Many interesting systems in several disciplines can be modeled as networks of nodes that can store and exchange data: pervasive systems, edge computing scenarios, and even biological and bio-inspired systems. These systems feature inherent complexity, and often simulation is the preferred (and sometimes the only) way of investigating their behavior; this is true both in the design phase and in the verification and testing phase. In this tutorial paper, we provide a guide to the simulation of such systems by leveraging Alchemist, an existing research tool used in several works in the literature. We introduce its meta-model and its extensible architecture; we discuss reference examples of increasing complexity; and we finally show how to configure the tool to automatically execute multiple repetitions of simulations with different controlled variables, achieving reliable and reproducible results.