The July 2019 Open Bioinformatics Foundation Public Board Meeting was held in person, as a Birds-of-Feather during the 2nd day lunch period of the 2019 BOSC.

Date, Location and Dial-In

Date and time: July 25, 12:45pm CEST Venue: Congress Center Basel, Switzerland, in the Dehli Room (ground floor, same room as BOSC) Dial-In for participating remotely: expired

Agenda

Old business:

1. Approve minutes from March 2018 Public Board Meeting

New business:

1. Term expirations and Elections to the Board ( electronic ballot)
   • Malvika Sharan, running for Board member at-large
   • Karen Cranston’s term as Board member at-large expired in 2018, and she chose not to run for another term.
   • The terms of several current Board members (Hilmar Lapp, Peter Cock, Chris Fields, Nomi Harris) are expiring this year, but are deferred to later this year for re-election.
2. Fiscal sponsor
   • Update on fiscal sponsor situation
   • Revamping the process for OBF’s financial reports
3. OBF Code of Conduct
4. Open floor
   • Opportunities to engage
   • Revisiting vision and mission

Minutes

The meeting minutes are available in the obf-docs Github repository.

Dear Biopythoneers,

Biopython 1.74 has been released and is available from our website and PyPI.

This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.

(Please note we will be dropping support for Python 2.7 in early 2020.)

Over half 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.

Note: This is a guest blog post from Angela Muraya, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the Africa Open Science Hardware Summit 2019. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. If you are hoping to attend an open source / open science bioinformatics event and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships . The next deadline is August 15, 2019.

We are pleased to announce the April 2019 OBF Travel Fellowship recipients. The OBF Travel Fellowship program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics. After carefully evaluating a competitive set of applications submitted from all around the globe, we were able to extend offers to five deserving applicants: Sara El-Gebali, Angela Wanjugu Muraya, Saket Choudhary, Aziz Khan and Vid Ayer. They have all accepted the award, and we are looking forward to hearing about their experiences.

If you’d like the opportunity to present your work at BOSC 2019 (which will take place in Basel, Switzerland, on July 24-25, the last two days of ISMB/ECCB 2019), now’s your chance! The late round of abstract submission is open, and we will be choosing a few abstracts for “Late-Breaking Lightning Talks” as well as posters.

BOSC welcomes submissions about all aspects of open source bioinformatics, open science and open data. More information, and a link to the EasyChair submission portal, can be found at /events/bosc/submit/ .

Above: the old BOSC page. Below: the new one.

If you’ve been around the OBF and BOSC community, you’re probably familiar with our slightly rusty old site, which ran on MediaWiki, the same open source software that runs Wikipedia. While they’re both awesome tools, we decided it was time for a refresh.

Over the last few months, our Outreachy Intern Deepashree Deshmukh designed and implemented the new OBF website(with supervision by OBF Board member Yo Yehudi). The goal was an attractive and easily-updatable site that can function as a community-oriented hub. Did we accomplish that? Your feedback on the new site is welcome!

This is a guest blog post from Md Kamruzzaman Sarker, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend 2nd U.S. Semantic Technologies Symposium Series (US2TS). 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 on 15 April 2019. 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.

This is a guest blog post from Lindsay Rutter, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a National Center for Biotechnology Information (NCBI) hackathon and the Plant and Animal Genome Conference (PAG). 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 on 15 April 2019. 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.

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.