Studying the complex phenomenon of pattern formation created by the gene expression is a big challenge in the field of developmental biology. This spatial self-organisation autonomously emerges from the morphogenetic processes and the hierarchical organisation of biological systems seems to play a crucial role. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful. In this paper we propose the adoption of the agent-based model as an approach capable of capture multi-level dynamics. Each cell is modelled as an agent that absorbs and releases substances, divides, moves and autonomously regulates its gene expression. As a case study we present an agent-based model of Drosophila melanogaster morphogenesis. We then propose a formalisation of the model which clearly describe its main components. We finally show simulation results demonstrating the capability of the model of reproducing the expression pattern of the embryo.