bsb 4.0.0a22

A package for modelling morphologically detailed neuronal microcircuits.

:closed_book: Read the documentation on https://bsb.readthedocs.io/en/latest

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

The BSB requires Python 3.8+.

pip

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

pip install "bsb>=4.0.0a0"

Developers

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

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

Usage

The scaffold framework is best used in a project context. Create a working directory for each of your modelling projects and use the command line to configure, reconstruct or simulate your models.

Creating a project

You can create a quickstart project using:

bsb new my_model --quickstart
cd my_model

Reconstructing a network

You can use your project to create reconstructions of your model, generating cell positions and connections:

bsb compile -p

This creates a network file and plots the network.

Simulating a network

The default project currently contains no simulation config.

Contributing

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

Known issues

Simulation interfaces are not reinstated yet in v4

Shouldn't be much work, famous last words.