Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)

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Accession:83319
This package provides a series of codes that simulate networks of spiking neurons (excitatory and inhibitory, integrate-and-fire or Hodgkin-Huxley type, current-based or conductance-based synapses; some of them are event-based). The same networks are implemented in different simulators (NEURON, GENESIS, NEST, NCS, CSIM, XPP, SPLIT, MVAspike; there is also a couple of implementations in SciLab and C++). The codes included in this package are benchmark simulations; see the associated review paper (Brette et al. 2007). The main goal is to provide a series of benchmark simulations of networks of spiking neurons, and demonstrate how these are implemented in the different simulators overviewed in the paper. See also details in the enclosed file Appendix2.pdf, which describes these different benchmarks. Some of these benchmarks were based on the Vogels-Abbott model (Vogels TP and Abbott LF 2005).
Reference:
1 . Vogels TP, Abbott LF (2005) Signal propagation and logic gating in networks of integrate-and-fire neurons. J Neurosci 25:10786-95 [PubMed]
2 . Brette R, Rudolph M, Carnevale T, Hines M, Beeman D, Bower JM, Diesmann M, Morrison A, Goodman PH, Harris FC, Zirpe M, Natschl├Ąger T, Pecevski D, Ermentrout B, Djurfeldt M, Lansner A, Rochel O, Vieville T, Muller E, Davison AP, El Boustani S, Destexhe A (2007) Simulation of networks of spiking neurons: a review of tools and strategies. J Comput Neurosci 23:349-98 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; GENESIS; NEST; C or C++ program; XPP; CSIM; NCS; SPLIT; MVASpike; SciLab; Brian; PyNN; Python;
Model Concept(s): Activity Patterns; Methods;
Implementer(s): Carnevale, Ted [Ted.Carnevale at Yale.edu]; Hines, Michael [Michael.Hines at Yale.edu]; Davison, Andrew [Andrew.Davison at iaf.cnrs-gif.fr]; Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr]; Ermentrout, Bard [bard_at_pitt.edu]; Brette R; Bower, James; Beeman, Dave; Diesmann M; Morrison A ; Goodman PH; Harris Jr, FC; Zirpe M ; Natschlager T ; Pecevski D ; Djurfeldt M; Lansner, Anders [ala at kth.se]; Rochel O ; Vieville T ; Muller E ; El Boustani, Sami [elboustani at unic.cnrs-gif.fr]; Rudolph M ;
/
destexhe_benchmarks
NCS
ncs_coba.in
                            
############################## Brain Definition ################################

BRAIN
	TYPE				B1_Brain
	JOB				Benchmark_IF_G-based_Syn
	FSV				10000
	DURATION			1
#	IGNORE_EMPTY			NO
	DISTANCE			NO
	SEED				-15
	STIMULUS_INJECT		poisson_stiminject1
	COLUMN_TYPE			AI_1
	REPORT				AI1_E1_Voltage
	REPORT				AI1_E2_Voltage
	REPORT				AI1_I_Voltage
END_BRAIN

############################### Define Column Shells #########################

COLUMN_SHELL
        TYPE                    AI_shell_1
        WIDTH                   300
        HEIGHT                  800
        LOCATION                0               0
END_COLUMN_SHELL

############################### Fill Columns #################################

COLUMN
        TYPE                    AI_1
        COLUMN_SHELL            AI_shell_1
        LAYER_TYPE              layer_E1
        LAYER_TYPE              layer_E2
        LAYER_TYPE              layer_I
        CONNECT
                                layer_E1   Excitatory      s1
                                layer_I    Inhibitory      s1
                                ExcitSyn1  0.02             0
        CONNECT
                                layer_I    Inhibitory      s1
                                layer_E1   Excitatory      s1
                                InhibSyn1  0.02             0

        CONNECT
                                layer_E1    Excitatory      s1
                                layer_E2    Excitatory      s1
                                ExcitSyn1   0.02             0
        CONNECT
                                layer_E2    Excitatory      s1
                                layer_E1    Excitatory      s1
                                ExcitSyn1   0.02             0

        CONNECT
                                layer_E2   Excitatory      s1
                                layer_I    Inhibitory      s1
                                ExcitSyn1  0.02             0
        CONNECT
                                layer_I    Inhibitory      s1
                                layer_E2   Excitatory      s1
                                InhibSyn1  0.02             0

END_COLUMN

############################### Define Layer Shells #########################

LAYER_SHELL
	TYPE				layer_shell_E1
	LOWER				0
	UPPER				35
END_LAYER_SHELL

LAYER_SHELL
	TYPE				layer_shell_E2
	LOWER				35
	UPPER				70
END_LAYER_SHELL

LAYER_SHELL
	TYPE				layer_shell_I
	LOWER				70
	UPPER				105
END_LAYER_SHELL

############################### Fill Layers ##################################

LAYER
	TYPE				layer_E1
	LAYER_SHELL			layer_shell_E1
       CELL_TYPE              	Excitatory      14
       CONNECT
                                	Excitatory      s1
                                	Excitatory      s1
                                	ExcitSyn1       0.02           0
END_LAYER

LAYER
	TYPE				layer_E2
	LAYER_SHELL			layer_shell_E2
       CELL_TYPE              	Excitatory      3186
       CONNECT
                                	Excitatory      s1
                                	Excitatory      s1
                                	ExcitSyn1       0.02             0
END_LAYER

LAYER
        TYPE                    layer_I
        LAYER_SHELL             layer_shell_I
        CELL_TYPE               Inhibitory      800
        CONNECT
                                Inhibitory      s1
                                Inhibitory      s1
                                InhibSyn1       0.02             0
END_LAYER

############################### Define Cells ################################
CELL
	TYPE				Excitatory
	COMPARTMENT			soma_exc		s1	0	0	0
END_CELL
CELL
	TYPE				Inhibitory
	COMPARTMENT			soma_inhib		s1	0	0	0
END_CELL

############################### Define Compartments ##########################
COMPARTMENT
        TYPE                    soma_exc
        SPIKESHAPE              AP_Hoff
        TAU_MEMBRANE            0.020           0.0
        R_MEMBRANE              200             0
        THRESHOLD               -50             0
        VMREST                  -60             0
END_COMPARTMENT

COMPARTMENT
        TYPE                    soma_inhib
        SPIKESHAPE              AP_Hoff
        TAU_MEMBRANE            0.020           0.0
        R_MEMBRANE              200             0
        THRESHOLD               -50             0
        VMREST                  -60             0
END_COMPARTMENT

############################### Define Synapse ##############################

SYNAPSE
	TYPE			ExcitSyn1
	SFD_LABEL		NO_SFD
	LEARN_LABEL		NO_LEARN
	SYN_PSG		PSGexcit
	MAX_CONDUCT		0.010		0.0
	DELAY			0.0000000001	0.0000000001
	SYN_REVERSAL		0		0
	ABSOLUTE_USE		0.250		0.0
END_SYNAPSE

SYNAPSE
	TYPE			InhibSyn1
	SFD_LABEL		NO_SFD
	LEARN_LABEL		NO_LEARN
	SYN_PSG		PSGinhib
	MAX_CONDUCT		0.100		0.0
	DELAY			0.0000000001	0.0000000001
	SYN_REVERSAL		-80		0
	ABSOLUTE_USE		0.250		0.0
END_SYNAPSE

############################### Short-term Synaptic Dynamics ###############

# Exc
SYN_FACIL_DEPRESS
        TYPE                    NO_SFD
        SFD                     NONE
        FACIL_TAU               0.0           0.0
        DEPR_TAU                0.0           0.0
END_SYN_FACIL_DEPRESS

############################### Synaptic waveform #########################

SYN_PSG
        TYPE                    PSGexcit
        PSG_FILE                /home/milindz/work/brain_model/EPSG_Vogels.txt
END_SYN_PSG

SYN_PSG
        TYPE                    PSGinhib
        PSG_FILE                /home/milindz/work/brain_model/IPSG_Vogels.txt
END_SYN_PSG

############################### Long-term Synaptic Dynamics ###############
SYN_LEARNING
        TYPE                    NO_LEARN
        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

############################### 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 -50 -55 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60 -60
END_SPIKESHAPE

############################### Define Stimulus ##########################
STIMULUS
	TYPE				poisson_stimulus1
	MODE				CURRENT
	PATTERN			FILE_BASED
	FILENAME			/home/milindz/work/brain_model/poiss_14rows.txt
	TIME_FREQ_INCREMENT		0.0025	1
	FREQ_ROWS			14
	CELLS_PER_FREQ		1
	DYN_RANGE			0	400
	TIMING				EXACT
	SAMESEED			NO
	AMP_START			3
	WIDTH				0.001
	TIME_START			0
	TIME_END			0.05
	FREQ_START			999999
END_STIMULUS

STIMULUS_INJECT
	TYPE				poisson_stiminject1
	STIM_TYPE			poisson_stimulus1
	INJECT				AI_1 layer_E1 Excitatory s1 1.0
END_STIMULUS_INJECT

############################### Define Reports ###########################

REPORT
	TYPE				AI1_E1_Voltage
	CELLS				AI_1 layer_E1 Excitatory s1
	# Probability of No. of cells being selected = 100%
	PROB				1
	REPORT_ON			VOLTAGE
	FILENAME			AI1_E1_Voltage.txt
	ASCII
	FREQUENCY			1
	TIME_START			0.0
	TIME_END			1
END_REPORT

REPORT
	TYPE				AI1_E2_Voltage
	CELLS				AI_1 layer_E2 Excitatory s1
	PROB				1
	REPORT_ON			VOLTAGE
	FILENAME			AI1_E2_Voltage.txt
	ASCII
	FREQUENCY			1
	TIME_START			0.0
	TIME_END			1
END_REPORT

REPORT
	TYPE				AI1_I_Voltage
	CELLS				AI_1 layer_I Inhibitory s1
	PROB				1
	REPORT_ON			VOLTAGE
	FILENAME			AI1_I_Voltage.txt
	ASCII
	FREQUENCY			1
	TIME_START			0.0
	TIME_END			1
END_REPORT