BlueCelluLab

BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)

https://github.com/bluebrain/bluecellulab

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Keywords from Contributors

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Biologically detailed neural network simulations and analysis API

README.rst

.. warning::
   The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
   Future development will take place at: https://github.com/openbraininstitute/BlueCelluLab

|banner|

BlueCelluLab
============

+----------------+------------+
| Latest Release | |pypi|     |
+----------------+------------+
| Documentation  | |docs|     |
+----------------+------------+
| License        | |license|  |
+----------------+------------+
| Build Status 	 | |tests|    |
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| Coverage       | |coverage| |
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| Gitter         | |gitter|   |
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| Paper          | |joss|     |
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| Zenodo         | |zenodo|   |
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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 using the BlueCelluLab software for your research, please cite the following paper (including for poster presentations): `BlueCelluLab: Biologically Detailed Neural Network Experimentation API `_

.. code-block::

    @article{Tuncel2024,
        doi = {10.21105/joss.07026},
        url = {https://doi.org/10.21105/joss.07026},
        year = {2024},
        publisher = {The Open Journal},
        volume = {9},
        number = {100},
        pages = {7026},
        author = {Anıl Tuncel and Werner Van Geit and Mike Gevaert and Benjamin Torben-Nielsen and Darshan Mandge and İlkan Kılıç and Aurélien Jaquier and Eilif Muller and Lida Kanari and Henry Markram},
        title = {BlueCelluLab: Biologically Detailed Neural Network Experimentation API},
        journal = {Journal of Open Source Software}
    }

If you need to cite a specific version, please use the DOI provided by `Zenodo `_, which you can access via the "Cite this repository" button at the top of the repository page.

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
=================

* `Python 3.8+ `_
* `Neuron 8.0.2+ `_

Installation
============

BlueCelluLab can be pip installed with the following command:

.. code-block:: python

    pip install bluecellulab

Quick Start
===========

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

.. code-block:: python

    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 ...

.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
   :alt: 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`:

.. code-block:: bash

    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.

Copyright
=========

Copyright (c) 2023-2024 Blue Brain Project/EPFL

This work is licensed under `Apache 2.0 `_

For MOD files for which the original source is available on ModelDB, any specific licenses on mentioned on ModelDB, or the generic License of ModelDB apply.

The licenses of the morphology files used in this repository are available on: https://zenodo.org/record/5909613


.. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
                :target: https://github.com/BlueBrain/BlueCelluLab/blob/main/LICENSE

.. |tests| image:: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main
   :target: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml
   :alt: CI

.. |pypi| image:: https://img.shields.io/pypi/v/bluecellulab.svg
               :target: https://pypi.org/project/bluecellulab/
               :alt: latest release

.. |docs| image:: https://readthedocs.org/projects/bluecellulab/badge/?version=latest
               :target: https://bluecellulab.readthedocs.io/
               :alt: latest documentation

.. |coverage| image:: https://codecov.io/github/BlueBrain/BlueCelluLab/coverage.svg?branch=main
                   :target: https://codecov.io/gh/BlueBrain/bluecellulab
                   :alt: coverage

.. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
                 :target: https://gitter.im/BlueBrain/BlueCelluLab
                 :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab

.. |joss| image:: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg
                :target: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff
                :alt: JOSS

.. |zenodo| image:: https://zenodo.org/badge/640805129.svg
                 :target: https://zenodo.org/badge/latestdoi/640805129

..
    The following image is also defined in the index.rst file, as the relative path is
    different, depending from where it is sourced.
    The following location is used for the github README
    The index.rst location is used for the docs README; index.rst also defined an end-marker,
    to skip content after the marker 'substitutions'.

.. substitutions
.. |banner| image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg

Owner

JOSS Publication

BlueCelluLab: Biologically Detailed Neural Network Experimentation API

Published

August 17, 2024

DOI

10.21105/joss.07026

Volume 9, Issue 100, Page 7026

Authors

Anıl Tuncel
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

Werner Van Geit
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland, Present address -> Foundation for Research on Information Technologies in Society (IT’IS), Zurich 8004, Switzerland

Mike Gevaert
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

Benjamin Torben-Nielsen
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland, Present address -> Roche Information Solutions, F. Hoffmann-La Roche AG, Basel, Switzerland

Darshan Mandge
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

İlkan Kılıç
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

Aurélien Jaquier
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

Eilif Muller
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland, Present address -> Université de Montréal, CHU Ste-Justine Research Center (Architectures of Biological Learning Lab), Montréal, Canada, Present address -> Mila Quebec AI Institute, Montréal, Canada

Lida Kanari
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland

Henry Markram
Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland, Laboratory of Neural Microcircuitry (LNMC), Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland

Editor

Beatriz Costa Gomes

Tags

neuroscience neural network simulation computational neuroscience SONATA NEURON Blue Brain Project

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Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "BlueCelluLab"
doi: 10.5281/zenodo.8113483
url: https://zenodo.org/doi/10.5281/zenodo.8113483
abstract: "The Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally."
authors:
  - family-names: "Tuncel"
    given-names: "Anil"
  - family-names: "Van Geit"
    given-names: "Werner"
  - family-names: "Gevaert"
    given-names: "Mike"
  - family-names: "Torben-Nielsen"
    given-names: "Benjamin"
  - family-names: "Mandge"
    given-names: "Darshan"
  - family-names: "Kilic"
    given-names: "Ilkan"
  - family-names: "Jaquier"
    given-names: "Aurélien"
  - family-names: "Muller"
    given-names: "Eilif"
  - family-names: "Kanari"
    given-names: "Lida"
  - family-names: "Markram"
    given-names: "Henry"
date-released: 2020-03-01
publisher: "Zenodo"

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