corebmtk 0.1.1

corebmtk

corebmtk

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

Currently, BMTK uses h.run and extracellular NEURON mechanisms, which are both incompatible with CoreNeuron.

corebmtk uses pc.psolve and takes an alternate approach to recording and storing output. The goal of this project was to maintain all of BMTK's functionality while allowing for the use of CoreNeuron. Recording modules remove the step phase and integrate into initialize and finalize to be compatilbe with pc.psolve.

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)

When using MPI you'll have to replace your config as well. This wrapper prevents loading of mechanisms prior to running with x86_64/special.

# conf = bionet.Config.from_json(config_file, validate=True)
conf = corebmtk.Config.from_json(config_file, validate=True)

Limitations

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

Implemented recording modules:

1. reports.SpikesReport
2. netcon_report
3. reports.MembraneReport (report.params['sections'] == 'soma')
4. reports.ECPReport

Modules NOT implemented

1. mods.MembraneReport (general)
2. reports.ClampReport
3. save_synapses

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"
    }

Acknowledgments

Thanks @gregglickert for kicking this project off.

BMTK