https://github.com/biosimulators/biosimulators_test_suite
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Science Score: 23.0%
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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
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○Academic publication links
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✓Committers with academic emails
1 of 10 committers (10.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Keywords
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Repository
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Basic Info
- Host: GitHub
- Owner: biosimulators
- License: mit
- Language: Python
- Default Branch: dev
- Homepage: https://docs.biosimulators.org/Biosimulators_test_suite/
- Size: 56 MB
Statistics
- Stars: 7
- Watchers: 6
- Forks: 2
- Open Issues: 29
- Releases: 90
Topics
Metadata Files
README.md
BioSimulators test suite
The BioSimulators test suite is a tool for validating that biosimulation software tools implement the BioSimulators conventions for biosimulation tools.
The test suite is composed of two parts:
A collection of example modeling projects. Each project is represented by a single COMBINE/OMEX archive that contains one or more simulation experiments described using the Simulation Experiment Description Markup Language (SED-ML) and one or more models described using a format such as the BioNetGen Language (BNGL) or the Systems Biology Markup Language (SBML).
Software for checking that biosimulation tools execute these projects according to the BioSimulators conventions.
- Simulation tools support the BioSimulators standard command-line arguments.
- Simulation tools support the BioSimulators conventions for Docker images.
- Simulation tools follow the BioSimulators conventions for executing simulations described by SED-ML files in COMBINE/OMEX archives.
- Simulation tools support the BioSimulators conventions for the outputs of SED-ML files in COMBINE/OMEX archives.
Installation instructions, tutorial, and API documentation
Installation instructions, tutorial, and API documentation are available here.
License
The software in this package is released under the MIT License. The modeling projects in this package are released under the Creative Commons 1.0 Universal (CC0) license.
Development team
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, the https://health.uconn.edu/cell-analysis-modeling/ at the University of Connecticut, and the Center for Reproducible Biomedical Modeling with assistance from the contributors listed here.
Contributing to the test suite
We enthusiastically welcome contributions to the test suite! Please see the guide to contributing and the developer's code of conduct.
Acknowledgements
This work was supported by National Institutes of Health award P41EB023912.
Questions and comments
Please contact the BioSimulators Team with any questions or comments.
Owner
- Name: BioSimulators
- Login: biosimulators
- Kind: organization
- Email: info@biosimulators.org
- Location: USA
- Website: https://biosimulators.org
- Twitter: BioSimulators
- Repositories: 20
- Profile: https://github.com/biosimulators
Enabling more comprehensive and more predictive biological models through standardized simulation tools
GitHub Events
Total
- Delete event: 1
- Push event: 2
- Pull request event: 2
- Create event: 1
Last Year
- Delete event: 1
- Push event: 2
- Pull request event: 2
- Create event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Karr | j****r@g****m | 455 |
| biosimulatorsdaemon | b****n@g****m | 92 |
| Lucian Smith | l****h@u****u | 14 |
| Ryann Jordan | r****7@g****m | 6 |
| Logan Drescher | 1****r | 3 |
| Eran | a****n@g****m | 2 |
| Bilal Shaikh | b****2@g****m | 2 |
| GMarupilla | 5****a | 2 |
| GMarupilla | m****a@m****m | 1 |
| moraru | m****u | 1 |
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 53
- Total pull requests: 24
- Average time to close issues: 10 days
- Average time to close pull requests: 7 days
- Total issue authors: 7
- Total pull request authors: 7
- Average comments per issue: 0.98
- Average comments per pull request: 0.88
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 7
Past Year
- Issues: 1
- Pull requests: 9
- Average time to close issues: N/A
- Average time to close pull requests: about 1 month
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.78
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 7
Top Authors
Issue Authors
- jonrkarr (40)
- bilalshaikh42 (4)
- danv61 (3)
- moraru (2)
- CodeByDrescher (2)
- gmarupilla (1)
- luciansmith (1)
Pull Request Authors
- dependabot[bot] (13)
- jonrkarr (8)
- CodeByDrescher (4)
- luciansmith (3)
- bilalshaikh42 (1)
- eagmon (1)
- gmarupilla (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 607 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 89
- Total maintainers: 2
pypi.org: biosimulators-test-suite
Tools for validating that biosimulation tools are consistent with the BioSimulators standards
- Homepage: https://github.com/biosimulators/Biosimulators_test_suite
- Documentation: https://biosimulators-test-suite.readthedocs.io/
- License: MIT License (MIT)
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Latest release: 0.1.88
published over 2 years ago
Rankings
Maintainers (2)
Dependencies
- pydata-sphinx-theme *
- sphinx >=1.8
- sphinxprettysearchresults *
- GabrielBB/xvfb-action v1 composite
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/create-release v1 composite
- actions/setup-java v2 composite
- actions/setup-python v2 composite
- ad-m/github-push-action master composite
- codecov/codecov-action v2 composite
- eWaterCycle/setup-singularity v6 composite
- biosimulators_utils *
- PyPDF2 *
- biosimulators_utils >=0.1.172
- cement *
- docker *
- natsort *
- numpy <1.23.0
- python_dateutil *
- pyyaml *
- simplejson *
- termcolor *
- parameterized * test