Biologically detailed neural network simulations and analysis.

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  • License: Apache Software License (Apache2.0)
  • Author: Blue Brain Project, EPFL
  • Tags computational neuroscience, simulation, analysis, SONATA, neural networks, neuron, Blue Brain Project
  • Requires: Python >=3.8
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BlueCelluLab

Latest Release

latest release

Documentation

latest documentation

License

license

Build Status

CI

Coverage

coverage

Gitter

Join the chat at https://gitter.im/BlueBrain/BlueCelluLab

Citation

zenodo

The Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells. Suitable use cases for BlueCelluLab include:

  • Scripting and statistical analysis for single cells or cell pairs.

  • Lightweight, detailed reporting on specific state variables after simulation.

  • Developing synaptic plasticity rules.

  • Validating dynamics of synaptic properties.

  • Automating in-silico whole-cell patching experiments.

  • Debugging, both scientifically and computationally.

Citation

When you use this BlueCelluLab software for your research, we ask you to cite the following reference(this includes poster presentations):

@software{bluecellulab_zenodo,
  author       = {Tuncel, Anil and Van Geit, Werner and Gevaert, Mike and Torben-Nielsen, Benjamin and Mandge, Darshan and Kilic, Ilkan and Jaquier, Aurélien and Muller, Eilif and Kanari, Lida and Markram, Henry},
  title        = {BlueCelluLab},
  month        = jul,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.8113483},
  url          = {https://doi.org/10.5281/zenodo.8113483}
}

Support

We are providing support on Gitter. We suggest you create tickets on the Github issue tracker in case you encounter problems while using the software or if you have some suggestions.

Main dependencies

Installation

BlueCelluLab can be pip installed with the following command:

pip install bluecellulab

Quick Start

The following example shows how to create a cell, add a stimulus and run a simulation:

from bluecellulab.cell import create_ball_stick
from bluecellulab import Simulation

cell = create_ball_stick()
sim = Simulation()
sim.add_cell(cell)
stimulus = cell.add_step(start_time=5.0, stop_time=20.0, level=0.5)

sim.run(25, cvode=False)
time, voltage = cell.get_time(), cell.get_soma_voltage()
# plotting time and voltage ...
Voltage plot

Tutorial

A more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the examples page.

API Documentation

The API documentation can be found on ReadTheDocs.

Running the tests

Testing is set up using tox:

pip install tox

tox -e py3  # runs the tests
tox -e lint  # runs the format checks

Contributing

We welcome contributions to BlueCelluLab! Please see the CONTRIBUTING.rst for guidelines on how to contribute.

Funding & Acknowledgements

The development and maintenance of this code is supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for anilbey from gravatar.com anilbey Avatar for aurelienjaquier from gravatar.com aurelienjaquier Avatar for ikilic from gravatar.com ikilic

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: Apache Software License (Apache2.0)
  • Author: Blue Brain Project, EPFL
  • Tags computational neuroscience, simulation, analysis, SONATA, neural networks, neuron, Blue Brain Project
  • Requires: Python >=3.8
Classifiers

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2.6.36

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