A challenge to understanding the mind and brain is to integrate biochemical, genetic, developmental and neuroscientific information. We present a system for integrated simulation of biochemistry, neurodevelopment and neural activity within a unifying framework of genetic control. Using this system, we have developed a novel model for the formation of topographic projections. We also simulate activity-dependent developmental processes which underlie receptive field refinement and ocular dominance column formation. As an illustration of the overall utility of integrated neurogenetic simulation, we show how axon guidance and learning together may explain the results of a critical study of topographic map development (Brown et al., 2000, Cell).