Pattern formation emerges during development from the interplay between gene regulatory networks (GRNs) acting at the single cell level and cell movements driving tissue level morphogenetic changes. As a result, the timing of cell specification and the dynamics of morphogenesis must be tightly cross-regulated. In the developing zebrafish, mesoderm progenitors will spend varying amounts of time (from 5 to 10hrs) in the tailbud before entering the pre-somitic mesoderm (PSM) and initiating a stereotypical transcriptional trajectory towards a mesodermal fate. In contrast, when dissociated and placed in vitro, these progenitors differentiate synchronously in around 5 hours. We have used a data-driven mathematical modelling approach to reverse-engineer a GRN that is able to tune the timing of mesodermal differentiation as progenitors leave the tailbud’s signalling environment, which also explains our in vitro observations. This GRN recapitulates pattern formation at the tissue level when modelled on cell tracks obtained from live-imaging a developing PSM. Our “live-modelling” framework also allows us to simulate how perturbations to the GRN affect the emergence of pattern in zebrafish mutants. We are now extending this analysis to cichlid fishes in order to explore the regulation of developmental time in evolution.