Professional Skills
Our project leaders and advanced postdoctoral researchers are dedicated to providing an interdisciplinary professional skills training within the qualification program of the IRTG. We define “professional skills” as the essential competencies and expertise required to perform successfully at the interface of cardiovascular biology and bioinformatics. This training includes the two major tasks “cardiovascular biology and pathophysiology” and “data analysis training”. All of the courses are specific for this IRTG and given by IRTG members.
cardiovascular biology, pathophysiology and human cardiovascular disease
The lecture series in cardiovascular biology, pathophysiology and human cardiovascular disease aims to establish a good foundation for cardiovascular research. The lecture will convey the essential basic knowledge on the cardiovascular system to all doctoral researchers who, most likely, did not acquire their Master´s degrees in the cardiovascular field but rather in other biomedical disciplines or bioinformatics. Understanding the current state of knowledge on molecular and cellular mechanisms governing organ function and dysfunction, will enable our early career scientists to generate valid hypotheses, design appropriate experiments and integrate the results of their own research into the current scientific context. The advanced pathophysiological part of the lectures extends also the knowledge of doctoral researchers in medicine who have in general a better understanding of the cardiovascular functions due to their training in physiology, pharmacology and basic cardiology.
Data Analysis Training
The rapid development of novel omics approaches nowadays facilitates a fast progress in molecular analyses down to the single cell level. In contrast to the relatively short time required to generate the data sets, particularly in the field of RNAseq, the data analysis presents a major obstacle slowing down the research progress. Many bioinformatic tools for data analysis have been developed by bioinformaticians in the programming languages R (e.g. the Seurat program package for scRNASeq) and Python (e.g. Scanpy). However, their widespread use by researchers outside bioinformatics communities is often limited. Basic knowledge on how to map sequencing reads to reference transcriptomes; arrange, import, normalize, and analyze data sets; and how to set up a suitable analysis pipeline, organizing all steps of data analysis in a consecutive manner is lacking. Obviously, there exists a broad gap between specialized researchers performing the molecular and functional investigations but lacking sufficient knowledge of basic bioinformatics analysis skills on one side and bioinformaticians on the other side, focusing rather on development of new computational tools than running standard analyses. In this IRTG we seek to fill this gap and develop early career researchers with expertise in functional and molecular analysis and solid basic bioinformatics skills for analysis of large omics data sets using dedicated software tools.
Practical courses in functional analysis of the cardiovascular system
Practical courses in functional analysis of the cardiovascular system will introduce methods to analyze cardiovascular function from the cellular level, via organs, to whole animal models including blood pressure measurement in mice, functional analysis of heart and kidney, angiogenesis assays, confocal microscopy, FACS, etc. Details such as suitability, resolution, sensitivity of methods etc. are also covered. In addition, we plan to address replacement methods for animal experimentation and therefore introduce the 3R principles. We will invite experts for iPSC-derived organoids such as engineered heart tissue, blood vessel organoids, respectively, to get insight into the current options and limitations of replacement methods. Once per cohort we will have the Cardiovascular Research Symposium. Doctoral researchers present a method they are using in their research to other members of the IRTG to foster discussion on the strengths and weaknesses of various methods and the ability to weigh alternatives. Doctoral researchers become familiar with the expertise available within other research groups of the IRTG3109, supporting collaboration and networking.