For many years, linear stability theory and the parabolized stability equations have been the methods of choice for predicting transition in boundary layers caused my modal growth. Recently, input-output analysis has been shown to be an effective tool for analyzing the sensitivity of boundary-layer instability to forcing in specific locations in a flow field, such as along a geometric wall. This type of analysis provides specific insight into the type of surface characteristics, including distributed surface roughness, to which the instability growth in the boundary layer is most sensitive. We develop this method for canonical flat-plate boundary and demonstrate how I/O analysis can be applied to predict modal and non-modal growth. We then explore how this method might be used to explore recent direct numerical simulations of the BOLT flight experiment.