Bioinformatics is fascinating: It enables us to use computer-based methods to gain insights into biology and medicine – for example, to decode the human genome. In order to learn more about bioinformatics methods and working methods, 17 (post-) doctoral students and group leaders participated in the first “RESIST Bioinformatics Summer School” which aim to teach the analysis of bulk and single-cell Transcriptomics using the programming language R and the MHH High Performance Computing Cluster “Leine”. It took place for the first time, from July 17 to 21 at the MHH, and was funded by RESIST.

The course leader was Prof. Dr. Thomas Otto from the University of Glasgow, who specializes in computational method development in the fields of immunology and infection. Participants were able to learn to generate and analyze data sets from RNA sequencing (RNA-Seq), involving both bulk (RNA-Seq-) and single cell data sets (sc-RNA-Seq). RNA sequencing, the determination of the nucleotide sequence of ribonucleic acids and their abundance, is an important technology for the study of cells and of disease. It opens up the possibility of conducting comparative studies – for example, between cells that have been infected by viruses and those that have not.

The Bioinformatics Summer School program ranged from a theoretical and practical introduction to the R programming language to exercises in sequencing the transcriptome – analyzing which genes are turned on and thus converted into mRNA – and various programs, for example Seurat for analyzing single-cell datasets. “The aim of the course was to teach the participants the basics and the “bioinformatics language”, so that they can now perform their analyses independently and get help on the Internet on their own if necessary.

The course was organized by Prof. Dr. Daniel Depledge, MHH Institute of Virology, who also taught two one-day courses on “Introduction to High Performance Computing” as a prerequisite for participation in the summer school. His course covered high-performance computing (HPC) topics ranging from basic commands for the Unix operating system to writing scripts for processing and analyzing bulk RNA sequencing data. Prof. Depledge was supported by Amy Fitzpatrick, a visiting researcher in his lab.

Dr. Carina Jürgens enjoyed the Bioinformatical Summer School: “It gave a good insight into the use of bioinformatics methods and the computational way of working. We got a heads up on how complicated it can be in terms of the administrative side to work on HPC. This will help us better assess planned experiments in the future. In addition, the course has contributed to the networking of colleagues working in bioinformatics,” says the postdoc from the MHH Department of Gastroenterology, Hepatology and Endocrinology. Dr. Anika Freise from the MHH Clinic for Gastroenterology, Hepatology, Infectiology and Endocrinology, is also enthusiastic: “Prof. Otto succeeded in giving a very informative and high-quality course despite some problems with the local infrastructure! Analyzing RNA sequencing data will definitely be easier and faster for me now.”