Author: Esther Plomp
This blog provides a short summary of the recent online Genomics Workshop at TU Delft. Due to the Corona regulations implemented at TU Delft all of 4TU.ResearchData’s Carpentry Workshops are now taking place online. The Genomics Workshop was no exception.The original plan was to hold the workshop in person in June, just like the first Genomics Workshop we organised in 2019. Due to the increased workload at that time, the decision was made to move the workshop to September (16, 17, 23 & 24, 9:00-13:00).
Moving a beginner friendly interactive programming course online was quite the challenge, but thanks to all the efforts of the team of instructors and helpers, it was still successful! Our instructors for this course were Raúl A. Ortiz Merino, Marcel van den Broek, Santosh Ilamparuthi, Esther Plomp and Carlos Teijeiro Barjas (SURF). Our helpers were Mario Beck, Nicolas Dintzner, Wijb Dekker, Maurits Kok, Sam Nooij (LUMC) and Carien Hilvering (Maastricht University).
The 22 participants, who tuned in from several different countries and time zones, received a crash course in project organization for genomics from Esther, cloud genomics from Carlos, shell for genomics from Santosh, and data wrangling and processing by Raúl and Marcel (see also the programme of the workshop on GitHub). Raúl and Marcel set up a local virtual environment at the TU Delft for the previous workshop, but this was not possible for this workshop. Instead, the Carpentries provided us with virtual Amazon Web Services (AWS) instances which contained the dataset and software that we needed for the workshop.
The course was held online through Zoom. Zoom is a great tool for these workshops, as it provides you with the option to open up mini meetings within your online meetings (breakout rooms). Breakout rooms can be used for more interaction between the participants when they are doing exercises or for helping participants out when they are stuck. We used the breakout rooms primarily for exercises in the first two days. During the ‘data wrangling and processing’ days we only used break out rooms if a participant got stuck. In general, participants, helpers and instructors were happy with this format. There were some pacing problems if a participant was stuck for a long time. We tried to resolve longer issues during breaks or by getting them back on track by documenting when individuals left for a break out room and came back, so that it was clear what they missed.
Collaborative notes were taken using a Google Doc instead of the etherpad that we normally use. In a Google Doc you can share screenshots when participants are stuck, a functionality that is not available in the etherpad. In the end we mostly solved issues by screen sharing in Zoom rather than exchanging screenshots. For the Google Docs we used the same format as the FAIR software workshop (held on the 8th of September). The Google Doc provided an overview for the participants of the programme of the day and the materials used, a way for them to introduce themselves and connect with the other participants, a platform for questions and a list of the commands that were used during the day. We also used Google Docs to ask the participants for feedback, rather than using the sticky notes that we normally use during physical workshops. Questions were also asked through the Zoom chat and we used the participant list buttons (yes and no) as a replacement for the sticky notes that we used previously as an indication whether participants were ready with their exercise or needed help.
Most of the participants of the course were graduate students. We provided the opportunity to obtain a certificate for anyone that wanted to take the course for credits in their graduate school programme. Out of the 22 participants, 15 requested such a certificate.
Despite being held online, we still had a lot of interaction with each other and we managed to get through most of the materials of the lessons! Onward to our next online basic programming workshop in October!