Note: The scaffold framework is still under heavy development. Please check the Known Issues section at the bottom for important issues that fell victim to our deadlines and will be solved at a later date.

BSB: A scaffold modelling framework

This package is intended to facilitate spatially, topologically and morphologically detailed simulations of brain regions 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 bsb

Developers

Developers best use pip's editable install. This creates a live link between the installed package and the local git repository:

 git clone git@github.com:dbbs-lab/bsb
 cd bsb
 pip install -e .[dev]
 pre-commit install

Usage

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

Command line interface (CLI)

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

bsb --config=mouse_cerebellum_cortex_noTouch.json compile -x=200 -z=200 -p

To run with different configurations, change the config argument to the relative path of a .json 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 bsb.core.Scaffold class. This object requires a bsb.config.ScaffoldConfig instance for its construction. To emulate the CLI functionality you can use the JSONConfig class and provide the relative path to the configuration file.

from bsb import Scaffold
from bsb.config import JSONConfig

config = new JSONConfig(file='mouse_cerebellum_cortex_noTouch.json')
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.compile_network()

Plotting network architecture

After calling compile_network the scaffold instance can be plotted:

scaffoldInstance.plot_network_cache()

Contributing

All contributions are very much welcome. Take a look at the contribution guide

Known issues

No configuration serialization

When modifying the config object through scripts and then saving it to file, you'll store the original configuration file text, and you won't actually serialize the modified object

We will fix this by version 4.0

If MPI is installed but mpi4py is not undefined behavior may occur

The amount of NEST virtual processes is determined by using mpi4py to get the amount of MPI processes. But if the package is not installed it is assumed no MPI simulations will be ran and the amount of virtual processes might be lower than expected when used in combination with OpenMP. Be sure to pip install using the [MPI] requirement tag.

lionelkusch/bsb