This is a guest post from Mihai Popescu, a GSoC student with CWL, which participates under the OBF umbrella. Cross-posted on the CWL forums: https://cwl.discourse.group/t/working-on-a-cwl-toil-project-with-the-open-bioinformatics-foundation/390

I am Mihai Popescu, a second year master student at VU Amsterdam in Parallel and Distributed Computer Systems. I am happy that my GSoC proposal got accepted and that I have started working on the project. I attended some CWL meetings since I submitted the proposal and I got to know a small part of the community. I would like to thank my mentor Michael for introducing me to the CWL community and answering a lot of my questions about workflows.

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:

It’s Google Summer of Code (GSoC) application time again - I’ll be leading the OBF GSoC application and org admin process this year alongside Sarthak Sehgal, Michael Crusoe, and Kai Blin. The OBF typically works as an umbrella organisation for other sub-projects - if you have an open + bio related code project that you think could use a student intern this year, please read on.

TL;DR: Please send ideas for half-sized projects (1.5 months, not 3 months) by Thursday 18 feb, New mailing list, Code of Conduct.

OBF was accepted as a mentoring organisation for Google Summer of Code this year. It was another good year for OBF, with Kai Blin, Michael R. Crusoe, Sarthak Sehgal, and Yo Yehudi as administrators. We hosted eight students all of which successfully completed their work:

1. Srijan Verma (mentors: Dmitry Petrov, Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers
2. Himanshi Mathur (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - Implementation of SVML in SIMDe ( final report, other blogs, SIMD Everywhere)
3. Boshen Yan (mentors: Amal Thomas, Marius Beek, Saket) - Implementing user-friendly search features in PysraDB ( final report, weekly writeup, work summary)
4. Shekhar Shukla (mentors: Oliver Alka, Hannes Röst, Timo Sachsenberg) - OpenMS R Package ( final report, blogs, OpenMS)
5. Francesco Porto (mentors: George Githinji, Erik Garrison, Pjotr Prins) - Parallel Graph Traversal for Variation Graphs
6. Eliza Martin (mentors: Dymitr Nowicki, Vlada Tyshchenko, Anton Kulaga) - Protein sequence and structural analysis CWL pipeline for comparative biology
7. Hidayat Ullah Khan (mentors: Jun Aruga, Evan Nemerson, Michael R. Crusoe) - SIMDe: Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension ( final report, mentee blogposts, SIMD Everywhere)
8. T. Waschischeck (mentors: Chris Bielow, Julianus Pfeuffer) - Using DeNovo Sequencing to Predict Protein Database Suitability ( final report, student blog, OpenMS)

This year, OBF received 5000 USD from Google for being a mentoring organisation. The funds from GSoC go into the general OBF Fund that is primarily used to sponsor OBF Event Fellowships which is a program aimed at increasing diverse participation at events promoting open science practices such as resource development and dissemination in the bioinformatics and biological research community.

OBF has been selected as a Google Summer of Code mentor organisation for the 5th consecutive time! We are proud to be hosting over 13 projects from various sub-organisations that aim to promote open science. This year OBF’s application was led by Sarthak Sehgal, Kai Blin, Yo Yehudi, and Michael Crusoe. Last year, GSoC 2019, was another good year with five students successfully completing their projects.

Call to students to apply for GSoC

OBF is welcoming students across the globe with a passion for open science to apply for GSoC. You can view the eligibility criteria here and the whole timeline here. The application portal opens on March 16 but feel free to contact the mentors of projects you are interested in already. It’s a fantastic opportunity to write code, learn about open source development, and be a part of a welcoming and diverse community, while earning a stipend! All information about OBF’s GSoC participation can be found here.

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.

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.

The Open Bioinformatics Foundation has been accepted as a mentoring organisation for the 2018 instance of the Google Summer of Code. OBF is acting as an umbrella for ten bioinformatics Open Source projects, making it possible to offer a very diverse set of student projects.

Are you a student and interested in applying for any of the projects? The student application period is open from March 12th through 27th from the official GSoC website. See the full timeline for details. Feel free to contact the mentors of projects you are interested in already, though.