{
  "manifest": {
    "$BASE_DIR": "${configdir}",
    "$OUTPUT_DIR": "$BASE_DIR/output",
    "$INPUT_DIR": "$BASE_DIR/inputs",
    "$NETWORK_DIR": "$BASE_DIR/network",
    "$COMPONENT_DIR": "$BASE_DIR/../biophys_components"
  },

  "run": {
    "tstop": 2000.0,
    "dt": 0.01,
    "dL": 20,
    "spike_threshold": -15,
    "nsteps_block":10000,
    "save_cell_vars": ["v","i_membrane"],
    "calc_ecp": false
  },

  "conditions": {
    "celsius": 34.0,
    "v_init": -80
  },

  "node_sets": {
    "save_cell_vars": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
  },

  "inputs": {
    "external_spikes": {
      "input_type": "spikes",
      "module": "nwb",
      "input_file": "$INPUT_DIR/stim_12_pulses.nwb",
      "node_set": "EXT",
      "trial": "trial_0"
    }
  },

  "output": {
    "log_file": "log.txt",
    "spikes_file": "spikes.h5",
    "spikes_file_csv": "spikes.csv",
    "output_dir": "$OUTPUT_DIR"
  },

  "reports": {
    "membrane_current": {
      "cells": "save_cell_vars",
      "variable_name": "i_membrane",
      "module": "membrane_report",
      "file_name": "i_membrane.h5",
      "sections": "soma",
      "enabled": true
    },

    "membrane_potential": {
      "cells": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
      "variable_name": "v",
      "module": "membrane_report",
      "file_name": "voltage.h5",
      "sections": "soma",
      "enabled": true
    },

    "syn_report": {
      "cells": "slice",
      "variable_name": "tau_FDR",
      "module": "netcon_report",
      "sections": "soma",
      "syn_type": "stp2syn"
    }
  },

  "target_simulator":"NEURON",

  "components": {
    "morphologies_dir": "$COMPONENT_DIR/morphologies",
    "synaptic_models_dir": "$COMPONENT_DIR/synaptic_models",
    "mechanisms_dir":"$COMPONENT_DIR/mechanisms",
    "biophysical_neuron_models_dir": "$COMPONENT_DIR/biophysical_neuron_templates",
    "point_neuron_models_dir": "$COMPONENT_DIR/point_neuron_templates"
  },

  "networks": {
    "nodes": [
      {
        "name": "slice",
        "nodes_file": "$NETWORK_DIR/slice_nodes.h5",
        "node_types_file": "$NETWORK_DIR/slice_node_types.csv"
      },
      {
        "name": "ext",
        "nodes_file": "$NETWORK_DIR/ext_nodes.h5",
        "node_types_file":  "$NETWORK_DIR/ext_node_types.csv"
      }

    ],

    "edges": [
      {
        "edges_file": "$NETWORK_DIR/ext_to_slice_edges.h5",
        "edge_types_file": "$NETWORK_DIR/ext_to_slice_edge_types.csv"
      }
    ]
  }
}
