Community

Thanks to OBF support with a travel grant, I was able to attend the first European CarpentryConnect event in Manchester CCMcr19 organized by The Software Sustainability Institute.

Colourful Manchester days post Pride weekend

The Carpentries is a global community with a mission to teach essential data and foundational computational skills to researchers for conducting efficient, open, and reproducible research. The community includes instructors, trainers, maintainers and many more helpers and supporters on a global scale.

The OBF Travel Fellowship program, established in 2016, aims to increase diverse participation at events related to open source bioinformatics. Applications are reviewed three times a year. Applicants may apply for attending any event that develops or promotes open source development and open science in the biological research community. It doesn’t have to be an OBF-related event, and it can be one that you already attended in the recent past. For example, if you attended BOSC 2019 and your travel expenses were not covered by your employer or university, you could apply for a travel fellowship to help defray those expenses (up to a maximum of $1000, in most cases). Travel fellowship awardees are required to write a blog post about their experience attending the event; you can see some past such posts on our blog.

As Europe experienced a record-breaking heat wave, BOSC 2019 attendees stayed cool in the Basel Congress Center (and many took breaks by floating down the Rhine). This was the 20th annual BOSC. In 2018, BOSC partnered with the Galaxy Community Conference in GCCBOSC2018; this year, it returned to ISMB as one of over a dozen “Communities of Special Interest” (COSIs).

BOSC 2019 opened on July 24 with chair Nomi Harris noting that over its 20 years, BOSC has been held in 12 different countries, 6 US states and 2 Canadian provinces. Next, Heather Wiencko introduced the Open Bioinformatics Foundation, BOSC’s parent organization, and Kai Blin discussed the OBF’s participation in Google’s Summer of Code. The two morning sessions focused on data–representing it, storing it, crunching it. Open Data was covered in another session later in the day.

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.

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.

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.