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!

Posted in Board, Community, OBF, Uncategorized | Tagged , , | Leave a comment

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

Posted in Board, Community, OBF | Tagged , , | Leave a comment

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


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

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , , , , , , | Leave a comment

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

Posted in Blogroll, Community, Travel Fellowship | Tagged , | Leave a comment

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

Next OBF Travel Fellowship application deadline is Dec 15!

The Open Bioinformatics Foundation 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. There are four application deadlines per year; the next will be December 15, 2017. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships. More information, including a link to the application form, can be found at https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md.

Posted in Community, General, OBF, Travel Fellowship | Tagged , , | 1 Comment

This is a guest blog post from Farah Zaib Khan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend our annual conference BOSC 2017 and its preceding Codefest in Prague, July 2017. 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 December 2017, you might want to apply?
Continue reading

Posted on by Farah Zaib Khan | Leave a comment

OBF visioning 2017

TL;DR: The OBF isn’t doing enough in public policy and advocacy around Open Science, and we are looking to recruit a new board member who is interested in this role. Is that you? If yes, then contact us.

At our October meeting, the OBF board took some time to think broadly about the OBF, current and future. We tried to answer the questions: What do we say we do? What do we actually do? What more do we wish we could do? We re-read our mission statement and list of public activities from the OBF main page, listed the current efforts of the board members and affiliates, and assessed how our actual work aligned with the stated goals of the organization. This was motivated by having board members who are new-ish to the OBF, as well as upcoming board elections.

Our general mission is fairly broad (“promoting the practice and philosophy of Open Source software development and Open Science within the biological research community”). We aim to do this through running / sponsoring BOSC and other open source events (codefests and Google Summer of Code); running a travel fellowship program; managing servers, mailing lists, domain names and other assets for our member projects; and by advocacy through policy and public statements.

With BOSC being our flagship event, it is not surprising that about 50% of our board time is spent on organizing this meeting, with our remaining effort about equally focused on the travel fellowship, server / domain management, and financials.

What more could we be doing? OBF could help facilitate other events, as we do for Google Summer of Code (GSoC). In this model, the board does not directly run the event, but instead provides support with financial management (e.g., reimbursements and payments) and advertising, while the hands-on organization is done by non-board members. In the case of GSoC, Kai Bin has been the OBF GSoC administrator for the past couple of years (thanks, Kai!). So, even though the board members don’t have bandwidth to organize other events, we could certainly help in a ‘producer’ role.

The big area where we aren’t doing enough is advocacy and communication. There is huge interest in Open Science, reproducibility, software sustainability and other similar topics, but the OBF is surprisingly silent. This doesn’t reflect a lack of interest (or opinion!) among the board members, but rather the difficulty in carving out time from other OBF jobs.

So, we are looking to recruit a new board member who is interested in policy and advocacy around Open Science. Does that sound like you? If you want to put your name forward, please email the board. The election will be held at the upcoming public board meeting in January. If you want more information, or want to contact one of us to talk about being on the board, see the OBF Board page.

Posted in Board, Community, General, OBF, Uncategorized | Tagged , | Leave a comment