// See also instructions at the bottom of this file.
// Small networks for visualization or debugging were run with
// the following parameters:
// int number_mossy_fibers = 6 // 540
// int number_granule_cells = 15 // 5355
// int number_Golgi_cells = 2 // 30
// float mossy_fiber_to_Golgi_cell_ratio = 3 // 18
// The numbers behind the // give the values used for large networks in the paper,
// but cannot be run with online graphical output on the screen.
// directory name for ascii output
str filename = "results/"
// chanmode for hsolver
int chanmode = 4 // 3
// cell numbers
int number_mossy_fibers = 6 // 540 // may be overwritten below
int number_granule_cells = 15 // 5355 // may be overwritten in Gran_layer_setup.g
int number_Golgi_cells = 2 // 30 // fixed
int number_stellate_cells = 0
// topographics : describes distances along the parallel-fiber axis (1D) only
// separation between adjacent Golgi cells
float Golgi_cell_separation = 300e-6 // meter
// ratio of number of mossy fibers over number of Golgi cells : an uneven number
float mossy_fiber_to_Golgi_cell_ratio = 3 // 18 // 9 // 3
number_mossy_fibers = {number_Golgi_cells} * {mossy_fiber_to_Golgi_cell_ratio}
// ratio of number of stellate cells over number of Golgi cells : an uneven number
int stellate_cell_to_Golgi_cell_ratio = 0 // 5
number_stellate_cells = {number_Golgi_cells} * {stellate_cell_to_Golgi_cell_ratio}
// separation between adjacent mossy fibers
float mossy_fiber_separation = {Golgi_cell_separation} / {mossy_fiber_to_Golgi_cell_ratio} // meter
// separation between adjacent stellate cells
float stellate_cell_separation = {Golgi_cell_separation} / {stellate_cell_to_Golgi_cell_ratio} // meter
// 4 mossy fibers can converge onto a single granule cell only when they fall
// within a circle with the following radius, the position of the created
// granule cell will be the midpoint of the 4 afferent mossy fibers
float mossy_fiber_to_granule_cell_connection_radius = 5 // in {mossy_fiber_separation} units
// probability that a granule cell is created for a combination of 4 valid mossy fiber positions
float P_mossy_fiber_to_granule_cell_connection = 1.0 // probability
// radius for mossy fiber to Golgi cell connections
float mossy_fiber_to_Golgi_cell_radius = {Golgi_cell_separation} / 2.0 // meter
// overlap of Golgi cell axons : integer
int Golgi_cell_axon_overlap = 1 // 1 // 3
// radius for Golgi cell to granule cell connections
float Golgi_cell_to_granule_cell_radius = \
{Golgi_cell_separation} * {Golgi_cell_axon_overlap} / 2.0 // meter
// radius for stellate cell to Golgi cell connections
float stellate_cell_to_Golgi_cell_radius = {Golgi_cell_separation} / 2.0 // meter
// length parallel fiber
float parallel_fiber_length = 5.0e-3 // meter
// mossy fiber input
float mossy_fiber_firing_rate = 50 // 10 // 25 // sec^-1
float mossy_fiber_refractory_period = 0.005 // sec
float interburst_interval = 0.1 // sec
float burst_duration = 0.01 // sec
float burst_intensity = 1.0 // multiplied by mossy_fiber_firing_rate
// synaptic probabilities
float P_mossy_fiber_to_Golgi_cell_synapse = 1.0 // probability
float P_granule_cell_to_Golgi_cell_synapse = 1.0 // 0.2 // 1.0 // probability
float P_Golgi_cell_to_granule_cell_synapse = 1.0 // probability
float P_mossy_fiber_to_granule_cell_synapse = {4.0 / number_mossy_fibers} // probability
float P_stellate_cell_to_Golgi_cell_synapse = 1.0 // probability
float P_granule_cell_to_stellate_cell_synapse = 0.1 // probability
// synaptic weights : the normalization is now done in RECALC of synchan !!!!
float weight_mossy_fiber_granule_cell_AMPA_synapse = 6.0
float weight_mossy_fiber_granule_cell_NMDA_synapse = 4.0
float weight_mossy_fiber_Golgi_cell_synapse = 0.0 // {dt} * 2.0 // 6.0
float weight_granule_cell_Golgi_cell_synapse = 45.0 // 18.0 // 15 // 6.0
float weight_granule_cell_stellate_cell_synapse = \
{weight_granule_cell_Golgi_cell_synapse * P_granule_cell_to_stellate_cell_synapse \
/ P_granule_cell_to_Golgi_cell_synapse}
float weight_Golgi_cell_granule_cell_GABAA_synapse = 45.0 // 30.0 // 45.0
float weight_Golgi_cell_granule_cell_GABAB_synapse = \
0.0 // {weight_Golgi_cell_granule_cell_GABAA_synapse / 2} // 0.0
float weight_stellate_cell_Golgi_cell_synapse = {weight_Golgi_cell_granule_cell_GABAA_synapse / 2}
// synaptic delays
float delay_mossy_fiber_granule_cell_synapse = 0.0
float delay_mossy_fiber_Golgi_cell_synapse = 0.0
float delay_granule_cell_Golgi_cell_synapse = 0.0
float delay_Golgi_cell_granule_cell_synapse = 0.0
float delay_stellate_cell_Golgi_cell_synapse = 0.0
float parallel_fiber_conduction_velocity = 0.5 // m/s
float time_axis_graph = 1.0
float weight_distribution = 0.15
float delay_distribution = 0.0
/*** INSTRUCTIONS ***/
/* Some parameters have to be consistent with each other.
The basic parameters are : (1) the number of Golgi cells (number_Golgi_cells),
(2) the ratio of the number of mossy fibers to the number of Golgi cells
(mossy_fiber_to_Golgi_cell_ratio), and (3) the span value for mossy fiber
ramification (mossy_fiber_to_granule_cell_connection_radius).
The number of mossy fibers (number_mossy_fibers) is derived from (1)
and (2), the number of granule cells (number_granule_cells) is derived
in Script Gran_layer_setup.g from number_mossy_fibers and (3).
Nevertheless, number_mossy_fibers and number_granule_cells must be correctly
initialized because these variables are used in some other scripts.
To know with which value number_granule_cells should be initialized,
you can run the simulation and abort it after script
Gran_layer_setup.g has been completed. The correct number is printed
on the screen by Gran_layer_setup.g ("made ... numbers of granule cells").
*/