Introduction to Project, Community and Outreach Manager

Hello MDAnalysis Community! I am excited to join the MDAnalysis team and serve as the new Project, Community and Outreach manager. This role was made possible through a Chan Zuckerberg Initiative award as part of the Essential Open Source Software for Science program: “EOSS5: Growing the MDAnalysis community sustainably: A dedicated project manager, teaching and outreach initiatives”.

As a short introduction, my name is Jenna Swarthout Goddard, and I recently completed my Ph.D. in Environmental Health at Tufts University, MA, USA. My research focused on using computational biological approaches to identify environmental pathways for infectious disease transmission. I self-identify as an animal and food enthusiast and am an avid (which does not necessarily equate to skilled) golfer.

I am looking forward to engaging with the MDAnalysis community and supporting MDAnalysis in expanding its outreach, mentorship and teaching efforts!

Google Summer of Code 2023

Google Summer of Code with
MDAnalysis 2023

MDAnalysis has been accepted as an organization for Google Summer of Code 2023! If you are interested in working with us this summer and you are new to open source, please read the advice and links below and write to us on the GSoC with MDAnalysis mailing list.

We are looking forward to all applications from any new and beginner open source contributors over 18 years old or students. Projects are scoped as either 175-hour (medium) or 350-hour (long) size. The duration can be extended from the standard 12 weeks to 22 weeks.

The application window deadline is April 4, 2023 - 18:00 UTC. As part of the application process you must familiarize yourself with Google Summer of Code 2023.

If you are interested in working with us please read on and contact us on our GSoC with MDAnalysis mailing list. Apply as soon as possible at; the application window opens on March 20, 2023 but potential GSoC Contributors are expected to familiarize themselves with application requirements and mentoring organizations as soon as possible. It’s also never too early to discuss application ideas with us!

Project Ideas

If you have your own idea about a potential project we’d love to work with you to develop this idea; please write to us on the mailing list to discuss it there.

We also have listed several possible projects for you to work on. Our initial list of ideas (see summaries in the table below) contains various projects of different scope and with different skill requirements. However, check the ideas page — we might add more ideas after the posting date of this post.

Our experience shows that having the listed skills increases the chances that a project will be completed successfully, so we use them as part of our decision criteria in choosing GSoC contributors.

project name difficulty project size description skills mentors
1 Generalise Groups hard 350 hours Generalise concept of groups Python, NetworkX, Molecular modelling @fiona-naughton, @richardjgowers, @yuxuanzhuang, @RMeli
2 Extend MDAnalysis Interoperability medium 350 hours Extend converters module to other relevant packages Python, Molecular Modelling @fiona-naughton, @hmacdope, @yuxuanzhuang, @RMeli
3 Benchmarking and performance optimization medium/hard 175 hours write benchmarks for automated performance analysis and address performance bottlenecks Python, Molecular Modelling @hmacdope, @orbeckst, @RMeli
4 Transport property calculations medium 350 hours write analysis code to calculate physical transport properties Python, Physics/Mathematics @orionarcher, @hmacdope
5 Implementation of parallel analysis framework hard 350 hours implement parallel framework in MDAnalysis Python, Parallel Programming, Molecular Modelling @yuxuanzhuang, @orbeckst, @RMeli

Information for prospective GSoC Contributors

You must meet our own requirements if you want to be a GSoC Contributor with MDAnalysis this year (read all the docs behind these links!). You must also meet the eligibility criteria. Our GSoC FAQ collects common questions from applicants.

The MDAnalysis community values diversity and is committed to providing a productive, harassment-free environment to every member. Our Code of Conduct explains the values that we as a community uphold. Every member (and every GSoC Contributor) agrees to follow the Code of Conduct.

As a start to get familiar with MDAnalysis and open source development you should follow these steps:

Watch the MDAnalysis Trailer

The MDAnalysis Trailer on YouTube is a one minute introduction to MDAnalysis.

Complete the Quick Start Guide

We have a Quick Start Guide explaining the basics of MDAnalysis. You should go through it at least once to understand how MDAnalysis is used. Continue reading the User Guide to learn more.

Introduce yourself to us

Introduce yourself on the mailing list. Tell us your GitHub handle, what you plan to work on during the summer or what you have already done with MDAnalysis.

Close an issue of MDAnalysis

You must have at least one commit in the development branch of MDAnalysis in order to be eligible, i.e., you must demonstrate that you have been seriously engaged with the MDAnalysis project. We have a list of easy bugs and suggested GSOC Starter issues to work on in our issue tracker on GitHub. We only accept one GSOC Starter issue per applicant so that everybody gets a chance. If you want to dive deeper, we encourage you to tackle some of the other issues in our issue tracker.

We also appreciate contributions which add more tests or update/improve our documentation.

Final remarks

We recommend you start your application by working on an issue. It will give you a better understanding of MDAnalysis as a project and improve the quality of your application.

To start developing for MDAnalysis have a look at our guide on contributing to MDAnalysis and write to us on the GSoC with MDAnalysis mailing list if you have more questions about setting up a development environment or how to contribute. We are also happy to chat on our MDAnalysis Discord server in the #gsoc channel (join with the public invitation link).

We look forward to working with you in GSoC 2023!

— MDAnalysis GSoC mentors (GitHub @MDAnalysis/gsoc-mentors, Discord @gsoc-mentor)

GSoC / Outreachy 2022 wrap-up

This year MDAnalysis participated in two programs with wonderful contributors from around the globe. We continued our participation in Google Summer of Code for another year and also participated in Outreachy for the first time. Huge thanks to these organisations for supporting MDAnalysis and the students.

Google Summer of Code / Outreachy 2022

Google Summer of Code

Our two outstanding GSoC contributors Aya Mohamed Alaa (@aya9aladdin), and Bjarne Feddersen (@BFedder) successfully completed their GSOC projects.

You can read more about their projects and packages in their blog posts:

— GSOC Mentors @jbarnoud @hmacdope @ojeda-e @IAlibay @fiona-naughton @orbeckst @lilyminium @richardjgowers

Google Summer of Code / Outreachy 2022


Uma Kadam (@umak1106) did the very first MDAnalysis Outreachy Internship with her project Improve MDAnalysis by implementing type hinting.

— Outreachy Mentors @jbarnoud @micaela-matta @richardjgowers


We have immensely enjoyed working with Aya, Bjarne and Uma and look forward to seeing how they continue to contribute to the MDAnalysis community, and wish them luck in their future endeavours.