NEURON launch.hoc

The launch.hoc file defines the parameters and simulation protocol for modeling fiber response to electrical stimulation in NEURON and is automatically populated based on parameters in Model and Sim. The launch.hoc file is created by the HocWriter class. Parameters defined in launch.hoc span the categories of: environment (i.e., temperature from Model), simulation time (i.e., time step, duration of simulation from Sim), fiber parameters (i.e., flags for fiber geometry and channels, number of fiber nodes from Model, Sim, and config/system/fiber_z.json), intracellular stimulation (i.e., delay from start of simulation, amplitude, pulse duration, pulse repetition frequency from Sim), extracellular stimulation (i.e., path to waveform file in n_sim/ folder which is always data/inputs/waveform.dat), flags to define the model parameters that should be recorded (i.e., Vm(t), Gating(t), Vm(x), Gating(x) from Sim), the locations at which to record the parameters (nodes of Ranvier for myelinated axons from Sim), and parameters for the binary search for thresholds (i.e., activation or block protocol, initial upper and lower bounds on the stimulation amplitude for the binary search, and threshold resolution for the binary search from Sim). The launch.hoc file loads Wrapper.hoc which calls all NEURON procedures. The launch.hoc file is created by the Python HocWriter class, which takes inputs of the Sim directory, n_sim/ directory, and an exception configuration. When the HocWriter class is instantiated, it automatically loads the fiber_z.json configuration file which contains all associated flags, parameters, and rules for defining a fiber’s geometry and channel mechanisms in NEURON.