A package for modelling morphologically detailed neuronal microcircuits.
Project description
: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 git@github.com: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 boilerplate projects using:
bsb new
It will ask you some information about the project, like a name and configuration template
and set up the most suited directory structure and key files for you. Afterwards, cd
into your project folder:
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 should create a network file and plot 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.
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