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:orphan:
Configuration file
==================
Configuration file defines the files describing the network, its input as well as run-time parameters. For convenience it is grouped into the following categories:
Manifest
++++++++
Includes custom path variables that may be used to build full paths to files. The special variable "${configdir}" in the "$BASE_DIR" stands for the directory where configuration file is located. Users may specify any valid directory for "$BASE_DIR" as well.
::
"manifest": {
"$BASE_DIR": "${configdir}",
"$OUTPUT_DIR": "$BASE_DIR/output",
"$INPUT_DIR": "$BASE_DIR/../../NWB_files",
"$NETWORK_DIR": "$BASE_DIR/network",
"$COMPONENT_DIR":"$BASE_DIR/../components"
},
Run
+++
Includes run time parameters
::
"run": {
"tstop":3000.0, # run time (ms)
"dt": 0.1, # time step (ms)
"dL": 20, # length of compartments (i.e., segments) (um)
"overwrite_output_dir": true, # if True: will overwrite the output directory; if False: will issue an error that directory exists
"spike_threshold": -15, # will record a spike when membrane voltage (mV) is exceeded
"nsteps_block":5000, # will write to disk data after this many steps
"save_cell_vars": ["v", "cai"], # save somatic variables in the list
"calc_ecp": true # calculate ExtraCellular Potential (ECP): True or False
},
Conditions
++++++++++
Includes information about the initial conditions:
::
"conditions": {
"celsius": 34.0, # temperature (C)
"v_init": -80 # initial membrane voltage (mV)
},
Node_id selections
++++++++++++++++++
Defines selections of cells. For example, this way can specify the cells (node_ids) for which variables will be saved
::
"node_id_selections": {
"save_cell_vars": [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]
},
Input
+++++
Defines spike_trains for the the external inputs
::
"input": [
{
"type": "external_spikes",
"format": "nwb",
"file": "$INPUT_DIR/lgn_spikes.nwb",
"source_nodes": "LGN",
"trial": "trial_0"
},
...
]
Output
++++++
Defines file names for the output
::
"output": {
"log_file": "$OUTPUT_DIR/log.txt", # log file
"spikes_ascii_file": "$OUTPUT_DIR/spikes.txt", # file for spikes in ascii format
"spikes_hdf5_file": "$OUTPUT_DIR/spikes.h5", # file for spikes in HDF5 format
"cell_vars_dir": "$OUTPUT_DIR/cellvars", # folder to save variables from individual cells
"ecp_file": "$OUTPUT_DIR/ecp.h5", # file to save extracellular potential
"output_dir": "$OUTPUT_DIR" # output directory
},
Components
++++++++++
The "components" grouping includes paths to directories containing building blocks of a network model
::
"components": {
"morphologies_dir": "$COMPONENT_DIR/biophysical/morphology", # morphologies
"synaptic_models_dir": "$COMPONENT_DIR/synaptic_models", # synaptic models
"mechanisms_dir": "$COMPONENT_DIR/mechanisms", # NEURON mechanisms
"biophysical_neuron_models_dir":"$COMPONENT_DIR/biophysical/electrophysiology", # parameters of biophysical models
"point_neuron_models_dir": "$COMPONENT_DIR/intfire", # parameters of point neuron models
"templates_dir": "$COMPONENT_DIR/hoc_templates" # NEURON HOC templates
},
Recording Extracelullar Electrode
+++++++++++++++++++++++++++++++++
Includes parameters defining extracellular electrodes
::
"recXelectrode": {
"positions": "$COMPONENT_DIR/recXelectrodes/linear_electrode.csv"
},
Networks
++++++++
Includes files defining nodes and edges:
::
"networks": {
"nodes": [
{
"name": "V1",
"nodes_file": "$NETWORK_DIR/v1_nodes.h5",
"node_types_file": "$NETWORK_DIR/v1_node_types.csv"
},
...
],
"edges": [
{
"target": "V1",
"source": "V1",
"edges_file": "$NETWORK_DIR/v1_v1_edges.h5",
"edge_types_file": "$NETWORK_DIR/v1_v1_edge_types.csv"
},
...
]
}
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