MDAnalysis 2024 Events - Recap of the User Group Meeting and Workshops

11 Sep 2024

As we near the last quarter of the year, we would like to reflect on the exciting events, including the recent MDAnalysis User Group Meeting and many workshops, that allowed us to connect with the MDAnalysis community throughout 2024.

MDAnalysis UGM (User Group Meeting)

From August 21-23, 2024, 65 MDAnalysis users and developers convened in London, United Kingdom for the second MDAnalysis UGM (User Group Meeting). Hosted at King’s College London in partnership with the Thomas Young Centre, the event featured presentations and open discussions about using and developing MDAnalysis, followed by a hackathon. Talks covered a broad range of topics including, but not limited to, materials science applications, drug discovery and therapeutics, machine learning and multiscale modeling, and tools for molecular dynamics simulation analysis.

For more details, we invite you to check out the MDAnalysis/UGM2024 GitHub repository, where many of the UGM presentations and hackathon materials may be accessed.

Awards

Based on attendees’ votes, the following recognitions were awarded to UGM participants:

Best Talk

• First Place - Raquel López-Ríos de Castro
• Second Place - Lexin Chen
• Third Place - Namir Oues
• Honorable Mentions - Michal H. Kolar, Matteo Degiacomi

Best Poster

• First Place - Asal Azar
• Second Place (TIE) - Simon Holtbrügge, Valerij Talagayev

All Star Pet (According to a pet photo contest on the #mda-pets channel on Discord)

• Pom (owned by Matteo Degiacomi)

Partners and Sponsors

We would like to thank our partners and sponsors for helping us make the 2024 MDAnalysis UGM such a success!

The Future of MDAnalysis UGMs

We would love for the MDAnalysis UGM to become an annual event. We are grateful to the Chan Zuckerberg Initiative (CZI) for supporting the 2023 and 2024 UGMs through our Essential Open Source for Science Round 5 award. However, as the 2-year grant is coming to a close, we are working hard to find ways to support potential future UGMs.

If you are interested in sponsoring, hosting at your own institution, or joining the organizing committee for any future UGMs, please get in touch with us on Discord (to join the Discord server, use the invitation link, https://discord.com/invite/fXTSfDJyxE), GitHub Discussions, or by emailing [email protected]!

MDAnalysis Training Workshops

This year was an exciting year for MDAnalysis, in that we were able to offer 4 different free online and hybrid training workshops!

Februrary 28th: Introduction to MDAnalysis and Molecular Nodes (Online)

Around 40 people joined us live on February 28, 2024 for an online workshop, during which 4 instructors (@fiona-naughton, @lilyminium, @yuxuanzhuang, @BradyAJohnston) introduced the MDAnalysis package and provided an interactive tutorial for visualizing MDAnalysis data in Molecular Nodes; the recording is available on our YouTube channel. All workshop materials and installation instructions are publicly available on the MDAnalysis/MDAnalysisWorkshop2-Intro0.5Day GitHub repository on the ‘feb24-ws’ branch.

May 10th: Introduction to Molecular Dynamics Trajectory Analysis using MDAnalysis

On May 10, 2024, 21 attendees convened in person at University College London (UCL) and another roughly 43 attendees joined online for a workshop walking participants through examples progressing from a beginner to an intermediate level. Instructors, @micaela-matta and @richardjgowers, showcased built-in analysis functions and walked participants through building custom analysis scripts; the recording of the intermediate lessons can be accessed on the MDAnalysis YouTube channel, and all workshop materials are on the MDAnalysisWorkshop-Intro1Day GitHub repo on the ‘may24-ws’ branch.

June 24th-25th: Moving from User to Developer: Analyzing Molecular Simulations and Building New Tools

In late June 2024, an MDAnalysis instructor team (@IAlibay, @orbeckst, @fiona-naughton, @yuxuanzhuang, @mikemhenry, @ianmkenney) partnered with the Molecular Sciences Software Institute (MolSSI) to offer a 2-day hybrid workshop at Arizona State University (ASU) in the Center for Biological Physics covering beginner to intermediate tutorials on the MDAnalysis library as well as tutorials on software development best practices provided by MolSSI instructors (@sjayellis, @armcdona). A total of 35 individuals attended in person, with another up to 76 attending online. All workshop materials are now publicly available in the MDAnalysisMolSSIWorkshop-Intermediate2Day GitHub repository under the ‘jun24-ws’ branch.

September 5th: MDAnalysis Intermediate Workshop, CCPBioSim Training Week

Rounding out the 2024 workshop series, @micaela-matta and @richardjgowers teamed up again for the CCPBioSim Training Week, hosted at the University of Sheffield in hybrid format, to teach participants how to build on basic MDAnalysis skills and learn about building more complex analysis scripts. There were 13 people registered for in-person attendance, and another 30 people registered for online participation. The materials for the workshop can be accessed on the MDAnalysisWorkshop-Intermediate1Day GitHub repo under the ‘ccpbiosim-24’ branch.

Acknowledgements

A special thanks goes out to the many partners and sponsors that helped us make these workshops possible:

We would like to again thank everyone who helped us make these workshops a success, including the participants, instructors, teaching assistants, and workshop organizers! If you or your organization are interested in partnering with MDAnalysis to organize future workshops, you are always welcome to fill out our Google form to discuss further.

To stay up-to-date on all MDAnalysis event offerings, be sure to follow our blog, X, LinkedIn, and Bluesky pages.

Outreachy 2024 Wrap-Up

09 Sep 2024

We would like to congratulate our wonderful Outreachy intern, Adetutu Oluwasanmi (@adetutudeborah), on successfully completing her Outreachy project with MDAnalysis.

You can read more about Adetutu’s project in her blog post:

• Adetutu: Outreachy 2024 - Develop a Communications Strategy for a Growing MDAnalysis User and Contributor Base

We have really enjoyed working with Adetutu and wish her the best in her future contributions to the MDAnalysis community and beyond!

We also thank Outreachy for supporting Adetutu and supporting MDAnalysis as an Outreachy organization for the second time. Unfortunately the Outreachy coordinators have announced that they are facing financial challenges that are putting the future of the program in jeaopardy; please read the Outreachy blog post for more details and to learn how the wider open source community can help secure the future of this impactful program!

— @jennaswa @micaela-matta (Outreachy mentors)

Outreachy 2024 - Develop a communications strategy for a growing MDAnalysis user and contributor base

04 Sep 2024

Goals of the Project

The goal of this project is to develop a comprehensive social media and communications strategy to grow the MDAnalysis user and contributor base. This involves conducting surveys with MDAnalysis users and developers to understand which communication channels they prefer to use to seek information about and engage with the MDAnalysis project. It also entails finding ways to boost participation and involvement from everyone in the MDAnalysis community and to also implement the setup of the MDAnalysis newsletter.

What I Did

At the start of the internship, I was able to explore MDAnalysis communication channels and document my observations, recommendations, and current analytics for each channel. I conducted keywords analysis, along with their frequencies, of the MDAnalysis mailing lists (now archived), Discord, and GitHub Discussions forum to gain insights into common questions and user needs within the MDAnalysis community. I delved into understanding how participants discover MDAnalysis workshops by gathering data from past MDAnalysis workshops. I also created a methods and definitions document to clarify the metrics used in my report and my approach to the tasks.

Moving forward, I drafted a survey plan, starting with a description of the MDAnalysis target audience and developing research questions to understand what we aim to learn from the survey. From the research questions, I developed the survey questions and answer options, and the Google form to collect data that will inform our communications strategy. Also, I created a survey outreach plan detailing the outreach and advertising channels we plan to use for distributing the survey, the survey participation plan, and the promotional content (blog post, email, and social media post).

We launched the survey form on August 1st and I sent follow-up reminders on August 15th and August 23rd respectively. While waiting for the survey responses, I developed a content strategy which included the proposed content plan and calendar for MDAnalysis. In the last week of the internship, I analyzed and wrote a summary of the survey results and how it can inform the MDAnalysis communication strategy.

The Current State

Currently, the initial survey results have been analyzed, and a summary has been prepared to inform the MDAnalysis communication strategy and a proposed content plan and calendar for MDAnalysis have been created.

What’s Left to Do

The next steps involve implementing the communications strategy based on the survey results and making adjustments to the strategy as needed. The survey results will guide the selection of communication channels and content types that will best engage the MDAnalysis community. Additionally, launching the MDAnalysis newsletter is another important part of the project. Beyond the internship, an ongoing effort will be needed to sustain the implementation of the communications strategy to grow MDAnalysis user and contributor’s base.

Challenges

One of the main challenges I encountered was drafting research and survey questions that would give the feedback needed to inform MDAnalysis communication strategy. It was important to ask the right questions to gather meaningful feedback from respondents. I was able to navigate this phase with the guidance and valuable input from my mentors and the MDAnalysis leadership.

Another challenge that I faced was ensuring active participation from the community in the survey. Beyond the initial outreach, my mentor and I sent follow-up reminders, and the survey was promoted during the MDAnalysis 2024 User Group Meeting. While the survey did receive a reasonable number of responses, broader participation from the community could have provided even more meaningful insights.

Lessons Learned

Here are some of the lessons I learned during the internship:

• Prioritize tasks/activities that directly contribute to the project goals. This will help you to stay focused and ensure the overall project goals are achieved.
• Before drafting survey questions, it’s important to first identify the key research questions.
• Learn to embrace and implement feedback from your mentors.
• Breakdown big goals into smaller, achievable weekly tasks. It helped me to stay on track and clearly identify the next steps.
• Communicate with your mentors. Don’t hesitate to ask questions and seek clarity when needed.
• Plan for multiple rounds of feedback and revisions when setting project timelines.
• Document your work and progress when working on a project.
• Be proactive.

Acknowledgements

I would like to extend my sincere gratitude to the Outreachy organizers for this incredible opportunity to contribute to the MDAnalysis project.

A special thanks to the MDAnalysis leadership team and my mentors, Jenna Swarthout Goddard (@jennaswa) and Micaela Matta (@micaela-matta), for their guidance and feedback throughout the internship. This experience has provided me with new skills I will carry forward in my future endeavors.

Finally, I want to express my gratitude to the entire MDAnalysis community for their participation in the survey and for helping make this project a success.

— @adetutudeborah