Training Infrastructure Feedback from Stefanie Dukowic-Schulze
Dr. Stefanie Dukowic-Schulze gave a training in the MSc Program "Translational Medical Research“ (TMR) at the Medical Faculty of Mannheim (University of Heidelberg).
Participants: 8 highly motivated students (7 TMR students plus 1 PhD student)
After repeated request for a bioinformatic introduction course, preferentially using Galaxy, we offered our first TMR course "Introduction to Bioinformatics“ as an extracurricular opportunity. The course highly benefitted from the provided Tlaas resource and from the instructor option to look up the current queues to which students submitted tasks.
Two whole on-site Saturdays (and self-study time around them) were filled with getting to know Galaxy, tools to process sequencing data and background information on common file formats and common issues in bioinformatics. We made use of the basic Galaxy tutorial "Galaxy 101 for everyone“ for preparation, and went in-class together through the concise Galaxy tutorials "Quality Control“ and "Mapping“, and parts of the "Whole transcriptome analysis of Arabidopsis thaliana“ tutorial to keep the on-site time focused on understanding inputs and outputs instead of re-cooking tutorials with more hours of processing time. Major life lessons came from re-processing individual published RNA-seq datasets which opened our eyes to issues regarding data access, using appropriate annotation files, and different final results depending on the pipelines used.
Thanks a lot to the whole Galaxy team for providing the service (Galaxy EU), the self-study-suitable tutorials with great explanations, and the well maintained tools to process data. This will definitely not be our last TMR Galaxy course!