https://github.com/bluebrain/connectome-analysis
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 5 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: agpl-3.0
- Language: Jupyter Notebook
- Default Branch: master
- Size: 31.7 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
[!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/connectome-analysis
Connectome Analysis
General functions to analyze connectomes from a topological perspective.
Documentation
See our documentation for detailed explanations including examples and tutorials.
See our source code for implementation details.
User installation
sh
pip install git+https://github.com/danielaegassan/connectome_analysis.git
Citation
If you use this software, kindly use the following BibTeX entry for citation:
@article{egas2024efficiency,
title={Efficiency and reliability in biological neural network architectures},
author={Egas Santander, Daniela and Pokorny, Christoph and Ecker, Andr{\'a}s and Lazovskis, J{\=a}nis and Santoro, Matteo and Smith, Jason P and Hess, Kathryn and Levi, Ran and Reimann, Michael W},
journal={bioRxiv},
pages={2024--03},
year={2024},
publisher={Cold Spring Harbor Laboratory},
doi = {10.1101/2024.03.15.585196}
}
Acknowledgements & Funding
The development of this software was 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 (c) 2023 Blue Brain Project / EPFL.
Development installation
- Clone this repository
Requirements:
Create a virtual environment and install the dependencies
sh
poetry install
CMake may have difficulties to find the right compilers to compile the C++ code. If that is the case, you have to specify the path to the compilers yourself:
sh
CC=/path/to/gcc CXX=/path/to/g++ poetry install
This is especially important on MacOS.
- Activate the virtual environment
sh
poetry shell
- Testing
sh
poetry run pytest tests
Documentation
The documentation is automatically generated from the content of the docs directory and from the docstrings of the public signatures of the source code. The documentation is updated and published as a Github project page automatically as part each release.
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
GitHub Events
Total
- Watch event: 1
- Fork event: 1
Last Year
- Watch event: 1
- Fork event: 1
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/setup-python v2 composite
- ./.github/actions/python-poetry-env * composite
- EndBug/add-and-commit v7 composite
- actions/checkout v2 composite
- actions/create-release v1 composite
- ./.github/actions/python-poetry-env * composite
- actions/checkout v2 composite
- ./.github/actions/python-poetry-env * composite
- actions/checkout v2 composite
- 163 dependencies
- black * develop
- jupyter ^1.0.0 develop
- mkdocs-material * develop
- mkdocstrings >=0.18 develop
- pytest * develop
- pytest-cov * develop
- pytest-github-actions-annotate-failures * develop
- seaborn * develop
- bigrandomgraphs >=0.0.4
- matplotlib *
- networkx *
- numpy *
- pandas *
- progressbar 2.5
- pyflagser *
- pyflagsercount >=0.2.41
- python >=3.8.3, <4
- scipy *
- tables *
- tqdm *
- bigrandomgraphs ==0.0.3
- blosc2 ==2.0.0
- cmake ==3.28.3
- colorama ==0.4.6
- contourpy ==1.1.1
- cycler ==0.12.1
- cython ==3.0.9
- fonttools ==4.50.0
- importlib-resources ==6.3.2
- kiwisolver ==1.4.5
- matplotlib ==3.7.5
- msgpack ==1.0.8
- networkx ==3.1
- numexpr ==2.8.6
- numpy ==1.24.4
- packaging ==24.0
- pandas ==2.0.3
- pillow ==10.2.0
- progressbar ==2.5
- py-cpuinfo ==9.0.0
- pyflagser ==0.4.5
- pyflagsercount ==0.4.0
- pyparsing ==3.1.2
- python-dateutil ==2.9.0.post0
- pytz ==2024.1
- scipy ==1.9.3
- six ==1.16.0
- tables ==3.8.0
- tqdm ==4.66.2
- tzdata ==2024.1
- zipp ==3.18.1