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release](https://img.shields.io/github/v/release/biosimulations/biomodels-qc)](https://github.com/biosimulations/biomodels-qc/releases)\n[![PyPI](https://img.shields.io/pypi/v/biomodels-qc)](https://pypi.org/project/biomodels-qc/)\n[![CI status](https://github.com/biosimulations/biomodels-qc/actions/workflows/ci.yml/badge.svg)](https://github.com/biosimulations/biomodels-qc/actions/workflows/ci.yml)\n[![Test coverage](https://codecov.io/gh/biosimulations/biomodels-qc/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulations/biomodels-qc)\n\n# BioModels-QC\nCommand-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.\n\nThe application can be installed locally or executed as a Docker image.\n\nThis application is intended to be used in conjuction with the best practices recommended [here](best-practices-for-curating-biomodels.md).\n\n## Local installation\n\n### Requirements\n* [Python](https://python.org) 3.9.0+\n* [pip](https://pip.pypa.io/) \u003e= 19.3\n* [Systems Biology Format Converter](http://sbfc.sourceforge.net/mediawiki/index.php/Main_Page)\n    * [Java](https://www.java.com/)\n* [Octave](https://www.gnu.org/software/octave/)\n    * [Mac OS installer](https://www.gnu.org/software/octave/download)\n    * Ubuntu: `apt-get install octave`\n    * [Windows installer](https://www.gnu.org/software/octave/download)\n* [Scilab](https://www.scilab.org/)\n    * [Mac OS installer](https://www.scilab.org/download/)\n    * Ubuntu: `apt-get install scilab`\n    * [Windows installer](https://www.scilab.org/download/)\n* [SVGLint](https://www.npmjs.com/package/svglint)\n    * [Node.js](https://nodejs.org/en/)\n        * [Mac OS installer](https://nodejs.org/en/download/)\n        * [Ubuntu instructions](https://github.com/nodesource/distributions/blob/master/README.md)\n        * [Windows installer](https://nodejs.org/en/download/)\n* [XPP](http://www.math.pitt.edu/~bard/xpp/xpp.html)\n    * [Mac OS instructions](http://www.math.pitt.edu/~bard/xpp/installonmac.html)\n    * Ubuntu: `apt-get install xppaut`\n    * [Windows instructions](http://www.math.pitt.edu/~bard/xpp/installonwindows.html)\n\nAfter installing the packages above, the following must be added to your system path:\n* `sbfConverter.sh` (Linux/Mac OS) or `sbfConverter.bat` (Windows)\n* `svglint`\n* `xppaut`\n\n### Installation\nRun the following command to install the package.\n```\npip install biomodels-qc\n```\n\n## Docker image\nRun the following command to pull the Docker image\n```\ndocker pull ghcr.io/biosimulations/biomodels_qc\n```\n\n## Tutorial\n\n### Convert the files for an entry to additional formats\nRun the following command to convert the files for an entry to additional formats such as BioPAX, MATLAB/Octave, and XPP.\n```\nENTRY_DIR=/path/to/directory-for-entry\nbiomodels-qc convert \"$ENTRY_DIR\"\n```\n\n### Validate an entry\nRun the following command to validate an entry of the BioModels database:\n```\nENTRY_DIR=/path/to/directory-for-entry\nbiomodels-qc validate \"$ENTRY_DIR\"\n```\n\n### Using the Docker image\nRun the following commands to use the BioModels-QC Docker image to execute the same conversion and validation operations.\n\n#### Convert the files for an entry to additional formats\n```\nENTRY_DIR=/path/to/directory-for-entry\\\ndocker run \\\n    --mount type=bind,source=\"$ENTRY_DIR\",target=/biomodels-entry \\\n    --interactive \\\n    --tty \\\n    --rm \\\n    ghcr.io/biosimulations/biomodels_qc \\\n        convert \\\n            /biomodels-entry\n```\n\n#### Validate an entry\n```\nENTRY_DIR=/path/to/directory-for-entry\nCONTAINER_TEMP_DIR=$(mktemp --directory)\ndocker run \\\n    --mount type=bind,source=\"$ENTRY_DIR\",target=/biomodels-entry \\\n    --volume /var/run/docker.sock:/var/run/docker.sock \\\n    --mount type=bind,source=\"$CONTAINER_TEMP_DIR\",target=/tmp \\\n    --env TEMP_DIR_HOST_PATH=$CONTAINER_TEMP_DIR \\\n    --interactive \\\n    --tty \\\n    --rm \\\n    ghcr.io/biosimulations/biomodels_qc \\\n        validate \\\n            /biomodels-entry\n```\n\n## Documentation\nDocumentation for the command-line program is available inline.\n\nRun the following command to obtain the help.\n```\nbiomodels-qc --help\n```\n\n### Using the Docker image\nRun the following command to use the BioModels-QC Docker image to obtain the help.\n```\ndocker run \\\n    --interactive \\\n    --tty \\\n    --rm \\\n    ghcr.io/biosimulations/biomodels_qc \\\n        --help\n```\n\n## API documentation\nAPI documentation is available [here](https://biosimulations.github.io/biomodels-qc/).\n\n## License\nThis package is released under the [MIT license](LICENSE).\n\n## Development team\nThis 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).\n\n## Contributing to BioModels-QC\nWe enthusiastically welcome contributions! Please see the [guide to contributing](CONTRIBUTING.md) and the [developer's code of conduct](CODE_OF_CONDUCT.md).\n\n## Acknowledgements\nThis work was supported by National Institutes of Health award P41EB023912.\n\n## Questions and comments\nPlease contact the [BioSimulations Team](mailto:info@biosimulations.org) with any questions or comments.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulations%2Fbiomodels-qc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosimulations%2Fbiomodels-qc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulations%2Fbiomodels-qc/lists"}