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A collection of scripts to assist with developing networks in BMTK (https://github.com/AllenInstitute/bmtk)
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bmtools
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README.md
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setup.py

README.md

bmtools

A collection of scripts to make developing networks in BMTK easier.

license

Getting Started

Installation

git clone https://github.com/tjbanks/bmtools
cd bmtools
python setup.py install

For developers who will be pulling down additional updates to this repository regularly use the following instead.

python setup.py develop

Example Use

> cd your_bmtk_model_directory
> python -m bmtools
Build, plot or debug BMTK models easily.

python -m bmtools.build
python -m bmtools.plot
python -m bmtools.debug
python -m bmtools.util

optional arguments:
  -h, --help  show this help message and exit
>  
> python -m bmtools.plot
Plot BMTK models easily.

python -m bmtools.plot

positional arguments:
  {positions,positions-old,connection-total,connection-divergence,connection-convergence,network-graph,raster,raster-old}
    positions           Plot cell positions for a given set of populations
    positions-old       Plot cell positions for hipp model (to be removed/model specific for testing)
    connection-total    Plot the total connection matrix for a given set of populations
    connection-divergence
                        Plot the connection percentage matrix for a given set of populations
    connection-convergence
                        Plot the connection convergence matrix for a given set of populations
    network-graph       Plot the connection graph for supplied targets (default:all)
    raster              Plot the spike raster for a given population
    raster-old          Plot the spike raster for hipp model (to be removed/model specific for testing)

optional arguments:
  -h, --help            show this help message and exit
>
> python -m bmtools.plot positions

bmtools

Planned future features

python -m bmtools.build
    Create a starting point network
    Download sample networks

python -m bmtools.plot
    Plot variable traces
    Plot spike rasters
    Plot cell positions
    Plot connection matricies
    
python -m bmtools.debug 
    list cell types available for single debug
    Run a single cell in the network
    Isolate a single cell in the network
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