We present an interactive, agent-based, multi-scale 3D model of a colony of E. coli bacteria. We simulate chemical diffusion on an agar plate which is inhabited by a colony of bacterial cells. The cells interact with a discrete grid that models diffusion of attractants and repellents, to which the cells react. For each bacterium, we simulate its chemotactic behaviour, making a cell either follow a gradient or tumble. Cell propulsion is determined by the spinning direction of the motors that drive its flagella. In an agent-based model, we have implemented the molecular elements that comprise the two key chemotactic pathways of excitation and adaptation, which, in turn, regulate the motors and influence a cells movement through the agar medium. We show four interconnected model layers that capture the biological processes from the colony layer down to the level of interacting molecules.