banner

BlueCelluLab

Latest Release

latest release

Documentation

latest documentation

License

license

Build Status

CI

Coverage

coverage

Gitter

Join the chat at https://gitter.im/openbraininstitute/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.

Copyright

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

Copyright (c) 2025 Open Brain Institute

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

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (2.6.100)

5 maintainers

PyPI data
Data sourced directly from PyPI's database.
Avatar for anilbey from gravatar.com anilbey Avatar for aurelienjaquier from gravatar.com aurelienjaquier Avatar for bbp.opensource from gravatar.com bbp.opensource
+2 more Avatar for ikilic from gravatar.com ikilic Avatar for obi.maintainer from gravatar.com obi.maintainer

Credits

Author: Blue Brain Project, EPFL

License

Apache Software License (Apache2.0)

Requires

Python >=3.10

Provides Extra

examples

Tags

computational neuroscience simulation analysis SONATA neural networks neuron Blue Brain Project

Classifiers

Report project as malware

Download files

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

Source Distribution

bluecellulab-2.6.99.tar.gz (568.7 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

bluecellulab-2.6.99-py3-none-any.whl (194.6 kB view details)

Uploaded Python 3

File details

Details for the file bluecellulab-2.6.99.tar.gz.

File metadata

  • Download URL: bluecellulab-2.6.99.tar.gz
  • Upload date:
  • Size: 568.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for bluecellulab-2.6.99.tar.gz
Algorithm Hash digest
SHA256 10f473a56aa292e6d5937ec0ba4e79ff02b89a46756d6d758512f5a28e859798
MD5 8f6751e89c07e21794293afcf41cb320
BLAKE2b-256 9e70b2690a75cabf1d0821a8bbb4bdc108d86793cf4038c73c7d7d709dd7e301

See more details on using hashes here.

File details

Details for the file bluecellulab-2.6.99-py3-none-any.whl.

File metadata

  • Download URL: bluecellulab-2.6.99-py3-none-any.whl
  • Upload date:
  • Size: 194.6 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for bluecellulab-2.6.99-py3-none-any.whl
Algorithm Hash digest
SHA256 ac94f5779fdbd6c032802f9599be0c5844966f22a2285a1912797b83245c7efb
MD5 96197082ae425cb22556c4709c1424c0
BLAKE2b-256 82e0240507c32e83bb38566eecba1fda6b1d1e1814673724659244804aae6f90

See more details on using hashes here.

Release history Release notifications | RSS feed

2.6.100

This release

2.6.99

2.6.98

2.6.97

2.6.96

2.6.95

2.6.94

2.6.93

2.6.92

2.6.91

2.6.90

2.6.89

2.6.88

2.6.87

2.6.86

2.6.85

2.6.84

2.6.83

2.6.82

2.6.81

2.6.80

2.6.79

2.6.78

2.6.77

2.6.76

2.6.75

2.6.74

2.6.73

2.6.72

2.6.71

2.6.70

2.6.69

2.6.68

2.6.67

2.6.66

2.6.65

2.6.64

2.6.63

2.6.62

2.6.61

2.6.60

2.6.59

2.6.58

2.6.57

2.6.56

2.6.55

2.6.54

2.6.53

2.6.52

2.6.51

2.6.50

2.6.49

2.6.48

2.6.47

2.6.46

2.6.45

2.6.44

2.6.43

2.6.42

2.6.41

2.6.40

2.6.39

2.6.38

2.6.37

2.6.36

2.6.35

2.6.34

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

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page