Example declarative specificationΒΆ
Here is an example parameter file (in YAML) that specifies a full simulation:
params: {}
nest_params: {}
session_models:
params:
reset_network: false
record: true
shift_origin: false
nest_params: {}
even_rate:
params:
simulation_time: 50.0
unit_changes:
- layers:
- input_layer
population_name: input_exc
change_type: constant
from_array: false
nest_params:
rate: 100.0
nest_params: {}
warmup:
params:
reset_network: true
record: false
simulation_time: 50.0
unit_changes:
- layers:
- l1
population_name: null
change_type: constant
from_array: false
nest_params:
V_m: -70.0
- layers:
- input_layer
population_name: input_exc
change_type: constant
from_array: false
nest_params:
rate: 100.0
nest_params: {}
arbitrary_rate:
params:
simulation_time: 50.0
unit_changes:
- layers:
- input_layer
population_name: input_exc
change_type: constant
from_array: true
nest_params:
rate: ./input_layer_rates_5x5x1.npy
nest_params: {}
simulation:
params:
sessions:
- warmup
- even_rate
- arbitrary_rate
output_dir: ./output
input_dir: ./params/input
nest_params: {}
kernel:
params:
extension_modules: []
nest_seed: 94
nest_params:
local_num_threads: 20
resolution: 1.0
print_time: true
overwrite_files: true
network:
params: {}
nest_params: {}
neuron_models:
params: {}
nest_params: {}
ht_neuron:
params:
nest_model: ht_neuron
nest_params:
g_peak_NaP: 0.5
g_peak_h: 0.0
g_peak_T: 0.0
g_peak_KNa: 0.5
g_KL: 1.0
E_rev_NaP: 55.0
g_peak_AMPA: 0.1
g_peak_NMDA: 0.15
g_peak_GABA_A: 0.33
g_peak_GABA_B: 0.0132
instant_unblock_NMDA: true
S_act_NMDA: 0.4
V_act_NMDA: -58.0
cortical_inhibitory:
params: {}
nest_params:
theta_eq: -53.0
tau_theta: 1.0
tau_spike: 0.5
tau_m: 8.0
l1_inh:
params: {}
nest_params: {}
l2_inh:
params: {}
nest_params: {}
cortical_excitatory:
params: {}
nest_params:
theta_eq: -51.0
tau_theta: 2.0
tau_spike: 1.75
tau_m: 16.0
l1_exc:
params: {}
nest_params: {}
l2_exc:
params: {}
nest_params: {}
input_exc:
params:
nest_model: poisson_generator
nest_params: {}
layers:
params:
type: null
nest_params:
rows: 5
columns: 5
extent:
- 8.0
- 8.0
edge_wrap: true
input_area:
params:
type: InputLayer
add_parrots: true
nest_params: {}
input_layer:
params:
populations:
input_exc: 1
nest_params: {}
l1_area:
params: {}
nest_params: {}
l1:
params:
populations:
l1_exc: 2
l1_inh: 1
nest_params: {}
l2_area:
params: {}
nest_params: {}
l2:
params:
populations:
l2_exc: 2
l2_inh: 1
nest_params: {}
synapse_models:
params: {}
nest_params: {}
static_synapse:
params:
nest_model: static_synapse_lbl
nest_params: {}
input_synapse_NMDA:
params:
target_neuron: ht_neuron
receptor_type: NMDA
nest_params: {}
input_synapse_AMPA:
params:
target_neuron: ht_neuron
receptor_type: AMPA
nest_params: {}
ht_synapse:
params:
nest_model: ht_synapse
target_neuron: ht_neuron
nest_params: {}
GABA_B_syn:
params:
receptor_type: GABA_B
nest_params: {}
AMPA_syn:
params:
receptor_type: AMPA
nest_params: {}
GABA_A_syn:
params:
receptor_type: GABA_A
nest_params: {}
NMDA_syn:
params:
receptor_type: NMDA
nest_params: {}
topology:
params:
projections:
- source_layers:
- input_layer
source_population: parrot_neuron
target_layers:
- l1
target_population: l1_exc
projection_model: input_projection_AMPA
- source_layers:
- input_layer
source_population: parrot_neuron
target_layers:
- l1
target_population: l1_inh
projection_model: input_projection_AMPA
- source_layers:
- input_layer
source_population: parrot_neuron
target_layers:
- l1
target_population: l1_inh
projection_model: input_projection_NMDA
- source_layers:
- l1
source_population: l1_exc
target_layers:
- l1
target_population: l1_exc
projection_model: horizontal_exc
- source_layers:
- l1
source_population: l1_exc
target_layers:
- l1
target_population: l1_inh
projection_model: horizontal_exc
- source_layers:
- l1
source_population: l1_exc
target_layers:
- l2
target_population: l2_exc
projection_model: FF_exc
- source_layers:
- l1
source_population: l1_exc
target_layers:
- l2
target_population: l2_inh
projection_model: FF_exc
nest_params: {}
recorder_models:
params: {}
nest_params:
record_to:
- file
- memory
withgid: true
withtime: true
spike_detector:
params:
nest_model: spike_detector
nest_params: {}
weight_recorder:
params:
nest_model: weight_recorder
nest_params:
record_to:
- file
- memory
withport: false
withrport: true
multimeter:
params:
nest_model: multimeter
nest_params:
interval: 1.0
record_from:
- V_m
recorders:
params:
population_recorders:
- layers: []
populations: []
model: multimeter
- layers:
- l2
populations:
- l2_inh
model: multimeter
- layers: null
populations:
- l2_exc
model: multimeter
- layers:
- l1
populations: null
model: multimeter
- layers: null
populations: null
model: spike_detector
projection_recorders:
- source_layers:
- input_layer
source_population: parrot_neuron
target_layers:
- l1
target_population: l1_exc
projection_model: input_projection_AMPA
model: weight_recorder
- source_layers:
- l1
source_population: l1_exc
target_layers:
- l1
target_population: l1_exc
projection_model: horizontal_exc
model: weight_recorder
nest_params: {}
projection_models:
params:
type: topological
nest_params:
allow_autapses: false
allow_multapses: false
allow_oversized_mask: true
horizontal_inh:
params: {}
nest_params:
connection_type: divergent
synapse_model: GABA_A_syn
mask:
circular:
radius: 7.0
kernel:
gaussian:
p_center: 0.25
sigma: 7.5
weights: 1.0
delays:
uniform:
min: 1.75
max: 2.25
input_projection:
params: {}
nest_params:
connection_type: convergent
mask:
circular:
radius: 12.0
kernel: 0.8
weights: 1.0
delays:
uniform:
min: 1.75
max: 2.25
input_projection_AMPA:
params: {}
nest_params:
synapse_model: input_synapse_AMPA
input_projection_NMDA:
params: {}
nest_params:
synapse_model: input_synapse_NMDA
horizontal_exc:
params: {}
nest_params:
connection_type: divergent
synapse_model: AMPA_syn
mask:
circular:
radius: 12.0
kernel:
gaussian:
p_center: 0.05
sigma: 7.5
weights: 1.0
delays:
uniform:
min: 1.75
max: 2.25
FF_exc:
params: {}
nest_params:
connection_type: convergent
synapse_model: AMPA_syn
mask:
circular:
radius: 12.0
kernel: 0.8
weights: 1.0
delays:
uniform:
min: 1.75
max: 2.25