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.