Metadata-Version: 2.1
Name: corebmtk
Version: 0.0.5
Summary: corebmtk
Home-page: https://github.com/tjbanks/corebmtk
Download-URL: 
Author: Tyler Banks
Author-email: tbanks@mail.missouri.edu
License: MIT
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

# 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. `reports.SpikesReport`
1. `netcon_report`
1. `reports.MembraneReport (report.params['sections'] == 'soma')`
1. `reports.ECPReport`

Modules NOT implemented

1. `mods.MembraneReport` (general)
1. `reports.ClampReport`
1. `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"
    }
```
