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.

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BOSC 2017 report

BOSC 2017 ( /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.

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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. [Read More]

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. [Read More]

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.

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).

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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.

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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.

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