Biologically detailed neural network simulations and analysis.

Navigation

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

Project description

banner

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

Paper

JOSS

Zenodo

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 using the BlueCelluLab software for your research, please cite the following paper (including for poster presentations): BlueCelluLab: Biologically Detailed Neural Network Experimentation API

@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

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

Release history Release notifications | RSS feed

2.6.36

2.6.35

2.6.34

This version

2.6.33

2.6.32

2.6.31

2.6.30

2.6.29

2.6.28

2.6.26

2.6.23

2.6.22

2.6.21

2.6.20

2.6.19

2.6.18

2.6.17

2.6.16

2.6.15

2.6.14

2.6.13

2.6.12

2.6.11

2.6.10

2.6.9

2.6.8

2.6.7

2.6.6

2.6.5

2.6.4

2.6.3

2.6.2

2.6.1

2.6.0

2.5.11

2.5.10

2.5.9

2.5.8

2.5.7

2.5.6

2.5.5

2.5.4

2.5.3

2.5.0

2.4.1

2.4.0

2.3.7

2.3.6

2.3.5

2.3.4

2.3.3

2.3.2

2.3.1

2.2.7

2.2.6

2.2.5

2.2.4

2.2.3

2.2.2

2.2.1

2.2.0

2.1.0

2.0.3

2.0.2

2.0.1

2.0.0

1.8.6

1.8.5

1.8.4

1.8.3

1.8.2

1.8.1

1.8.0

1.7.6

1.7.5

1.7.4

1.7.3

1.7.2

1.7.1

1.7.0

1.6.5

1.6.4

1.6.3

1.6.2

1.6.1

1.6.0

1.5.3

1.5.2

1.5.1

1.5.0

1.4.1

1.3.16

1.3.15

1.3.14

1.3.13

1.3.12

1.3.11

1.3.10

1.3.9

1.3.8

1.3.7

1.3.6

1.3.5

1.3.4

1.3.3

1.3.2

1.3.1

1.3.0

1.2.9

1.2.8

1.2.7

1.2.6

1.2.5

1.2.4

1.2.3

1.2.2

1.2.1

1.2.0

1.1.1

1.1.0

1.0.3.dev1 pre-release

1.0.2

1.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bluecellulab-2.6.33.tar.gz (506.0 kB view details)

Uploaded Source

Built Distribution

bluecellulab-2.6.33-py3-none-any.whl (120.3 kB view details)

Uploaded Python 3

File details

Details for the file bluecellulab-2.6.33.tar.gz.

File metadata

  • Download URL: bluecellulab-2.6.33.tar.gz
  • Upload date:
  • Size: 506.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.0 CPython/3.12.5

File hashes

Hashes for bluecellulab-2.6.33.tar.gz
Algorithm Hash digest
SHA256 69c9c87fd1ec2380b28d9a9a227c956974ccc44820c59a3d5eeba2f37ce2b2ac
MD5 3fcb06c395d6074b9a212c42f1243511
BLAKE2b-256 b1163d2a8484634d46df5f618a00a4feaf7ee4175e0fed84e10cbc61e822519b

See more details on using hashes here.

File details

Details for the file bluecellulab-2.6.33-py3-none-any.whl.

File metadata

File hashes

Hashes for bluecellulab-2.6.33-py3-none-any.whl
Algorithm Hash digest
SHA256 0f384ee072889fdbcd120fa9172ae3ed20e5ad66ebc962cb46e777a990493a76
MD5 c3e2d2032671283e3a539b6440dea5fc
BLAKE2b-256 e6f216663551ec72c0a1f6d249dfc055c64ea20de9a329e9566700f21c9c16cf

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page