Since knowledge about processes in living cells increases, modelling and simulation techniques are used to get new insights into these processes. This book describes visualisation techniques that were developed to ease the modelling procedure and support the analysis of simulation results. The biological background is introduced in the first chapter which is followed by a short description of the software package that does contain the developed analysis and visualisation techniques. These techniques include automatic graph representations of biochemical pathways that are part of such processes, the 3D visualisation of simulation time series data simultaneously with these graphs and correlation methods for the analysis of the relationships between time series. This book is suitable for beginners and experts that are interested in graph theory, visualisation and software engineering.