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).
[Read More]About the OBF
The Open Bioinformatics Foundation (OBF) is a non-profit, volunteer-run group that promotes open source software development and Open Science within the biological research community. Membership in the OBF is free and open to anyone who wants to help promote open source or open science in a biological field.
OBF runs the annual Bioinformatics Open Source Conference (BOSC).
BOSC 2025 will be July 21-22, 2025, in Liverpool, UK (as part of ISMB/ECCB 2025). BOSC 2024 took place July 15-16, 2024, as part of ISMB 2024 in Montréal, Canada.
OBF Event Awards
The OBF Event Fellowship program aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community.
OBF Travel Fellowship - CWL week in London
This is a guest blog post from Anton Khodak, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a week long Common Workflow Language (CWL) workshop in London, November 2016. This was a natural continuation of Anton’s work on porting tools to the CWL as one of the OBF’s Google Summer of Code 2016 students. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 April 2017 - if you’re planning to attend the OBF’s annual Bioinformatics Open Source Conference (BOSC) 2017 in Prague, you might want to apply?
[Read More]
OBF Public Board of Directors Meeting
The OBF has at least one public board meeting per year, in part to vote on important business issues, and in part to publicly discuss items relevant to the OBF community. The latest public OBF Board of Director’s meeting took place October 4, 2016. It was attended by Board members Hilmar Lapp, Peter Cock, Nomi Harris, Chris Fields, and Karen Cranston, as well as guests Heather Wiencko (Board candidate), Michael Crusoe, Spencer Bliven, and Robert Gilmore.
The agenda, and tentative minutes (taken by then-secretary Peter Cock) are available from the OBF wiki. The following is a summary:
[Read More]Minutes:2016 Oct ConfCall
Agenda Venue: To be held by conference call on Oct 4, 2016, 12.30pm EDT (16:30 UTC, 17:30 BST, 18:30 CEST, 9.30am PDT) Dial-in Information: +1-857-216-2939 PIN: 62534 http://www.uberconference.com/hlapp
Old business May 2015 BoD meeting minutes Amendments to the 2013 Financial Report 2014 Financial Report New business Term expirations and Elections for the Board ( electronic ballot) Heather Wiencko, running for election to the Board. Hilmar Lapp, President of the Board. Running for re-election.
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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.
[Read More]
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.
[Read More]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.
[Read More]
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.
[Read More]
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.
[Read More]
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 1.67 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.
[Read More]