installers and/or wheels should be available later. (Update: Compiled wheel packages now available 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 PyPy v5.7, PyPy3.5 v5.8 beta, and Jython 2.7 (although we are deprecating support for Jython).

New Logo:

Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our original logo (with two yellow snakes) and the current Python logo, this shows a yellow and blue snake forming a double helix.

[Biopython Logo]

Setup changes:

We now explicitly recommend installation using pip, rather than the classic “python setup.py install” approach. In a related change, we now 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 (except on Jython).

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:

Bio.AlignIO now supports Mauve’s eXtended Multi-FastA (XMFA) file format under the format name “mauve” (contributed by Eric Rasche).

Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return text-mode handles for use under Python 3.

Two new arguments for reading and writing blast-xml files have been added to the Bio.SearchIO functions (read/parse and write, respectively). They are use_raw_hit_ids and use_raw_query_ids. Check out the relevant SearchIO.BlastIO documentation for a complete description of what these arguments do.

Bio.motifs was updated to support changes in MEME v4.11.4 output.

The Bio.Seq sequence objects now have a .count_overlap() method to supplement the Python string like non-overlap based .count() method.

The Bio.SeqFeature location objects can now be compared for equality.

In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously _DistanceMatrix) has a new method .format_phylip() to write Phylip-compatible distance matrix files (contributed by Jordan Willis).

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, PEP257 and best practice standard coding style.

Acknowledgements:

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

  • Aaron Kitzmiller (first contribution)
  • Adil Iqbal (first contribution)
  • Allis Tauri
  • Andrew Guy
  • Ariel Aptekmann (first contribution)
  • Ben Fulton
  • Bertrand Caron (first contribution)
  • Chris Rands
  • Connor T. Skennerton
  • Eric Rasche
  • Eric Talevich
  • Francesco Gastaldello
  • François Coste (first contribution)
  • Frederic Sapet (first contribution)
  • Jimmy O’Donnell (first contribution)
  • Jared Andrews (first contribution)
  • John Kern (first contribution)
  • Jordan Willis (first contribution)
  • João Rodrigues
  • Kai Blin
  • Markus Piotrowski
  • Mateusz Korycinski (first contribution)
  • Maximilian Greil
  • Michiel de Hoon
  • morrme (first contribution)
  • Noam Kremen (first contribution)
  • Patrick Kunzmann
  • Peter Cock
  • Rasmus Fonseca (first contribution)
  • Rodrigo Dorantes-Gilardi (first contribution)
  • Sacha Laurent (first contribution)
  • Sourav Singh
  • Ted Cybulski (first contribution)
  • Tiago Antao
  • Wibowo ‘Bow’ Arindrarto
  • Zheng Ruan

Thank you all.

P.S. You can follow @Biopython on Twitter

Checksums:

 

$ md5sum biopython-1.70.*
feff7a3e2777e43f9b13039b344e06ff  biopython-1.70.tar.gz
6307ab27c257fe69b9dae4bfc3052f49  biopython-1.70.zip
$ shasum -a 256 biopython-1.70.*
4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b  biopython-1.70.tar.gz
34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f  biopython-1.70.zip

 

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Travel award recipients for April 2017

We had a huge response to this round of the OBF travel award. After reviewing the applications, the OBF board selected four recipients. Three applicants accepted awards, and all plan to use the funds to attend this year’s BOSC, to take place July 22-23 in Prague.

Congratulations to our spring 2017 recipients:

  • Sourav Singh, who will participate in the Codefest and present the Biopython Project Update 2017 talk
  • Jonathan Sobel, presenting on a citizen science project named BeerDeCoded, carried out by members of the Swiss non-profit called the Hackuarium
  • Jiwen Xin, presenting the BioThings Explorer project, which integrates genomic data via public APIs

We encourage everyone at BOSC to come out and support our award winners! After BOSC, watch for blog posts from each of the awardees.

The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. See the OBF travel award page for details and link to application.

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BOSC 2017 keynote speakers

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2017, and our first sponsors.

But first a final reminder – today (Thursday 13 April 2017) is our deadline for submitting a full length talk abstract to BOSC 2017.

Dawn Field

Dawn Field is a Lamberg International Guest Professor at Göteborg University’s Department of Marine Sciences. Previously she was a senior research fellow at the NERC Centre for Ecology and Hydrology, Head of the Molecular Evolution and Bioinformatics Group at the Centre for Ecology and Hydrology in Wallingford, UK, and a research associate at the Smithsonian Institution. She is also a founder of the Genomic Standards Consortium, the Genomic Observatories Network and Ocean Sampling Day.

Dr. Field is credited with introducing the concept of a biological code, or “biocode” – the sum of all DNA on earth. In their book Biocode: The New Age of Genomics, she and coauthor Neil Davies describe the rapid rise of genomics, how it is revealing the scale and diversity of life on Earth, and future possibilities and implications.

Dr. Field’s advocacy for open data and interoperability is epitomized by her past leadership of the Genomics Standards Consortium (GSC), which aims to facilitate genomic data integration, discovery and comparison through international community-driven standards.

The title of Dr. Field’s keynote talk is “Understanding the Biocode: Global Sharing of Data.”

Nick Loman

Nick Loman is known as a vocal proponent of open genomic data in healthcare. A Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, Dr. Loman explores the use of cutting-edge genomics and metagenomics approaches to human pathogens. He promotes the use of open data to facilitate the surveillance and treatment of infectious disease.

Dr. Loman helped establish real-time genomic surveillance of Ebola in Guinea and Zika in Brazil (via the ZiBRA project, which states that “Data will be subject to open release as it is generated”). In another recent project, real-time genomic data was used to analyze a small outbreak of Salmonella enteritidis in the UK. Through this sharing of genomic datasets, researchers were able to confirm that the cases were linked to a larger, national-scale outbreak. Dr. Loman is one of the authors of Poretools, and he regularly shares cutting-edge Nanopore data and protocols for using it. In collaboration with Lex Nederbragt, Dr. Loman is developing an open-source repository of sequencing and bioinformatics benchmarking datasets called Seqbench.

BOSC 2017 Sponsors

We are grateful to and welcome The Hyve (open source solutions for bioinformatics) and Mozilla Science Lab (a community of researchers, developers, and librarians making research open and accessible), as the first sponsors for BOSC 2017.

If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.

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Biopython 1.69 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.69 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

Continue reading

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