Training Infrastructure Feedback from Dr. Tuan Leng Tay


From 22 to 26 February 2021, I ran a full-time bioinformatics workshop during the practical “Block Week” for 23 Master of Biology students at the University of Freiburg, Freiburg im Breisgau. The OM-02 course is an elective module for Master students in their first semester tailored to help them identify a specialisation to pursue subsequent research internships and their thesis work. All students came from different backgrounds and training in their undergraduate studies, and have not had prior exposure to bioinformatics analyses or coding. I started by giving an introduction to the Galaxy platform for -omics analysis and focussed specifically on the following tutorials found on https://training.galaxyproject.org/:

  • From peaks to genes
  • Quality Control
  • Mapping
  • Reference-based RNA-Seq data analysis

This course was previously conducted in a computer lab at the Faculty of Biology and required at least two persons (including the main lecturer and teaching assistant) to rove and assist a class of up to 15 per day as students worked through the assigned tutorials individually. Due to the pandemic, this year’s practical course took place over Zoom. Taking advantage of the TIaaS infrastructure for which we were allocated four servers, each with 32 cores and 240 GB of RAM, we were able to smoothly work through the tutorials remotely. The possibility to monitor the progress of each job was a welcome feature as this allowed me to keep up with the students’ progress despite the remote format. In addition, I had recruited four PhD student tutors familiar with Galaxy to guide 3-4 students in breakout rooms during the hands-on sessions. The tutors also used their own research data to demonstrate the practical applications of the course content.

To combat Zoom fatigue, I shortened all lectures by half and held open book quizzes and recap sessions to promote self-learning and understanding of the training material. The interactive and relaxed atmosphere created by inclusive pedagogical methods ensured that all students participated both verbally and in writing to reinforce their key learning points.

Finally, many thanks to the Galaxy TIaaS and the GTN material, without which this course would not have been possible!

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