Biological systems involve a wide amount of different molecular interactions. Each interaction can in turn present a deep level of mechanistic details. Most modelling methods can encompass only one of those two dimensions, that is the width or depth of biological systems. Rule-based modelling is a powerful method in that regard as it can model large systems with mechanistically detailed interactions. The advantage of including mechanistic details is that they allow a clear tracking of causal chains of events between biomolecules. This translates into a precise pinpointing of upstream regulators and a better understanding of complex biological systems.