Scaffold: A scaffold model for the cerebellum

This package is intended to facilitate spatially, topologically and morphologically detailed simulations of the cerebellum developed by the Department of Brain and Behavioral Sciences at the University of Pavia.

Installation

Pip

This software can be installed as a Python package from PyPI through pip.

 pip install dbbs-scaffold

Usage

The scaffold model can be used through the command line interface or as a python package.

Command line interface (CLI)

Run the scaffold in the command line with subcommand compile to compile a network architecture.

scaffold --config=mouse_cerebellum.ini compile -p

To run with different configurations, change the config argument to the relative path of a .ini config file. The -p flag indicates that the compiled network should be plotted afterwards and can be omitted.

Python package

The central object is the scaffold.Scaffold class. This object requires a scaffold.config.ScaffoldConfig instance for its construction. To emulate the CLI functionality you can use the ScaffoldIniConfig class and provide the relative path to the configuration file.

from scaffold import Scaffold
from scaffold.config import ScaffoldIniConfig

config = new ScaffoldIniConfig('mouse_cerebellum.ini')
scaffoldInstance = new Scaffold(config)

This scaffold instance can then be used to perform the subcommands available in the CLI by calling their corresponding functions:

scaffoldInstance.compileNetworkArchitecture()

Plotting network architecture

After calling compileNetworkArchitecture the scaffold instance can be passed to plotNetwork from the scaffold.plotting module for plotting:

from scaffold.plotting import plotNetwork

plotNetwork(scaffoldInstance)