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.

Some were announcement specific, where nowadays blogs and Twitter work quite well. Others were development specific (including automatic commit logs from central source code repositories), but now most OBF Project discussions are on GitHub. While the main project mailing lists used to have a lot of user support traffic, much of that has moved to external Q&A style sites like BioStars, StackExchange, or StackOverflow. What this means is that the OBF software projects probably only need a single mailing list each.

Based on http://mailman.open-bio.org/mailman/listinfo here are the current publicly listed OBF hosted mailing lists.

Miscellaneous active public lists (propose to retain in some form):

Miscellaneous active but non-public lists (propose to retain in some form):

BioPerl (propose to merge to a single list):

BioJava (propose to merge to a single list):

Biopython (propose to merge to a single list):

BioRuby (propose to merge to a single list):

BioSQL (propose to merge to a single list):

EMBOSS (propose to merge to a single list):

DAS (propose to merge to a single list, or close and archive):

Dormant lists, including legacy projects (propose to close and archive):

If this affects you directly (e.g. any project leaders we have not been able to contact yet), please write to the OBF board. Since mailman is currently unreliable, board at open-bio.org might not work. Please CC our fall back address of obf-board at Google Groups.

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.

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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

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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.

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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.

Posted in Blogroll, Board, Community, General, Mailing lists, OBF, Uncategorized | Tagged , , , , | 1 Comment

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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