Both activity-dependent (AD) and activity-independent (AI) processes play important roles in neural development. For example, in the development of the vertebrate visual system, molecular guidance cues that are largely activity-independent provide a rough topography of early projections, while activity-dependent refinement of termination zones occurs later on through correlated retinal activity. A key question concerns the nature of the interaction between these processes. Recent knockout experiments involving the ß2 subunit of nicotinic acetylcholine receptors and bone morphogenic protein (BMP) suggest that these two processes make genuinely separate contributions - but leave open the precise nature of their interaction. In this article we show how a novel, computational framework (dubbed INTEGRATE) can illuminate the scope and limits of the AI-AD interaction, including facts about critical periods and timing.