Defer perturbations until after the start of a simulation

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Defer perturbations until after the start of a simulation

Post by ted »

When running simulations of a model that is not spontaneously active, i.e. has a stable resting potential, it is generally a good idea to initialize the model to its steady state, and delay the onset of perturbations such as stimuli (current clamps, synaptic activations etc.) until t (h.t to all you Pythonists) is at least 5 or 10 ms. This allows verification that state variables are indeed properly initialized. If the model _is_ spontaneously active, it is best to defer perturbations until the simulation has run long enough for activity to stabilize. Likewise, plots of any variable vs. t, and phase plane plots, should genearlly include a bit of "baseline activity" before the start of any perturbation. These recommendations will seem like standard practice to modelers who have a background in experimental biology, but experience has shown them to be new ideas to many who come from mathematics or the physical sciences.
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