Using a Multi-agent systems paradigm, the present project develops, validates and exploits a computational testbed that simulates micro-biological complex systems, namely the aggregation patterns of the social amoeba Dyctiostelium discoideum. We propose a new design and implementation for managing discrete simulations with autonomous agents on a microscopic scale, thus focusing on their social behavior and mutual interactions. Then, the dependence on the main physical variables is tested, namely density and number of amoebas; in addition, we analyze the robustness of the dynamics against various noise sources. Along with these results, we suggest a methodology for further studies that make use of our validated model.