https://github.com/bluebrain/sonata-extension
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (9.0%) to scientific vocabulary
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Repository
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: apache-2.0
- Language: AGS Script
- Default Branch: master
- Homepage: https://sonata-extension.readthedocs.io/en/latest/
- Size: 5.16 MB
Statistics
- Stars: 3
- Watchers: 37
- Forks: 4
- Open Issues: 6
- Releases: 1
Topics
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/sonata-extension
sonata-extension
This documentation covers circuit and simulation related file format used at Blue Brain. It is an extension to the SONATA format as described per http://dx.doi.org/10.1371/journal.pcbi.1007696
As the Blue Brain Project aims at reconstructing the entire mouse brain this format has been extended to support:
- vasculature models
- glial cell models
- glia to glia cell connectivity
- tripartite neuroglial connectivity
- gliovascular connectivity
- neuromodulatory projections
- plasticity
- gap junctions
In addition, this documentation covers all the properties used by models delivered by the Blue Brain Project in more details compared to the original publication. Some technical extension have been added to improve composability of network models (model being built separately and assembled later).
The definition of the various stimuli and reports supported by Neuron and CoreNeuron are covered as well in more details than the original publication.
The reference implementation to load data for this extension is provided by libsonata
How-to:
- To update the documentation, update the rst files located in the source directory.
- To update the version number, modify the "version" entry in package.json.
- To locally build the documentation, just run
tox -e docs.
Funding & Acknowledgement
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) 2022-2024 Blue Brain Project/EPFL
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
- Delete event: 1
- Issue comment event: 2
- Push event: 6
- Pull request review event: 13
- Pull request review comment event: 9
- Pull request event: 5
- Create event: 3
Last Year
- Watch event: 1
- Delete event: 1
- Issue comment event: 2
- Push event: 6
- Pull request review event: 13
- Pull request review comment event: 9
- Pull request event: 5
- Create event: 3
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 15
- Total pull requests: 97
- Average time to close issues: 2 months
- Average time to close pull requests: 26 days
- Total issue authors: 6
- Total pull request authors: 17
- Average comments per issue: 4.67
- Average comments per pull request: 1.33
- Merged pull requests: 85
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 53
- Average time to close issues: about 2 months
- Average time to close pull requests: 20 days
- Issue authors: 2
- Pull request authors: 10
- Average comments per issue: 2.5
- Average comments per pull request: 1.09
- Merged pull requests: 49
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- anilbey (3)
- 1uc (1)
- james-isbister (1)
- mgeplf (1)
- KeremKurban (1)
- joni-herttuainen (1)
Pull Request Authors
- WeinaJi (21)
- matz-e (11)
- joni-herttuainen (9)
- mgeplf (9)
- joseph-tharayil (6)
- jorblancoa (5)
- KeremKurban (2)
- bbpgithubaudit (2)
- seirios (2)
- arnaudon (1)
- anilbey (1)
- GianlucaFicarelli (1)
- ferdonline (1)
- edasubert (1)
- eleftherioszisis (1)
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Dependencies
- sphinx >=2.0.0
- sphinx-autorun *
- sphinx-bluebrain-theme *