https://github.com/alleninstitute/sonata
Collaboration between BBP and AIBS
Science Score: 67.0%
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
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: plos.org -
✓Committers with academic emails
8 of 13 committers (61.5%) from academic institutions -
✓Institutional organization owner
Organization alleninstitute has institutional domain (alleninstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary
Keywords from Contributors
Repository
Collaboration between BBP and AIBS
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- License: bsd-3-clause
- Language: Python
- Default Branch: master
- Size: 139 MB
Statistics
- Stars: 57
- Watchers: 20
- Forks: 36
- Open Issues: 38
- Releases: 0
Metadata Files
README.md
SONATA Data Format
The SONATA Data Format is a Scalable Open Data Format for multiscale neuronal network models and simulation output, jointly developed by the Allen Institute for Brain Science (AIBS) and the Blue Brain Project (BBP) of the École polytechnique fédérale de Lausanne (EPFL).
The design and architecture of SONATA builds on both organizations’ expertise with large-scale high-performance network simulation, visualization and analysis. It was designed for memory and computational efficiency, as well as to work across multiple platforms. Even though AIBS and BBP use different approaches to modeling and use different tools, the format allows networks built by one institute to be simulated by the other and vice versa. We provide specification documentation, open-source reference APIs, and model and simulation output examples with the intention of catalyzing support and adoption of the format in the modeling community.
We really welcome user input, please use our user survey form. Registering allows us to communicate with SONATA users and is encouraged, but not required: registration link.
The SONATA Data Format provides:
Facilities for representing nodes (cells) and edges (synapses/junctions) of a network. It uses table-based data structures, hdf5 and csv, to represent nodes, edges and their respective properties. Furthermore, indexing procedures are specified to enable fast, parallelizable, and efficient partial lookup of individual nodes and edges. The use of hdf5 provides efficiency both in file size and IO time. The format includes specific properties and naming conventions, but also allows modelers to extend node and edge model properties as they desire, to ensure models can be used with a variety of simulation frameworks and use cases.
A JSON-based file format for configuring simulations, including specifying variables to record from, and stimuli to apply.
A systematic schema for describing simulation output/reports making it easy for users to exchange their simulation output data, and moreover the underlying hdf5 based format permits efficient storage of variables such as spike times, membrane potential, and Ca2+ concentration.
For further details on SONATA, see:
https://github.com/AllenInstitute/sonnet/blob/master/docs/SONATADEVELOPERGUIDE.md
See the paper about SONATA: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007696.
Please cite SONATA as follows:
Dai et al. The SONATA data format for efficient description of large-scale network models. PLoS Comput Biol 16(2): e1007696. https://doi.org/10.1371/journal.pcbi.1007696
Software Development Tools
pySONATA - A Python based API for reading and writing SONATA files.
libSONATA - A C++ API for reading SONATA files, with Python bindings.
NDX Simulation Output - An NWB extension for converting NWB:N files to and from SONATA.
Software that has SONATA support (not exhaustive)
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Watch event: 4
Last Year
- Watch event: 4
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| kaeld | k****d@a****g | 40 |
| Juan Hernando Vieites | j****o@e****h | 34 |
| Padraig Gleeson | p****n@g****m | 12 |
| Arseny V. Povolotsky | a****y@e****h | 10 |
| eilif | e****r@e****h | 4 |
| xpliu16 | x****6@g****m | 4 |
| kael | y****u@e****m | 2 |
| Andrew Davison | a****n@u****r | 2 |
| alex4200 | a****z@e****h | 2 |
| Aleksei Sanin | a****n@e****h | 2 |
| Mizzou Neuro | l****b@m****u | 1 |
| Nicolai Haug | n****g@y****m | 1 |
| Sergey Gratiy | s****g@a****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 56
- Total pull requests: 47
- Average time to close issues: 10 months
- Average time to close pull requests: 3 months
- Total issue authors: 14
- Total pull request authors: 16
- Average comments per issue: 4.3
- Average comments per pull request: 0.57
- Merged pull requests: 35
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pgleeson (17)
- salvadord (9)
- hernando (8)
- arsenius7 (7)
- asanin-epfl (3)
- kaeldai (2)
- wvangeit (2)
- Hjorthmedh (2)
- chr-pok (1)
- SteMasoli (1)
- anirban6908 (1)
- maartensc (1)
- alex4200 (1)
- JY-Gao (1)
Pull Request Authors
- kaeldai (19)
- hernando (5)
- arsenius7 (4)
- asanin-epfl (3)
- pgleeson (3)
- apdavison (3)
- MarikeReimer (2)
- mgeplf (1)
- alex4200 (1)
- nicolossus (1)
- matz-e (1)
- alkino (1)
- latimerb (1)
- joni-herttuainen (1)
- wvangeit (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 143 last-month
- Total dependent packages: 1
- Total dependent repositories: 2
- Total versions: 2
- Total maintainers: 1
pypi.org: sonata
SONATA Data Format API
- Homepage: https://github.com/AllenInstitute/sonata
- Documentation: https://sonata.readthedocs.io/
- License: BSD License
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Latest release: 0.0.2
published over 6 years ago