simulation_configECP_vpsi_vclamp.json

{
  "manifest": {
    "$BASE_DIR": "${configdir}",
    "$OUTPUT_DIR": "$BASE_DIR/outputECP",
    "$COMPONENTS_DIR": "$BASE_DIR/components"
  },
  "target_simulator": "NEURON",
  "run": {
    "tstart": 0.0,
    "tstop": 15000.0,
    "dt": 0.05,
    "dL": 200000.0,
    "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"
    },
    "pyr_vclamp": {
      "input_type": "voltage_clamp",
      "module": "SEClamp",
      "node_set": "vclamp_cells",
      "amps":[[0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0], [0,0,0]],
      "durations": [[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000],[100000, 100000, 100000]],
      "rs": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01]
    }
  },
  "output": {
    "log_file": "log.txt",
    "output_dir": "$OUTPUT_DIR",
    "spikes_file": "spikes.h5"
  },
  "reports": {

    "ecp": {
      "cells": "all",
      "variable_name": "v",
      "module": "extracellular",
      "electrode_positions": "$COMPONENTS_DIR/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp.h5",
      "electrode_channels": "all"
      },
    "syn_report": {
      "cells": [0,50,100,200,300,400,500,600,700,750],
      "variable_name": "igaba",
      "module": "netcon_report",
      "sections": "all",
      "syn_type": "interD2pyrD_SOM2P_STFD"
      },
    "membrane_report": {
      "cells": [0,50,100,200,300,400,500,600,700,750],
      "module": "membrane_report",
      "sections": "soma",
      "variable_name": ["v"],
      "file_name": "cell_vars.h5"
    },
    "control_syn_report": {
      "cells": [1,751],
      "variable_name": "igaba",
      "module": "netcon_report",
      "sections": "all",
      "syn_type": "interD2pyrD_SOM2P_STFD"
      },
    "control_membrane_report": {
      "cells": [1,751],
      "module": "membrane_report",
      "sections": "soma",
      "variable_name": ["v"],
      "file_name": "control_cell_vars.h5"
    }

  },
  "node_sets_file": "$BASE_DIR/node_sets.json",
  "network": "$BASE_DIR/circuit_config.json"
}