//genesis
// This is the main script for setting up and running a network.
float dt = 10e-6
str label = "IMTEK"
str filename = "./"
setclock 0 {dt}
setclock 1 50e-6
float tmax = 0.15
str name
include defaults.g
// making the neurons
/* Make L5P pyramidal cell */
include ../L5P37C/L5P_make.g
create_L5P /L5P 0 0 0
/* Make L5P pyramidal cell without tuft or backpropagating spike */
include ../L5P37C-notuft/L5P_notuft_make.g
create_L5Pnotuft /L5Pnotuft -0.00004 0 0.0002
/* Make neuron with narrow spikes */
include ../L5P37C-onlybasal/L5P_onlybasal_make.g
create_L5Ponlybasal /L5Ponlybasal 0.00004 0 0.0001
/* Make additional inhibitory neuron */
create_L5Ponlybasal /L5Ponlybasal2 -20e-6 -30e-6 0.0003
/* Make additional excitatory neuron */
create_L5Pnotuft /L5Pnotuft2 20e-6 30e-6 0.0003
cd ../Network_5neuron_IMTEK
/* Set up graphical and ascii output */
include ../Output/L5P_view.g
add_xcell /L5P
add_xcell /L5Ponlybasal
add_xcell /L5Pnotuft
add_xcell /L5Ponlybasal2
add_xcell /L5Pnotuft2
//include ../Output/L5P_graph.g
// add_xgraph /L5P
// add_xgraph /L5Ponlybasal
// add_xgraph /L5Pnotuft
// add_xgraph /L5Ponlybasal2
// add_xgraph /L5Pnotuft2
include ../Output/L5P_ascout.g
add_ascout /L5P
add_ascout /L5Ponlybasal
add_ascout /L5Pnotuft
add_ascout /L5Ponlybasal2
add_ascout /L5Pnotuft2
/* Set up electrode arrays */
include ../Electrodes/electrodesIMTEK_make.g
include ../Electrodes/electrodes_connect.g
// connect_to_electrodes L5P
// connect_to_electrodes L5Ponlybasal
// connect_to_electrodes L5Pnotuft
// connect_to_electrodes L5Ponlybasal2
// connect_to_electrodes L5Pnotuft2
useclock /electrode_array 1
useclock /electrode_array/##[] 1
/* Setup the hines solvers */
include Network_hsolve.g
make_hsolve /L5P
make_hsolve /L5Ponlybasal
make_hsolve /L5Pnotuft
make_hsolve /L5Ponlybasal2
make_hsolve /L5Pnotuft2
include ../Output/L5P_graphsolve.g
add_xgraph /L5P
add_xgraph /L5Ponlybasal
add_xgraph /L5Pnotuft
add_xgraph /L5Ponlybasal2
add_xgraph /L5Pnotuft2
/* generate for each compartment of L5P an associated fibre */
randseed 54321 // 12345
// make the fibres using L5P as template neuron
include ../Fibres/Fibres_make
make_fibres /Excitatory_fibres /L5P/p#
make_fibres /Inhibitory_fibres /L5P/p#
// connect the fibres to the neurons
include ../Fibres/Fibres_connect
connect_horizontally /Excitatory_fibres/FF/fibre[] \
/L5P/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.5} 0
connect_horizontally /Excitatory_fibres/FBintra/fibre[] \
/L5P/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.5} 0.02
connect_horizontally /Inhibitory_fibres/FF/fibre[] \
/L5P/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.25} 0.002
connect_horizontally /Inhibitory_fibres/FBintra/fibre[] \
/L5P/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.25} 0.033 // 0.025
connect_horizontally /Excitatory_fibres/FF/fibre[] \
/L5Ponlybasal/p#[][TYPE=compartment]/AMPA \
0.1 {weight_AMPA_synapse * 0.15} 0
connect_horizontally /Excitatory_fibres/FBintra/fibre[] \
/L5Ponlybasal/p#[][TYPE=compartment]/AMPA \
0.1 {weight_AMPA_synapse * 0.10} 0.02
connect_horizontally /Inhibitory_fibres/FF/fibre[] \
/L5Ponlybasal/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.7} 0.002
connect_horizontally /Inhibitory_fibres/FBintra/fibre[] \
/L5Ponlybasal/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.7} 0.033
connect_horizontally /Excitatory_fibres/FF/fibre[] \
/L5Pnotuft/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.8} 0
connect_horizontally /Excitatory_fibres/FBintra/fibre[] \
/L5Pnotuft/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.8} 0.02
connect_horizontally /Inhibitory_fibres/FF/fibre[] \
/L5Pnotuft/p#[][TYPE=compartment]/GABA \
0.02 {weight_GABA_synapse * 0.4} 0.002
connect_horizontally /Inhibitory_fibres/FBintra/fibre[] \
/L5Pnotuft/p#[][TYPE=compartment]/GABA \
0.02 {weight_GABA_synapse * 0.4} 0.033
// I keep the same connections for new neurons 4 and 5
// and do not include them in feedback
connect_horizontally /Excitatory_fibres/FF/fibre[] \
/L5Ponlybasal2/p#[][TYPE=compartment]/AMPA \
0.4 {weight_AMPA_synapse * 0.15} 0
connect_horizontally /Excitatory_fibres/FBintra/fibre[] \
/L5Ponlybasal2/p#[][TYPE=compartment]/AMPA \
0.1 {weight_AMPA_synapse * 0.10} 0.02
connect_horizontally /Inhibitory_fibres/FF/fibre[] \
/L5Ponlybasal2/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.7} 0.002
connect_horizontally /Inhibitory_fibres/FBintra/fibre[] \
/L5Ponlybasal2/p#[][TYPE=compartment]/GABA \
0.025 {weight_GABA_synapse * 0.7} 0.033
connect_horizontally /Excitatory_fibres/FF/fibre[] \
/L5Pnotuft2/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.8} 0
connect_horizontally /Excitatory_fibres/FBintra/fibre[] \
/L5Pnotuft2/p#[][TYPE=compartment]/AMPA \
0.05 {weight_AMPA_synapse * 0.8} 0.02
connect_horizontally /Inhibitory_fibres/FF/fibre[] \
/L5Pnotuft2/p#[][TYPE=compartment]/GABA \
0.02 {weight_GABA_synapse * 0.4} 0.002
connect_horizontally /Inhibitory_fibres/FBintra/fibre[] \
/L5Pnotuft2/p#[][TYPE=compartment]/GABA \
0.02 {weight_GABA_synapse * 0.4} 0.033
include ../Output/L5P_history.g
add_history /L5P
add_history /L5Ponlybasal
add_history /L5Pnotuft
add_history /L5Ponlybasal2
add_history /L5Pnotuft2
include nsynapses
include ../Fibres/Firing_rate_profile.g
// This gives different weights to the afferent fibres according to their depth (layer) in neocortex
make_firing_rate_profile /Excitatory_fibres/FF 0.0008 0.0002 2 0 0.0004 1 10
make_firing_rate_profile /Excitatory_fibres/FBintra 0.001 0.0002 2 0 0.0004 1 10
make_firing_rate_profile /Inhibitory_fibres/FF 0.0008 0.0004 1 0 0.0002 2 45
make_firing_rate_profile /Inhibitory_fibres/FBintra 0.001 0.0004 1 0 0.0002 2 45
include ../Fibres/Harsch-Robinson_modulation.g
// This gives a temporal profile to the spike rate of the subcortical afferent fibres
Harsch_Robinson_modulation 30 0.1
// This gives a temporal profile to the intracortical fibers
include ../Fibres/Firing_rate_modulation.g
resched
randseed 12345
// current injection
//setfield /L5P/soma inject 20e-12 // 800e-12
reset
// just a check, recording electrode positions
include ../Electrodes/electrode-positions.g
// step 25 -t
//quit