August 3, 2020

Taking summer school online

A conversation with Marta Lloret, The European Bioinformatics Institute

bio excel logo


The Bioexcel Summer School on Biomolecular Simulations teaches students how to use software for molecular modeling and simulations using a combination of lectures and hands-on tutorials. It was held virtually for the first time this summer. In moving online, they received more than 80 complete applications, which is twice as many as received for in-person sessions. Most applicants were still based in Europe, but some were also from the U.S., Africa and Asia. Participation was capped at 30 students due to limitations in the number of available virtual machines.


The one-week course contained pre-recorded lectures (now available on their YouTube channel), live question and answer sessions, live tutorials, and a forum for students to ask questions and socialize. Each day was six to eight hours, including breaks. Participants could view the lectures on their own time and then logged in at specified times for 20-minute question and answer sessions. The course also included optional coffee break socials, which were attended by most participants. Topics of discussion included how the pandemic impacted their work, quantum computing, innovations in their field, and careers in industry. This last discussion was not a part of the original program, but arose from a poll asking participants what they wanted to discuss. Posters were saved as PDF files in a shared Google Drive folder and each had a thread for discussion. Participants gave brief presentations about their posters on the first day to introduce their work.

The tutorials took on one of two formats: the trainer would either lead the participants step-by-step through a module or give an introduction at the beginning and then let the students do the work at their own pace. One mode of instruction was not overwhelmingly preferred by the participants over the other. Nearly all of the participants attended each of the tutorials.

Lessons Learned

Trainers were concerned about being able to help students without being able to see their screens, but they were able to troubleshoot using copied and pasted error messages. The biggest challenges typically had to do with installation issues, but these were resolved beforehand. Students were also eager to answer each other’s questions via chat. It can be difficult to manage multiple windows containing Zoom, tutorial instructions, and the console - keep screen space in mind when planning tutorials. In the end, transitioning online is not as hard as you might think. You need to find ways to interact with participants and test your technology beforehand. It’s hard work, but it’s doable. Moving online requires more planning, which could be because we’re not accustomed to it, but also because it requires more preparation time to test platforms and write detailed instructions for tutorials. Participants were really happy with it - in an exit survey, 92% of respondents rated the course as excellent or very good.

Future Plans

The organizers are considering holding the school online again with the same basic structure. In the future, they want to provide opportunities for participants to build stronger relationships. They’ll consider moving the social times to the beginning or end of the day so that people can self-select to be there. They’d like to keep the participant number to about 30 due to the number of available virtual machines and also to be able to address everyone’s questions. They’ll also consider providing trainings to the instructors about best practices in online teaching.