This post is guest-posted by Federica Trevisan, an OBF GSoC student with the Wellcome Trust. Cross-posted with Federica’s blog: https://federikovi.medium.com/my-google-summer-of-code-2021-c795dd0cc794

My Google Summer of Code 2021

Well yes, I am part of GSoC 2021 💻☀️

What is Google Summer of Code

In a nutshell, GSoC is a remote program founded in 2005, in which Google connects students and organisations during the summer break from classes. In this global program the students work with an open source organization on a 10 week programming project during their break from school. In this way students can gain technical experience on real projects by “flipping bits not burgers” . It’s also a competitive program; this year only the 27% of students who submitted at least a proposal got accepted.¹

OBF students and mentors at an OBF kickoff call

Every year the OBF applies to participate as a mentoring organisation for Google Summer of Code, a paid work experience program where students get the chance to do paid work on an open source project and open source organisations host the students to work on their projects. This year, eight projects have participated under the OBF umbrella - read more about these fantastic students and their work below:

Birds of a Feather (BoFs) are informal, self-organized meetups focused on specific topics. They are a great way to meet other like-minded community members and have an in-depth discussion on a topic of shared interest.

BoFs at ISMB/ECCB 2021 will take place each day of the meeting except the last day, at the same time as the poster session (not ideal, we know–but there are only so many viable hours in the day), from 15:20-16:20 UTC. We recommend that you choose either Thursday, July 29 (the first day of BOSC) or Wednesday, July 28 (the day before BOSC).

Thanks to funding from our sponsors, we are opening a special call for applications to the BOSC-OBF Event Support Fund. This fund aims to increase participation of members from groups otherwise underrepresented in BOSC or in bioinformatics community events in general, including but not limited to underrepresented demographic groups (country of residence and citizenship), ethnic background (historically underrepresented and other minority groups), career stages, gender identity and expression, people with disabilities and members from low income/resource organisations.

The Open Bioinformatics Foundation (OBF) Event Fellowship program supports and encourages diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Sona Charles, a Scientist (Bioinformatics) at ICAR-Indian Institute of Spices Research, India, was supported to participate in the Great Lakes Bioinformatics (GLBIO) 2021 Conference by this award granted to her in the application round-1 of 2021. Find more information here.

In this pandemic stricken world when all conferences are taking place virtually and don’t require traveling, it has become more accessible for international participants like me. However, the cost for registration, video-conferencing accessories and childcare remain the same. Luckily, I came across the Open Bioinformatics Foundation Event Fellowship, when I was hoping to attend the Great Lakes Bioinformatics (GLBIO) 2021 Conference. I had already submitted a poster entitled “ Sequence-Based Prediction of Phytophthora- Host Interaction Using Machine Learning Methods” to the conference, which was accepted. I went ahead and applied for the event fellowship at Open Bioinformatics Foundation for its first round of 2021. Two weeks later (after the application review phase), I was informed by the Chair of OBF Event Fellowship that I was awarded the fellowship.

Biopython 1.79 has been released and is available from our website and PyPI.

This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1.

The major changes in this version are listed below:

- The Seq and MutableSeq classes in Bio.Seq now inherit from the same base class, ensuring their mutual consistency. In addition, both classes now store sequence data as bytes and bytearray objects, respectively.

There’s still a chance to submit your abstract in the Late Poster round, which closes June 3 at 11:59pm ET!

What about late-breaking lightning talks? Unfortunately/fortunately, we got so many high-quality abstracts in the early round, we were not able to save any talk slots for the late round. Talk slots will open up only if some early-round speakers decide not to attend the conference.

Abstract format. To be considered for a poster, you only need to submit a 200-word short abstract. However, you should feel free to add a PDF (2 pages max) that better describes your work! Your PDF should include the title, author name(s), open source license, and code or project URL (even though this information is also requested on the submission form). Accepted abstracts are published on the BOSC website as-is.

The OBF is committed to providing a harassment-free and respectful environment for all members of our community. To ensure that we are clearly describing norms, rules, and recommended practices for all our participants and members, we have provided a first draft of the OBF Code of Conduct and shared it recently in our newsletter.

You can find the draft together with our request for comments on this pull request (see a preview here). If you have not already, please take a few minutes to add your comments in this pull request by June 4th, 2021.

The following outlines a potential new grant programme, subject to approval by the OBF membership in a formal vote, which the OBF board would hope to launch this year.

Motivation

In 2016, the OBF introduced a “Travel Fellowship” to help individuals attend meetings, aiming to improve diversity in the bioinformatics community. Awardees were reimbursed (with receipts) after the event in which they participated, with a standard cap of USD $1000. The Travel Fellowship was later renamed the “Event Fellowship” reflecting that with the COVID-19 pandemic (and hopefully longer-term changes in scientific conferences to promote the participation of diverse members in online events and reduce carbon emissions), attending events no longer automatically means travelling in person.

BOSC is organized entirely by volunteers. We are lucky to have these amazing people on the Organizing Committee this year!

Jason Williams( @JasonWilliamsNY) is a new member of the BOSC Organizing Committee, though he’s been a BOSC participant and an abstract reviewer for years. Jason was a BOSC panelist in 2015 on a panel about increasing diversity in open source bioinformatics, and again in 2018 for a panel about training and documentation in open source bioinformatics.