I am an associate professor at the Faculty of Medicine, University of Debrecen, Hungary, and I have been using the Galaxy platform to teach the basics of RNA-seq data analysis to 2nd year Molecular Biology MSc students since 2016. The goal of my course is to help students move from the concept of “RNA-seq is awesome, it gives us lots of data” to a solid understanding of how the sequencing process works, how the raw data looks like, and how we can get from the raw reads to the heart of the biological processes.
Practically none of the students have the skills to use Linux or R, so Galaxy is an ideal platform to jump-start their training – it also gives us more time to play with some other tools and databases for result interpretation, such as the Integrated Genomics Viewer, the UCSC and Ensembl Genome browsers, the Reactome database, the ConsensusPathDB, GeneCards, etc.
Although I have access to a simplified in-house Galaxy server, I prefer using the Freiburg Galaxy server (https://usegalaxy.eu),
because it is more realistic for the students with all the tools, genomes, shared workflows and datasets available.
This was the first year I used the TIaaS service at Freiburg, and it was definitely a leap from the previous years, since the jobs were completed much faster during the course, making it a very pleasant teaching experience. Although I use my own training materials, I check the Galaxy Training Network materials regularly for ideas – it is a superb collection, and if students are interested in an analysis beyond the course topics, it’s nice to be able to direct them to GTN for easy self-training. Every year 15-20 Hungarian and 5-10 international students take this Galaxy-based course – and this year we also organized a more advanced course for interested PhD students.
I am very grateful to the people behind the Galaxy project, and especially to the Freiburg Galaxy team for spearheading the training efforts and providing this service to biologists, teachers and students. Knowing how much time and effort goes into a training material, I truly appreciate the ever increasing selection of the GTN materials.
Thank you very much!