BOODLE (BiOlOgical DeveLopment Environment) is a long-term project to complement morphometric empirical studies in the field of developmental biology by means of interactive modelling and simulation techniques. BOODLE aims at providing viable behaviour models of cells that fit recorded time series of morphogenetic stages. This information is critical for driving empirical studies and for simulating the emergence of pathological abnormalities. In this paper, we present a BOODLE prototype that covers the whole functionality of the envisioned system. The application usage cycle starts with importing scan data of embryos of model organisms. Next, it allows the user/experimenter to work with the imported model, for instance to add meta data, to refine annotations, and even to automatically or manually populate the captured volumes with virtual cells. Finally, the user/experimenter is given the opportunity to run simulation experiments. To outline how the pipeline works in particular, we have setup a mockup toy experiment that optimises cell parameters such that a population of cells develops in accordance with several preset transient states. For all stages of the modelling and simulation process, BOODLE provides accessible interfaces and visualisations. These include visual programming and configuration of individual cells’ behaviours and physical properties. In this paper, we show how all these aspects together realise a prototype for a Biologist-in-the- Loop simulation for the creation, automated optimisation and analysis of cellular behaviour models.