brian2modelfitting
Model fitting toolbox for the Brian 2 simulator
Science Score: 33.0%
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
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○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
4 of 8 committers (50.0%) from academic institutions -
○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords from Contributors
Repository
Model fitting toolbox for the Brian 2 simulator
Basic Info
- Host: GitHub
- Owner: brian-team
- License: other
- Language: Python
- Default Branch: master
- Homepage: https://brian2modelfitting.readthedocs.io
- Size: 2.15 MB
Statistics
- Stars: 17
- Watchers: 7
- Forks: 6
- Open Issues: 13
- Releases: 1
Metadata Files
README.md
brian2modelfitting
Model fitting toolbox for Brian 2 simulator.
The package brian2modelfitting allows the user to find the best fit of the unknown free parameters for recorded traces and spike trains. It also supports simulation-based inference, where instead of point-estimated parameter values, a full posterior distribution over the parameters is computed.
By default, the toolbox supports a range of global derivative-free optimization methods, that include popular methods for model fitting: differential evolution, particle swarm optimization and covariance matrix adaptation (provided by the Nevergrad, a gradient-free optimization platform) as well as Bayesian optimization for black box functions (provided by scikit-optimize, a sequential model-based optimization library). On the other hand, simulation-based inference is the process of finding parameters of a simulator from observations by taking a Bayesian approach via sequential neural posterior estimation, likelihood estimation or ration estimation (provided by the sbi), where neural densitiy estimator, a deep neural network allowing probabilistic association between the data and underlying parameter space, is trained. After the network is trained, the approximated posterior distribution is available.
Documentation
The full documentation is available at http://brian2modelfitting.readthedocs.org.
Testing status
Installation
Install brian2modelfitting from the Python package index via pip:
pip install brian2modelfitting
The basic install only supports the optimization methods provided by the Nevergrad library. To install additional
algorithms, support for simulation-based inference, and other features, you can install the optional dependencies:
| extra | description | install command |
|---------|---------------------------------------------------------------------------------------|-------------------------------------------|
| sbi | simulation-based inference with sbi | pip install 'brian2modelfitting[sbi]' |
| skopt | optimization with sckikit-optimize | pip install 'brian2modelfitting[skopt]' |
| algos | additional algorithms for Nevergrad | pip install 'brian2modelfitting[algos]' |
| efel | FeatureMetric with eFEL electrophysiology features | pip install 'brian2modelfitting[efel]' |
| test | framework to run the test suite | pip install 'brian2modelfitting[test]' |
| docs | framework to build the documentation | pip install 'brian2modelfitting[docs]' |
| all | all of the above dependencies | pip install 'brian2modelfitting[all]' |
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License
The model fitting toolbox is released under the terms of the CeCILL 2.1 license and is available here.
Use
Please report issues at the GitHub issue tracker or at the Brian 2 discussion forum.
Owner
- Name: Brian simulator
- Login: brian-team
- Kind: organization
- Location: Paris, France
- Website: https://briansimulator.org
- Repositories: 25
- Profile: https://github.com/brian-team
GitHub Events
Total
- Issues event: 1
- Watch event: 2
Last Year
- Issues event: 1
- Watch event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Marcel Stimberg | m****g@i****r | 225 |
| Aleksandra Teska | a****a@g****m | 148 |
| antelk | a****0@f****r | 117 |
| Eslam Khaled | e****4@g****m | 5 |
| romainbrette | r****e@i****r | 3 |
| Dan Goodman | d****b@t****t | 2 |
| Marcel Stimberg | m****g@s****r | 1 |
| thesamovar | d****n@e****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 40
- Total pull requests: 37
- Average time to close issues: 5 months
- Average time to close pull requests: 24 days
- Total issue authors: 8
- Total pull request authors: 5
- Average comments per issue: 1.1
- Average comments per pull request: 2.89
- Merged pull requests: 33
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mstimberg (20)
- romainbrette (9)
- bdevans (4)
- akapet00 (3)
- Jasmine969 (1)
- gvignoud (1)
- eslam69 (1)
- michmgee (1)
Pull Request Authors
- mstimberg (24)
- akapet00 (9)
- eslam69 (2)
- alTeska (1)
- pb663 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 19 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 3
pypi.org: brian2modelfitting
Modelfitting Toolbox for the Brian 2 simulator
- Homepage: https://github.com/brian-team/brian2modelfitting
- Documentation: https://brian2modelfitting.readthedocs.io/
- License: CeCILL-2.1
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Latest release: 0.4
published about 6 years ago
Rankings
Maintainers (3)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- brian2 >=2.2
- nevergrad >=0.4
- numpy >=1.21
- pandas *
- scikit-learn >=0.22
- tqdm *