Several complex biological phenomena are to be modelled in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events plays an essential role. Key examples are embryogenesis and morphogenesis processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. This paper introduces a practical framework for modelling and simulating these scenarios. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie's direct method. As an example of application of our framework, we model the first stages of Drosophila Melanogaster development, which generate the early spatial pattern of gene expression, and we show the correctness of our model comparing the simulation results with real data of gene expression and spatial/temporal resolution acquired in free on-line sources.