Community

About a year ago, the OBF shared plans to get more involved with the open science community, and followed up by recruiting two board members for this purpose. Since then, we’ve tried to keep up momentum and community engagement - during GCCBOSC, we held an OBF Birds of Feather meeting, allowing members of the board to meet with attendees and discuss their needs and interests. As a result of this meeting, we ended up with our new community-designed logo and launched a community newsletter (incidentally, issue 2 of the newsletter is going to be released within the next few days - feel free to suggest a news item).

We have successfully crowd-sourced a new OBF logo! The process started at the OBF Birds of a Feather meeting at GCCBOSC 2018 when the OBF leaders announced that we were seeking a new logo design. Two BoF participants immediately started sketching ideas, as well as a third community member who was not at the BoF but saw our tweet. The designs (which you can see here) were put up for a public vote. Aleix Lafita’s narrowly won and was adopted as our new OBF logo! We are currently working on possible variations on the logo for special events or causes (for example, a rainbow version).

This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the GCCBOSC 2018 meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. Our August call recently closed, the current call closes 15 December 2018, you might want to apply?

How should I start describing the fruitful experience in this amazing city… First time ever in Portland, second time attending BOSC… I knew I was signing up for a great time but did not know much about the uncanny beauty of this picturesque city.

First of all, I would like to thank the Open Bioinformatics Foundation (OBF) for providing partial funding to support my travel expenses (though an OBF Travel Fellowship award). I would also like to thank my PhD supervisors Andrew Lonie and Richard O. Sinnott for the remaining expenditure.

This year, the Galaxy Community Conference (GCC) and the Bioinformatics Community Conference (BOSC) met together to form the first Bioinformatics Community Conference. At GCCBOSC 2018, participants were able to meet and collaborate with a broad community of bioinformatics developers and users who focus on open, interoperable software tools and libraries that facilitate scientific research.

Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC attracted nearly 300 participants from around the world. The meeting started with two days of training workshops (Figure 1). The main meeting had some parallel sessions and some joint sessions, including well-received keynote talks by Tracy Teal, Fernando Pérez and Lucia Peixoto, as well as a panel discussion about documentation and training. Posters, demos and Birds of a Feather sessions ( BoFs) gave participants opportunities to engage in discussions about topics of mutual interest. After the main meeting, many attendees stayed for up to four additional collaboration days (the CollaborationFest, or CoFest). Figure 1. Participants at one of the GCCBOSC training workshops. (All GCCBOSC photographs in this post are from Bérénice Batut’s Flickr album, under a CC-BY-SA license.) Figures 2,3. Attendees and presenters mingled at the poster/demo sessions.

It was really great to meet so many of you at GCCBOSC this year! We will soon have a couple of Travel Fellowship blog posts talking about the conference, so we won’t provide too much of a general overview at this point, but we would like to share a little more about one of the Bird of Feather (BoF) events we ran - specifically the OBF community BoF. The aim of this BoF was to engage anyone who was:

Dear Biopythoneers,

I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:

https://biopython.org/wiki/Download https://pypi.python.org/pypi/biopython/1.72

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).

We had another great round of applications for the OBF Travel Fellowship this spring. After reviewing the applications, the OBF Board selected three recipients, who have all accepted the award.

Congratulations to our spring 2018 recipients:

• Anisha Keshavan –  attended the eLife Innovation Sprint. Anisha is a postdoctoral fellow at the University of Washington, where she develops open source code, including citizen scientist platforms for image quality classification and image segmentation ( update - see blog post).
• Farah Zaib Khan – attending GCCBOSC2018 including the CollaborationFest. Farah is a Common Workflow Language contributor based at the University of Melbourne. She has recently been working on a project to record the provenance of CWL workflows, and first attended BOSC in 2017 ( update - see blog post).
• Tendai Mutangadura – attending GCCBOSC2018 including the CollaborationFest. Tendai is a first-time BOSC attendee who works at the University of Missouri and focuses on studying disease-causing mutations in canine genomics ( update - see blog post).

Watch this space for blog posts from each of the awardees ( update - links added above).

The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices.  We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one, as you will find out.