RNA-Seq Training feedback from Simon Moxon


I am an associate professor at the University of East Anglia in the UK and I have been wanting to teach undergraduate biology students some practical skills in next generation sequencing analysis since I started my position in 2016. I was put off by having to teach all of the prerequisites required such as using the Linux command line, working with R etc. There was also a real reluctance from the students to learn these more technical skills and I didn’t want risk alienating them before we even started looking at any sequencing data. Another big barrier for us was the difficulty in setting up accounts for 60 undergrads on our HPC facilities so I had to find an alternative method for teaching.

I knew from the start that Galaxy would be the ideal platform to teach students and I had previously looked into setting up my own Galaxy server using on demand cloud services but the lack of transparency in calculating costs had put me and the school (who would have to pick up the bill) off taking this route. I then learnt about Training Infrastructure as a Service (TIaaS) which would allow me to run sessions using a private queue thus allowing students to run jobs within a short timeframe and allow an interactive teaching experience for the students without waiting for queued jobs to complete.

TIaaS was perfect for us, I taught 60 students to analyse and interpret RNA-Seq datasets over 3 x 3-hour practical sessions and received really good feedback. At no point in the sessions were students waiting more than a few minutes for jobs to complete on the subsampled published datasets that I had given them. I created my own teaching materials for this course but there is already an excellent guide “Reference-based RNA-Seq data analysis” on the Galaxy Training Network that I could have used or adapted. I am really pleased with how everything went and very grateful for the TIaaS at UseGalaxy.eu. I hope that this experience has made my students less scared of and more interested in continuing to build skills in bioinformatics.

Thank you to the Freiburg Galaxy team for all of your help with setting this up, I would highly recommend TIaaS to anyone thinking of setting up any future Galaxy training!

Simon Moxon

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