# Attempt at a test program. This has one column with three layers, each # with excitatory and inhibitory cells. Layer A is connected to B, and B to C. # Sine stimulus is applied to A, and output of C is recorded. ############################## Define Brain ################################ BRAIN TYPE Brain JOB c2 FSV 10000 DISTRIBUTE EqualSynapse DURATION 1.5000 SEED 999999 STIMULUS_INJECT StInject1 COLUMN_TYPE AI_1 COLUMN_TYPE AI_2 CONNECT AI_1 layer_A Excitatory s1 AI_2 layer_B Excitatory s1 ExcitSyn1 0.1 3 REPORT ReportIn REPORT ReportOut END_BRAIN ############################### Define Column Shells ######################### COLUMN_SHELL TYPE AI_shell_1 WIDTH 300 HEIGHT 800 LOCATION 100 50 END_COLUMN_SHELL COLUMN_SHELL TYPE AI_shell_2 WIDTH 300 HEIGHT 800 LOCATION 0 0 END_COLUMN_SHELL ############################### Fill Columns ################################# COLUMN TYPE AI_1 COLUMN_SHELL AI_shell_1 LAYER_TYPE layer_A LAYER_TYPE layer_B CONNECT layer_A Excitatory s1 layer_B Excitatory s1 ExcitSyn1 0.1 3 END_COLUMN COLUMN TYPE AI_2 COLUMN_SHELL AI_shell_2 LAYER_TYPE layer_A LAYER_TYPE layer_B CONNECT layer_A Excitatory s1 layer_B Excitatory s1 ExcitSyn1 0.1 3 END_COLUMN ############################### Define Layer Shells ######################### LAYER_SHELL TYPE layer_shell_A LOWER 0 UPPER 35 END_LAYER_SHELL LAYER_SHELL TYPE layer_shell_B LOWER 35 UPPER 65 END_LAYER_SHELL ############################### Fill Layers ################################## LAYER TYPE layer_A LAYER_SHELL layer_shell_A CELL_TYPE Excitatory 500 CELL_TYPE Inhibitory 100 CONNECT Excitatory s1 Inhibitory s1 ExcitSyn1 0.1 3 END_LAYER LAYER TYPE layer_B LAYER_SHELL layer_shell_B CELL_TYPE Excitatory 500 CELL_TYPE Inhibitory 100 CONNECT Excitatory s1 Inhibitory s1 ExcitSyn1 0.1 3 END_LAYER ############################### Define Cells ################################ CELL TYPE Excitatory COMPARTMENT soma_e1 s1 0 0 END_CELL CELL TYPE Inhibitory COMPARTMENT soma_i1 s1 0 0 END_CELL ############################### Define Compartments ########################## COMPARTMENT TYPE soma_e1 SPIKESHAPE AP_Hoff SPIKE_HALFWIDTH 10 0 TAU_MEMBRANE 0.015 0.0 R_MEMBRANE 200 0 THRESHOLD -40 0 LEAK_REVERSAL 0 0 LEAK_CONDUCTANCE 0 0 VMREST -65 0 CA_INTERNAL 100 0 CA_EXTERNAL 0 0 CA_SPIKE_INCREMENT 300 0 CA_TAU 0.07 0.0 CHANNEL ahp-2 CHANNEL m-1 CHANNEL a-1 CHANNEL a-2 END_COMPARTMENT COMPARTMENT TYPE soma_i1 SPIKESHAPE AP_Hoff SPIKE_HALFWIDTH 10 0 TAU_MEMBRANE 0.015 0.001 R_MEMBRANE 200 3 THRESHOLD -40 1 LEAK_REVERSAL 0 0 LEAK_CONDUCTANCE 0 0 VMREST -60 1 CA_INTERNAL 20 0 CA_EXTERNAL 0 0 CA_SPIKE_INCREMENT 100 5 CA_TAU 0.1 0.001 CHANNEL ahp-2 CHANNEL m-1 CHANNEL a-1 END_COMPARTMENT ############################### Define Channels ############################# CHANNEL Kahp TYPE ahp-2 REVERSAL_POTENTIAL -80 0 M_INITIAL 0.0 0.0 M_POWER 2 CA_SCALE_FACTOR 0.000125 0 CA_EXP_FACTOR 2 0 CA_HALF_MIN 2.5 0 CA_TAU_SCALE_FACTOR 0.003 0.0000 UNITARY_G 0.054 0 STRENGTH 0.1 0.0 END_CHANNEL CHANNEL Km TYPE m-1 REVERSAL_POTENTIAL -80 0 M_INITIAL 0.1 0.0 M_POWER 1 E_HALF_MIN_M -44 0 SLOPE_FACTOR_M 40 20 8.8 SLOPE_FACTOR_M_STDEV 0 TAU_SCALE_FACTOR_M 0.303 UNITARY_G 0.084 0 STRENGTH 0.03 0 END_CHANNEL CHANNEL Ka TYPE a-1 REVERSAL_POTENTIAL -80 0 M_INITIAL 0.3 0.0 M_POWER 2 E_HALF_MIN_M -21.3 0 SLOPE_FACTOR_M 35 SLOPE_FACTOR_M_STDEV 0.0 V_TAU_VOLTAGE_M 100.000000 V_TAU_VOLTAGE_M_STDEV 0.000000 V_TAU_VALUE_M 0.000200 9999.000000 V_TAU_VALUE_M_STDEV 0.00000 H_INITIAL 0.7 0.0 H_POWER 1 E_HALF_MIN_H -58 0 SLOPE_FACTOR_H 8.2 SLOPE_FACTOR_H_STDEV 0.0 V_TAU_VOLTAGE_H -21.000000 -1.000000 10.000000 21.000000 V_TAU_VOLTAGE_H_STDEV 0.0 V_TAU_VALUE_H 0.05000 0.01000 0.15000 0.20000 2.5000 V_TAU_VALUE_H_STDEV 0.0000 UNITARY_G 0.120 0 STRENGTH 0.05 0 END_CHANNEL CHANNEL Ka TYPE a-2 REVERSAL_POTENTIAL -80 0 M_INITIAL 0.3 0.0 M_POWER 2 E_HALF_MIN_M -21.3 0 SLOPE_FACTOR_M 35 SLOPE_FACTOR_M_STDEV 0.0 V_TAU_VOLTAGE_M 100.000000 V_TAU_VOLTAGE_M_STDEV 0.000000 V_TAU_VALUE_M 0.0002 9999.000000 V_TAU_VALUE_M_STDEV 0.00000 H_INITIAL 0.7 0.0 H_POWER 1 E_HALF_MIN_H -58 0 SLOPE_FACTOR_H 8.2 SLOPE_FACTOR_H_STDEV 0.0 V_TAU_VOLTAGE_H -21.000000 -1.000000 10.000000 21.000000 V_TAU_VOLTAGE_H_STDEV 0.0 V_TAU_VALUE_H 0.005000 0.001000 0.015000 0.020000 0.250000 V_TAU_VALUE_H_STDEV 0.0000 UNITARY_G 0.120 0 STRENGTH 0.05 0 END_CHANNEL ############################### Define Synapse ############################## SYNAPSE TYPE ExcitSyn1 SFD_LABEL F2 SYN_PSG PSGexcit LEARN_LABEL 0HEBB MAX_CONDUCT 0.01 DELAY 0.0008 0.0012 SYN_REVERSAL 0 0 ABSOLUTE_USE 0.250 0.0 RSE_INIT 0.5 0.5 PREV_SPIKE_RANGE 0.1 0.1 END_SYNAPSE SYNAPSE TYPE InhibSyn1 SFD_LABEL F0 SYN_PSG PSGinhib LEARN_LABEL 0HEBB MAX_CONDUCT 0.05 DELAY 0.0008 0.0012 SYN_REVERSAL 0 0 ABSOLUTE_USE 0.32 0.0 END_SYNAPSE ############################### Short-term Synaptic Dynamics ############### SYN_FACIL_DEPRESS TYPE F0 SFD NONE FACIL_TAU 0.0 0.0 DEPR_TAU 0.0 0.0 END_SYN_FACIL_DEPRESS SYN_FACIL_DEPRESS TYPE F1 SFD FACIL FACIL_TAU 0.376 0.0 DEPR_TAU 0.045 0.0 END_SYN_FACIL_DEPRESS SYN_FACIL_DEPRESS TYPE F2 SFD DEPR FACIL_TAU 0.021 0.0 DEPR_TAU 0.706 0.0 END_SYN_FACIL_DEPRESS SYN_FACIL_DEPRESS TYPE F3 SFD BOTH FACIL_TAU 0.062 0.031 DEPR_TAU 0.144 0.08 END_SYN_FACIL_DEPRESS ############################### Synaptic waveform ######################### SYN_PSG TYPE PSGexcit PSG_FILE /home/jbm/EPSC.txt END_SYN_PSG SYN_PSG TYPE PSGinhib PSG_FILE /home/jbm/IPSC.txt END_SYN_PSG ############################### Long-term Synaptic Dynamics ############### SYN_LEARNING TYPE 0HEBB LEARNING NONE NEG_HEB_WINDOW 0.04 0.0 POS_HEB_WINDOW 0.04 0.0 POS_HEB_PEAK_DELTA_USE 0.01 0.0 NEG_HEB_PEAK_DELTA_USE 0.005 0.0 POS_HEB_PEAK_TIME 0.01 0.0 NEG_HEB_PEAK_TIME 0.01 0.0 END_SYN_LEARNING SYN_LEARNING TYPE +-HEBB LEARNING BOTH NEG_HEB_WINDOW 0.04 0.0 POS_HEB_WINDOW 0.04 0.0 POS_HEB_PEAK_DELTA_USE 0.01 0.0 NEG_HEB_PEAK_DELTA_USE 0.005 0.0 POS_HEB_PEAK_TIME 0.01 0.0 NEG_HEB_PEAK_TIME 0.01 0.0 END_SYN_LEARNING ############################### Define spikeshapes ####################### SPIKESHAPE TYPE AP_Hoff VOLTAGES -38 -35 -30 -20 -7 15 30 20 7 -8 -16 -22 -28 -33 -37 -40 -43 -45 -47 -49 -50 END_SPIKESHAPE ############################### Define Stimulus ########################## STIMULUS TYPE Stim1 MODE CURRENT PATTERN SINE TIMING EXACT SAMESEED NO AMP_START 0.5 VERT_TRANS 0.0 TIME_START 0.0 TIME_END 3.4025 FREQ_START 10 END_STIMULUS STIMULUS_INJECT TYPE StInject1 STIM_TYPE Stim1 INJECT AI_1 layer_A Excitatory s1 1.0 END_STIMULUS_INJECT ############################### Define Reports ########################### REPORT TYPE ReportIn ASCII CELLS AI_1 layer_A Excitatory s1 PROB 1.0 REPORT_ON VOLTAGE FILENAME in.out FREQUENCY 1 TIME_START 0.0 TIME_END 3.4025 END_REPORT REPORT TYPE ReportOut ASCII CELLS AI_1 layer_B Excitatory s1 PROB 1.0 REPORT_ON VOLTAGE FILENAME out.out FREQUENCY 1 TIME_START 0.0 TIME_END 3.4025 END_REPORT