simulation_simulation_config.json

{
  "manifest": {
    "$BASE_DIR": "${configdir}",
    "$OUTPUT_DIR": "$BASE_DIR/output"
  },
  "target_simulator": "NEURON",
  "run": {
    "tstart": 0.0,
    "tstop": 15000.0,
    "dt": 0.1,
    "dL": 20.0,
    "spike_threshold": -15.0,
    "nsteps_block": 5000
  },
  "conditions": {
    "celsius": 31.0,
    "v_init": -70.0
  },
  "inputs": {
    "vpsi_inh_spikes": {
      "input_type": "spikes",
      "module": "sonata",
      "input_file": "$BASE_DIR/vpsi_inh_spikes.h5",
      "node_set": "vpsi_inh"
    },
    "thalamus_pyr_spikes": {
      "input_type": "spikes",
      "module": "sonata",
      "input_file": "$BASE_DIR/thalamus_pyr_spikes.h5",
      "node_set": "thalamus_pyr"
    },
    "thalamus_som_spikes": {
      "input_type": "spikes",
      "module": "sonata",
      "input_file": "$BASE_DIR/thalamus_som_spikes.h5",
      "node_set": "thalamus_som"
    },
    "thalamus_cr_spikes": {
      "input_type": "spikes",
      "module": "sonata",
      "input_file": "$BASE_DIR/thalamus_cr_spikes.h5",
      "node_set": "thalamus_cr"
    },
    "shell_spikes": {
      "input_type": "spikes",
      "module": "sonata",
      "input_file": "$BASE_DIR/shell_spikes.h5",
      "node_set": "shell"
    }
  },
  "output": {
    "log_file": "log.txt",
    "output_dir": "$OUTPUT_DIR",
    "spikes_file": "spikes.h5"
  },
  "reports": {
    "v_report": {
      "variable_name": "v",
      "cells": "all",
      "module": "membrane_report",
      "sections": "soma"
    }
  },
  "node_sets_file": "$BASE_DIR/node_sets.json"
}