corebmtk 0.0.4

corebmtk

corebmtk

A module to allow BMTK to function with Core Neuron before official support.

Installation

pip install --upgrade corebmtk

Usage

In your run_network.py BMTK script replace your BioSimulator with a CoreBioSimulator.

import corebmtk

# sim = bionet.BioSimulator.from_config(conf, network=graph)
sim = corebmtk.CoreBioSimulator.from_config(conf, network=graph)

Limitations

Some recoring mechanisms are not yet implemented. See run output for more info.

Implemented recording modules:

1. Spikes
2. Membrane recording
3. ECP

Troubleshooting

When using ECP recording: CoreNEURON cannot simulate a model that contains the extracellular mechanism

Change your ecp report to use "module": "ecp" instead of "module": "extracellular"

    "ecp": {
      "cells": "all",
      "variable_name": "v",
      "module": "ecp",
      "electrode_positions": "./components/recXelectrodes/linear_electrode.csv",
      "file_name": "ecp.h5",
      "electrode_channels": "all"
    }