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BlueCelluLab
============
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| Latest Release | |pypi| |
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| Documentation | |docs| |
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| License | |license| |
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| Build Status | |tests| |
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| Gitter | |gitter| |
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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 <https://doi.org/10.21105/joss.07026>`_
.. 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 <https://zenodo.org/records/8113483>`_, which you can access via the "Cite this repository" button at the top of the repository page.
Support
=======
We are providing support on `Gitter <https://gitter.im/BlueBrain/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/BlueBrain/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.
Main dependencies
=================
* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_
* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_
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 <https://github.com/BlueBrain/BlueCelluLab/blob/main/examples/README.rst>`_.
API Documentation
=================
The API documentation can be found on `ReadTheDocs <https://bluecellulab.readthedocs.io>`_.
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 <https://github.com/BlueBrain/BlueCelluLab/blob/main/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 <https://www.apache.org/licenses/LICENSE-2.0.html>`_
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
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.. substitutions
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"description": "|banner|\n\nBlueCelluLab\n============\n\n+----------------+------------+\n| Latest Release | |pypi| |\n+----------------+------------+\n| Documentation | |docs| |\n+----------------+------------+\n| License | |license| |\n+----------------+------------+\n| Build Status \t | |tests| |\n+----------------+------------+\n| Coverage | |coverage| |\n+----------------+------------+\n| Gitter | |gitter| |\n+----------------+------------+\n| Paper | |joss| |\n+----------------+------------+\n| Zenodo | |zenodo| |\n+----------------+------------+\n\nThe Blue Brain Cellular Laboratory is designed for simulations and experiments on individual cells or groups of cells.\nSuitable use cases for BlueCelluLab include:\n\n* Scripting and statistical analysis for single cells or cell pairs.\n\n* Lightweight, detailed reporting on specific state variables after simulation.\n\n* Developing synaptic plasticity rules.\n\n* Validating dynamics of synaptic properties.\n\n* Automating in-silico whole-cell patching experiments.\n\n* Debugging, both scientifically and computationally.\n\nCitation\n========\n\nWhen using the BlueCelluLab software for your research, please cite the following paper (including for poster presentations): `BlueCelluLab: Biologically Detailed Neural Network Experimentation API <https://doi.org/10.21105/joss.07026>`_\n\n.. code-block::\n\n @article{Tuncel2024,\n doi = {10.21105/joss.07026},\n url = {https://doi.org/10.21105/joss.07026},\n year = {2024},\n publisher = {The Open Journal},\n volume = {9},\n number = {100},\n pages = {7026},\n author = {An\u0131l Tuncel and Werner Van Geit and Mike Gevaert and Benjamin Torben-Nielsen and Darshan Mandge and \u0130lkan K\u0131l\u0131\u00e7 and Aur\u00e9lien Jaquier and Eilif Muller and Lida Kanari and Henry Markram},\n title = {BlueCelluLab: Biologically Detailed Neural Network Experimentation API},\n journal = {Journal of Open Source Software}\n }\n\nIf you need to cite a specific version, please use the DOI provided by `Zenodo <https://zenodo.org/records/8113483>`_, which you can access via the \"Cite this repository\" button at the top of the repository page.\n\nSupport\n=======\n\nWe are providing support on `Gitter <https://gitter.im/BlueBrain/BlueCelluLab>`_. We suggest you create tickets on the `Github issue tracker <https://github.com/BlueBrain/BlueCelluLab/issues>`_ in case you encounter problems while using the software or if you have some suggestions.\n\nMain dependencies\n=================\n\n* `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`_\n* `Neuron 8.0.2+ <https://pypi.org/project/NEURON/>`_\n\nInstallation\n============\n\nBlueCelluLab can be pip installed with the following command:\n\n.. code-block:: python\n\n pip install bluecellulab\n\nQuick Start\n===========\n\nThe following example shows how to create a cell, add a stimulus and run a simulation:\n\n.. code-block:: python\n\n from bluecellulab.cell import create_ball_stick\n from bluecellulab import Simulation\n\n cell = create_ball_stick()\n sim = Simulation()\n sim.add_cell(cell)\n stimulus = cell.add_step(start_time=5.0, stop_time=20.0, level=0.5)\n\n sim.run(25, cvode=False)\n time, voltage = cell.get_time(), cell.get_soma_voltage()\n # plotting time and voltage ...\n\n.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png\n :alt: Voltage plot\n\nTutorial\n========\n\nA more detailed explanation on how to use BlueCelluLab, as well as other examples can be found on the `examples page <https://github.com/BlueBrain/BlueCelluLab/blob/main/examples/README.rst>`_.\n\nAPI Documentation\n=================\n\nThe API documentation can be found on `ReadTheDocs <https://bluecellulab.readthedocs.io>`_.\n\nRunning the tests\n=================\n\nTesting is set up using `tox`:\n\n.. code-block:: bash\n\n pip install tox\n\n tox -e py3 # runs the tests\n tox -e lint # runs the format checks\n\nContributing\n============\n\nWe welcome contributions to BlueCelluLab! Please see the `CONTRIBUTING.rst <https://github.com/BlueBrain/BlueCelluLab/blob/main/CONTRIBUTING.rst>`_ for guidelines on how to contribute.\n\nFunding & Acknowledgements\n==========================\n\nThe development and maintenance of this code is supported by funding to the Blue Brain Project, a research center of the \u00c9cole polytechnique f\u00e9d\u00e9rale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.\n\nCopyright\n=========\n\nCopyright (c) 2023-2024 Blue Brain Project/EPFL\n\nThis work is licensed under `Apache 2.0 <https://www.apache.org/licenses/LICENSE-2.0.html>`_\n\nFor 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.\n\nThe licenses of the morphology files used in this repository are available on: https://zenodo.org/record/5909613\n\n\n.. |license| image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg\n :target: https://github.com/BlueBrain/BlueCelluLab/blob/main/LICENSE\n\n.. |tests| image:: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml/badge.svg?branch=main\n :target: https://github.com/BlueBrain/BlueCelluLab/actions/workflows/test.yml\n :alt: CI\n\n.. |pypi| image:: https://img.shields.io/pypi/v/bluecellulab.svg\n :target: https://pypi.org/project/bluecellulab/\n :alt: latest release\n\n.. |docs| image:: https://readthedocs.org/projects/bluecellulab/badge/?version=latest\n :target: https://bluecellulab.readthedocs.io/\n :alt: latest documentation\n\n.. |coverage| image:: https://codecov.io/github/BlueBrain/BlueCelluLab/coverage.svg?branch=main\n :target: https://codecov.io/gh/BlueBrain/bluecellulab\n :alt: coverage\n\n.. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg\n :target: https://gitter.im/BlueBrain/BlueCelluLab\n :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab\n\n.. |joss| image:: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff/status.svg\n :target: https://joss.theoj.org/papers/effd553ca48734a2966d9d7ace3b05ff\n :alt: JOSS\n\n.. |zenodo| image:: https://zenodo.org/badge/640805129.svg\n :target: https://zenodo.org/badge/latestdoi/640805129\n\n..\n The following image is also defined in the index.rst file, as the relative path is\n different, depending from where it is sourced.\n The following location is used for the github README\n The index.rst location is used for the docs README; index.rst also defined an end-marker,\n to skip content after the marker 'substitutions'.\n\n.. substitutions\n.. |banner| image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/source/logo/BlueCelluLabBanner.jpg\n",
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