Parameters

Parameters:

Parameters is used to specify parameter values for neurons and connections. It is also used to specify external inputs.

Neuron and connection parameter commands:

• edit_neurons {<neurons to edit>} <param 1 name> <param 1 value>, <param 2 name> <param 2 value>, ...
  This command sets the parameter values for a group of neurons, for any number of specified parameters. Every type of neuron has different parameters which will be covered later.
  • Note the {} notation in choosing <from> and <to>. This is a way of specifying specifically which neurons should be used. Neurons can be specified by using the name of a group, by using pythons : notation, by specifying individual id numbers, or a combination. Examples of use are included above.
• edit_connection <connection to edit (connection name)> <param 1 name> <param 1 value>, <param 2 name> <param 2 value>, ...
  This command sets the parameter values for a connection, for any number of specified parameters. Every type of synapse has different parameters which will be covered later.

External stimulus parameter commands:

• estim {<neurons to stimulate>} {<timesteps to stimulate>} <stimulus voltage (float)>
  The command will present a constant external stimulus, of the specified value, to the specified neurons at the specified times.
• ostim {<neurons to stimulate>} {<timesteps to stimulate>} <max stimulus volatage (float)> <duration (int)> <centered on which neuron (int)> <standard deviation (int)>
  This command will present stimulus in a normal distribution fashion, centered on one neuron. It will only effect the specified neurons and will last for the specified duration ({<timesteps to stimulate>} here refers to the start time of this stimulus). The center neuron will recieve the maximum stimulus, and the stimulus will drop off for neurons further out based on the standard deviation.
• sniff {<neurons to stimulate>} {<timesteps to stimulate>} <max stimulus volatage (float)> <frequency> <centered on which neuron (int)> <standard deviation (int)>
  This command attempts to replicate the stimulation received by the olfactory bulb due to respiration. The stimulus rises with inhalation and falls with exhalation, following a sinusoidal pattern with the specified frequency. Furthermore, the stimulus is also presented in a normal distribution, centered on one neuron. At the peak of inhalation, the center neuron will receive the maximum stimulus, and this stimulus will drop off for other neurons based on the standard deviation.

Examples of external stimulus:

Example 1

Consider:

Simulator_setup:
timestep 1
final_timestep 70

Model_structure:
group basic Sensory 25

Parameters:
edit_neurons {Sensory}    time_constant 10, sigmoid_center 2, sigmoid_slope 0.01

# Simulate neurons 2,7,12,17,22 every 6 timesteps with 1V
estim {2:25:5} {::6} 1

Output:
plot neuron voltage raw {:} {:}
plot neuron raster raster {:} {:}
end

Outputted plots: Voltages of all neurons: Raster plot:

Example 2

Consider:

Simulator_setup:
timestep 1
final_timestep 500

Model_structure:
group basic OSN 100
group basic extra 100
connect OSN_to_extra basicS {OSN} {extra} 0.9


Parameters:
edit_neurons {OSN}    time_constant 1,   sigmoid_center 0.7, sigmoid_slope 0.15
edit_neurons {extra}    time_constant 1,   sigmoid_center 0.7, sigmoid_slope 0.15
edit_connection OSN_to_extra initial_weight 0.013,  E 70, tau1 1, tau2 4

# Simulate OSN neurons every in an oscillatory pattern with frequency 8Hz, 
# centered on neuron 50, with a deviation of 20, and maximum of 1V
sniff {OSN} {50:450} 1. 8 50 20

Output:
plot neuron voltage raw {OSN} {:}
plot neuron raster raster {OSN} {:}
end

Outputted plots: Voltages of all neurons in group OSN: Raster plot of all neurons in group OSN: