PointNet

PointNet is a simulation engine that utilizes NEST to run large-scale point neuron network models. Features including:

• Run the same simulation on a single core or in parallel on an HPC cluster with no extra programming required.

• Supports any spiking neuron models (rates models in development) available in NEST or with user contributed modules.

• Records neuron spiking, multi-meter recorded variables into the optimized SONATA data format.

Inputs

Inputs can be specified in the “inputs” sections of the simulation config, following the rules specified in the SONATA Data format.

Spike-Trains

Cells with model_type value virtual are equivalent to NEST’s spike_generator models which will play a pre-recorded series of spikes throughout the simulation. You may use either a SONATA spike-train file, an NWB file, or a space-separated csv file with columns node_id, population, and timestamps. Examples of how to create your own spike-train files can be found here.

{
    "LGN_spikes": {
        "input_type": "spikes",
        "module": "sonata",
        "input_file": "./inputs/lgn_spikes.h5",
        "node_set": {"population": "lgn"}
    }
}

• module: either sonata, hdf5, csv, or nwb: depending on the format of the spikes file

• node_set: used to filter which cells will receive the inputs

• input_file: path to file contain spike-trains for one or mode node

Current-Clamps

May use one step current clamp on multiple nodes, or have one node receive multiple current injections.

{
    "current_clamp_1": {
        "input_type": "current_clamp",
        "module": "IClamp",
        "node_set": "biophys_cells",
        "amp": 0.1500,
        "delay": 500.0,
        "duration": 500.0
    }
}

• module: Always IClamp

• node_set: used to filter which cells will receive the inputs

• amp: injection in pA

• delay: onset of current injection in ms

• duration: duration of current injection in ms

Outputs

Spikes

By default all non-virtual cells in the circuit will have all their spikes at the soma recorded.

Membrane and Intracellular Variables

Used to record the time trace of specific cell variables, usually the membrane potential (v). This is equivalent to NEST’s multimeter object.

{
    "membrane_potential": {
        "module": "multimeter_report",
        "cells": {"population": "V1"},
        "variable_name": "V_m"
        "file_name": "cai_traces.h5"
    }
}

• module: either mutlimeter_report or membrane_report, both the same

• variable_name: name of variable being recorded, will depend on the nest cell model.

• cells: a node_set filter out what cells to record.

• file_name: name of file where traces will be recorded, under the “output_dir”. If not specified the the report title

  will be used, eg “calcium_concentration.h5” and “membrane_potential.h5”