bsb 4.0.0a2

A package for modelling morphologically detailed neuronal microcircuits.

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

The BSB requires Python 3.8+.

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 [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 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

Contributing

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

Known issues

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

The BSB determines the amount of NEST virtual processes 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.

Topology module scripting requires workarounds

If you're using the topology module to define regions and partitions from scripts you cannot use the child class constructors but have to use the root Region and Partition constructors with a cls kwarg and you will have to update the _partitions variable manually for regions:

from bsb.topology import Region, Partition

r = Region(cls="group", partitions=[])
r._partitions = []
p = Partition(cls="layer", region=r)
r._partitions.append(p)

Everything works fine from the config though so we recommend defining the topology in a config file while we work on a fix!