Advances in experimental techniques, including behavioral paradigms using rich stimuli under closed loop conditions and the interfacing of neural systems with external inputs and outputs, reveal complex dynamics in the neural code and require a revisiting of standard concepts of representation. High-throughput recording and imaging methods along with the ability to observe and control neuronal subpopulations allow increasingly detailed access to the neural circuitry that subserves neural representations and the computations they support. How do we harness theory to build biologically grounded models of complex neural function?