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Transient growth and resolvent analyses are routinely used to assess non-asymptotic properties of fluid flows. In particular, resolvent analysis can be interpreted as a special case of viewing flow dynamics as an open system in which free-stream turbulence, surface roughness, and other irregularities provide sources of input forcing. We offer a comprehensive summary of the tools that can be employed to probe the dynamics of fluctuations around a laminar or turbulent base flow in the presence of such stochastic or deterministic input forcing and describe how input-output techniques enhance resolvent analysis. Specifically, physical insights that may remain hidden in the resolvent analysis are gained by detailed examination of input-output responses between spatially-localized body forces and selected linear combinations of state variables. This differentiating feature plays a key role in quantifying the importance of different mechanisms for bypass transition in wall-bounded shear flows and in explaining how turbulent jets generate noise. We highlight the utility of a stochastic framework, with white or colored inputs, in addressing a variety of open challenges including transition in complex fluids, flow control, and physics-aware data-driven turbulence modeling. Applications with time- or spatially-periodic base flows are discussed and future research directions are outlined.