bsb-core

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

BSB: A component framework for neural modelling

Developed by the Department of Brain and Behavioral Sciences at the University of Pavia, the BSB is a component framework for neural modelling, which focuses on component declarations to piece together a model. The component declarations can be made in any supported configuration language, or using the library functions in Python. It offers parallel reconstruction and simulation of any network topology, placement and/or connectivity strategy.

Installation

The BSB requires Python 3.9+.

pip

Any package in the BSB ecosystem can be installed from PyPI through pip. Most users will want to install the main bsb framework:

pip install "bsb"

Advanced users looking to control install an unconventional combination of plugins might be better off installing just this package, and the desired plugins:

pip install "bsb-core"

Note that installing bsb-core does not come with any plugins installed and the usually available storage engines, or configuration parsers will be missing.

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-core
 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

This will create a my_model folder for you with some starter files. It should contain:

• network_configuration.yaml: A configuration file in which your network will be described.
• A pyproject.toml file: This file uses the TOML syntax to set configuration values for the BSB.
• A placement.py and connectome.py files if you want to make your own components.

Reconstructing a network

Within your project folder, you can create reconstructions of your model, generating cell positions and connections:

bsb compile

The compile command should produce a network file located in your project folder based on your configuration file.

Simulating a network

The starter project contains no simulation configuration but the documentation provides tutorials for the neural simulators supported by the BSB.

Contributing

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

Acknowledgements

This research has received funding from the European Union’s Horizon 2020 Framework Program for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3) and Specific Grant Agreement No. 785907 (Human Brain Project SGA2) and from Centro Fermi project “Local Neuronal Microcircuits” to ED. The project is also receiving funding from the Virtual Brain Twin Project under the European Union's Research and Innovation Program Horizon Europe under grant agreement No 101137289.

We acknowledge the use of EBRAINS platform and Fenix Infrastructure resources, which are partially funded from the European Union’s Horizon 2020 research and innovation programme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project) and through the ICEI project under the grant agreement No. 800858 respectively.

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