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We have recently applied to Google for the OBF to be part of the Google Summer of Code 2019 programme, again with Kai Blin and Michael Crusoe as joint administrators. Last year, OBF GSoC 2018, was another good year with five students successfully completing their projects:

• Synchon Mandal (mentor Moritz Beber) “Adding methods to cobrapy for improved constraint-based metabolic modelling.” ( first blog bost; final report)
• Sophia Mersmann (mentors Oliver Alka, Julianus Pfeuffer, and Timo Sachsenberg) “Improve Posterior Error Probability Estimation For Peptide Search Engine Results” (blog posts; final report)
• Edgar Garriga Nogales (mentors Paolo Di Tommaso, Michael R. Crusoe, and Stian Soiland-Reyes) “Implement the support for Research Object specification into Nextflow framework” ( repository; homepage; final report).
• Sarthak Sehgal (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) “Frontend Website Student Project for BioJS” ( repository; blog posts; final report).
• Megh Thakkar (mentors Yo Yehudi, Dennis Schwartz, and Rowland Mosbergen) “Backend Website Student Project for BioJS” ( repository; blog posts; final report).

In some cases there isn’t a single code repository to link to, rather their work included pull requests to the main project etc.

We had a great round of OBF travel fellowship candidates in our last round of applications, and after review we extended offers to three deserving applicants: Malvika Sharan, Lindsay Rutter, and Sarker Kamruzzaman. They’ve all accepted the award, and we’re looking forward to hearing about their experiences!

Congratulations to our December 2018 recipients:

Malvika Sharan will be attending BOSC at ISMB 2019 in Basel this July. Abstract submissions have only just opened, but she intends to submit an abstract expanding on the idea “Inclusiveness in Open Science” that she spoke about last year ( slides). She’s been active in the BOSC community for several years, participating in abstract review and BoF organisation, and she plans to continue this for 2019.

Farah presents CWLProv at GCCBOSC 2018

The next round of our OBF Travel Fellowships just ended on the 15th of December! This round we have introduced a Review Chair coming from the midst of our community that will help us in reviewing the applications. The role will be filled by Farah Zaib Khan, one of our OBF Travel Fellowship alumni. Farah has successfully applied for the Fellowship twice before. Thanks in part to this support, she has become a central community member both of the Bioinformatics Open Source Conference and the Open Bioinformatics Foundation itself.

Dear Biopythoneers,

Biopython 1.73 has been released and is available from our website and PyPI.

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.

As in recent releases, more of our code is now explicitly available under either our original " Biopython License Agreement", or the very similar but more commonly used “3-Clause BSD License”.  See the LICENSE.rst file for more details.

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).

We recently discovered that the application to join the OBF (linked from the OBF membership page) was not working. It broke some time after August 31. We have now replaced it and it is working once again.

If you applied for OBF membership between September 1 and yesterday, please go to the new form (https://goo.gl/x9KYWL) and resubmit your application. We apologize for the inconvenience!

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.

BOSC 2019 will be part of ISMB 2019 Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. As we reported, the experiment was a success–participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years. However, we also concluded that there are some advantages to meeting with ISMB–for example, it attracts more students and postdocs, and the presence of other COSI tracks provides a wider range of scientific topics. Moreover, unlike the GCC 2018 venue, the venue already chosen for GCC 2019 has a number of drawbacks: we wouldn’t be able to run similarly-sized parallel sessions; registration prices wouldn’t be as affordable as in 2018; and the venue would not be able to accommodate the larger (160 people) and longer (four days) CollaborationFest that was one of the highlights of GCCBOSC 2018.For these and other reasons, the BOSC organizing committee concluded that the best way to serve the broadest community of potential BOSC attendees will be to partner with ISMB some years and GCC some years. We therefore plan to hold BOSC 2019 in Basel as part of ISMB. We hope to partner with GCC in 2020 at a North American site to be determined, or in 2021 in Europe.Wherever we hold future BOSCs, you can be sure that they will include a wide range of topics in open science and open source bioinformatics, and we hope that they will draw an ever-diversifying mix of attendees. As always, we welcome your feedback about what you liked in past BOSCs and your suggestions for the future. Feel free to email us ( bosc@open-bio.org) or tweet (@OBF_BOSC).