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

  "run": {
    "tstop": 4000.0,
    "dt": 0.1,
    "dL": 20.0,
    "spike_threshold": -15,
    "nsteps_block": 10000
  },

  "target_simulator":"NEURON",

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

  "node_sets": {
    "biophys_cells": {
      "model_type": "biophysical"
    },
    "virtual_cells": {
      "model_type": "virtual"
    }
  },

  "inputs": {
    "exc_spikes": {
      "input_type": "spikes",
      "module": "h5",
      "input_file": "$INPUT_DIR/exc_spike_trains.h5",
      "node_set": "virt"
    }
  },

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

  "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"
  },

  "reports": {
    "membrane_potential": {
      "cells": "biophys_cells",
      "variable_name": "v",
      "module": "membrane_report",
      "file_name": "v_report.h5",
      "sections": "soma"
    },

    "intracell_ca": {
      "cells": "biophys_cells",
      "variable_name": "cai",
      "module": "membrane_report",
      "file_name": "cai_report.h5",
      "sections": "soma"
    }
  },

    "networks": {
      "nodes": [
        {
          "nodes_file": "$NETWORK_DIR/bio_nodes.h5",
          "node_types_file": "$NETWORK_DIR/bio_node_types.csv"
        },
        {
          "nodes_file": "$NETWORK_DIR/virt_nodes.h5",
          "node_types_file": "$NETWORK_DIR/virt_node_types.csv"
        }
      ],

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