High-throughput methods, particularly sequencing, changed the face of genome analysis. These advances in technology drove a shift of focus in molecular biology. The desire to understand single functional entities, such as single genes, is replaced by how all genes, gene products and other functional units in the genome work together to produce a phenotype. This new quest for understanding the processes in the cell as relationships and interplay between functional entities is an application of system biology in molecular and cell biology context. Our ambition is to be able to produce these biological insights for systems biology from raw data in a reproducible and scalable manner, regardless of the number of samples and the diversity of data types.