https://github.com/biosimulations/biomodels-qc
Quality control tool for the BioModels repository of biochemical models
https://github.com/biosimulations/biomodels-qc
biomodels computational-model numerical-simulation quality-control systems-biology testing validation
Last synced: 2 months ago
JSON representation
Quality control tool for the BioModels repository of biochemical models
- Host: GitHub
- URL: https://github.com/biosimulations/biomodels-qc
- Owner: biosimulations
- License: mit
- Created: 2022-03-29T14:32:02.000Z (about 4 years ago)
- Default Branch: dev
- Last Pushed: 2025-05-21T18:33:40.000Z (about 1 year ago)
- Last Synced: 2026-01-27T14:57:22.169Z (4 months ago)
- Topics: biomodels, computational-model, numerical-simulation, quality-control, systems-biology, testing, validation
- Language: Python
- Homepage: https://biosimulations.github.io/biomodels-qc
- Size: 17.9 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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# BioModels-QC
Command-line application for quality controlling entries in the [BioModels database](https://www.ebi.ac.uk/biomodels/) and converting the primary files for entries in the database into additional formats such as BioPAX, MATLAB/Octave, and XPP.
The application can be installed locally or executed as a Docker image.
This application is intended to be used in conjuction with the best practices recommended [here](best-practices-for-curating-biomodels.md).
## Local installation
### Requirements
* [Python](https://python.org) 3.9.0+
* [pip](https://pip.pypa.io/) >= 19.3
* [Systems Biology Format Converter](http://sbfc.sourceforge.net/mediawiki/index.php/Main_Page)
* [Java](https://www.java.com/)
* [Octave](https://www.gnu.org/software/octave/)
* [Mac OS installer](https://www.gnu.org/software/octave/download)
* Ubuntu: `apt-get install octave`
* [Windows installer](https://www.gnu.org/software/octave/download)
* [Scilab](https://www.scilab.org/)
* [Mac OS installer](https://www.scilab.org/download/)
* Ubuntu: `apt-get install scilab`
* [Windows installer](https://www.scilab.org/download/)
* [SVGLint](https://www.npmjs.com/package/svglint)
* [Node.js](https://nodejs.org/en/)
* [Mac OS installer](https://nodejs.org/en/download/)
* [Ubuntu instructions](https://github.com/nodesource/distributions/blob/master/README.md)
* [Windows installer](https://nodejs.org/en/download/)
* [XPP](http://www.math.pitt.edu/~bard/xpp/xpp.html)
* [Mac OS instructions](http://www.math.pitt.edu/~bard/xpp/installonmac.html)
* Ubuntu: `apt-get install xppaut`
* [Windows instructions](http://www.math.pitt.edu/~bard/xpp/installonwindows.html)
After installing the packages above, the following must be added to your system path:
* `sbfConverter.sh` (Linux/Mac OS) or `sbfConverter.bat` (Windows)
* `svglint`
* `xppaut`
### Installation
Run the following command to install the package.
```
pip install biomodels-qc
```
## Docker image
Run the following command to pull the Docker image
```
docker pull ghcr.io/biosimulations/biomodels_qc
```
## Tutorial
### Convert the files for an entry to additional formats
Run the following command to convert the files for an entry to additional formats such as BioPAX, MATLAB/Octave, and XPP.
```
ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc convert "$ENTRY_DIR"
```
### Validate an entry
Run the following command to validate an entry of the BioModels database:
```
ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc validate "$ENTRY_DIR"
```
### Using the Docker image
Run the following commands to use the BioModels-QC Docker image to execute the same conversion and validation operations.
#### Convert the files for an entry to additional formats
```
ENTRY_DIR=/path/to/directory-for-entry\
docker run \
--mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
--interactive \
--tty \
--rm \
ghcr.io/biosimulations/biomodels_qc \
convert \
/biomodels-entry
```
#### Validate an entry
```
ENTRY_DIR=/path/to/directory-for-entry
CONTAINER_TEMP_DIR=$(mktemp --directory)
docker run \
--mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
--volume /var/run/docker.sock:/var/run/docker.sock \
--mount type=bind,source="$CONTAINER_TEMP_DIR",target=/tmp \
--env TEMP_DIR_HOST_PATH=$CONTAINER_TEMP_DIR \
--interactive \
--tty \
--rm \
ghcr.io/biosimulations/biomodels_qc \
validate \
/biomodels-entry
```
## Documentation
Documentation for the command-line program is available inline.
Run the following command to obtain the help.
```
biomodels-qc --help
```
### Using the Docker image
Run the following command to use the BioModels-QC Docker image to obtain the help.
```
docker run \
--interactive \
--tty \
--rm \
ghcr.io/biosimulations/biomodels_qc \
--help
```
## API documentation
API documentation is available [here](https://biosimulations.github.io/biomodels-qc/).
## License
This package is released under the [MIT license](LICENSE).
## Development team
This package was developed by the [Karr Lab](https://karrlab.org) at the Icahn School of Medicine at Mount Sinai and the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org).
## Contributing to BioModels-QC
We enthusiastically welcome contributions! Please see the [guide to contributing](CONTRIBUTING.md) and the [developer's code of conduct](CODE_OF_CONDUCT.md).
## Acknowledgements
This work was supported by National Institutes of Health award P41EB023912.
## Questions and comments
Please contact the [BioSimulations Team](mailto:info@biosimulations.org) with any questions or comments.