corebmtk
Project description
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.
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:
reports.SpikesReport
netcon_report
reports.MembraneReport (report.params['sections'] == 'soma')
reports.ECPReport
Modules NOT implemented
mods.MembraneReport
(general)reports.ClampReport
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.
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