Obf

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2016: Jennifer Gardy Dr. Jennifer Gardy is both a scientist and science communicator. She holds a PhD in Bioinformatics, and is an Assistant Professor of Population and Public Health at the University of British Columbia and a Senior Scientist at the British Columbia Centre for Disease Control (BCCDC). At the BCCDC, she pioneered a new way of investigating outbreaks of infectious diseases – “genomic epidemiology”, which uses a pathogen’s genome sequence as a tool for understanding how an infectious disease spreads. [Read More]

We are very pleased to announce our new Open Bioinformatics Foundation (OBF) Travel Fellowship program. The program is designed to enable people, whether long-standing members of our community or newcomers, to participate in eligible events for which costs would otherwise be prohibitive. This includes our annual Bioinformatics Open Source Conference (BOSC). Although not limited to specific groups of people, the program constitutes another major step for us in our ongoing efforts to increase the diversity in our communities in particular, and in the open source / open science bioinformatics community in general. [Read More]

Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016. Dates: July 8-9, 2016 Location: Orlando, FL Web site: /wiki/BOSC_2016 Email: bosc@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Twitter: @OBF_BOSC and @OBF_News Important Dates: Call for one-page abstracts opens: March 1, 2016 Abstract submission deadline: April 1, 2016 - extended to Monday 4 April 2016 Travel fellowship application deadline: April 15, 2016 Authors notified: May 6, 2016 Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue) BOSC 2016: July 8-9, 2016, Orlando, FL ISMB 2016: July 8-12, 2016, Orlando, FL The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. [Read More]

The Open Bioinformatics Foundation (OBF) is pleased to announce that we’ve finally entered the 21st century and upgraded our membership form from paper (yep!) to an online form. Membership in the OBF is free, and is open to anyone who has attended BOSC or can otherwise demonstrate commitment to OBF’s goals. The information you enter on the form, including your email address, will be treated confidentially - we are in the business of promoting open source and open science, not in selling email addresses. [Read More]

Source distributions and Windows installers for Biopython 1.66 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI). This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, although support for Python 2.6 is now deprecated. It has also been tested on PyPy 2.4 to 2.6, PyPy3 version 2.4, and Jython 2.7. Further work on the Bio.KEGG and Bio.Graphics modules now allows drawing KGML pathways with transparency. [Read More]

We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2), improvement of codes, and bug fixes. Here is a brief summary of changes. Ruby 2.0.0, 2.1, 2.2 support. Some features are removed because of remote service discontinuance or difficulty of code maintenance. Refactoring of code. Bio::SPTR is renamed as Bio::UniProtKB. Bug fixes. In addition, many changes have been made, including incompatible changes. [Read More]

Every year, BOSC includes a panel discussion that offers all attendees the chance to engage in conversation with the panelists and each other. Two months ago we announced the theme of the BOSC 2015 panel would be " Open Source, Open Door: increasing diversity in the bioinformatics open source community". Our complete list of panellists is: Panel chair Mónica Muñoz-Torres ( @monimunozto) is the lead biocurator at Berkeley Bioinformatics Open-Source Projects (BBOP). [Read More]

The next public Board of Directors Meeting of the OBF will take place on May 12th, 2015, at 17:00 UTC (1pm EDT, 10am PDT, 19:00 CEST, see World Clock). The developing agenda for the meeting is posted, as are the dial-in details. We will have Board elections at this meeting. The terms of Directors Jason Stajich and Chris Dagdigian expire, and they will both step down from the Board. As most of you will know, both have provided truly extraordinary service to the OBF, from the earliest beginnings of the organization and in fact the very community around it. [Read More]

The Bioinformatics Open Source Conference (BOSC) has always been about community. Launched in 2000, BOSC aims to provide a forum for both bioinformatics developers and users to share ideas and code and learn about the latest developments in open source bioinformatics and open science. Our goal this year is to welcome even greater participation, opening the door even wider to participants who have historically been underrepresented in the world of open source bioinformatics and, therefore, at BOSC. [Read More]

(This is a repost of a BLOG on Google Open Source news about Google’s open source student programs and software releases) One of our goals with GSoC is to inspire young developers to participate in open source development, hopefully continuing well beyond the summer. Pjotr Prins from the Open Bioinformatics Foundation shared this story with us about a GSoC 2012 student who has continued leading the development of a software tool used in laboratories around the world. [Read More]