Command-line application for quality controlling entries in the BioModels database 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.
- Python 3.9.0
- pip >= 19.3
- Systems Biology Format Converter
- Octave
- Mac OS installer
- Ubuntu:
apt-get install octave
- Windows installer
- Scilab
- Mac OS installer
- Ubuntu:
apt-get install scilab
- Windows installer
- SVGLint
- XPP
- Mac OS instructions
- Ubuntu:
apt-get install xppaut
- Windows instructions
After installing the packages above, the following must be added to your system path:
sbfConverter.sh
(Linux/Mac OS) orsbfConverter.bat
(Windows)svglint
xppaut
Run the following command to install the package.
pip install biomodels-qc
Run the following command to pull the Docker image
docker pull ghcr.io/biosimulations/biomodels_qc
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 "$ENTRY_DIR"
Run the following command to validate an entry of the BioModels database:
ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc validate "$ENTRY_DIR"
Run the following commands to use the BioModels-QC Docker image to execute the same conversion and validation operations.
ENTRY_DIR=/path/to/directory-for-entry\
docker run \
--mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
--interactive \
--tty \
--rm \
ghcr.io/biosimulations/biomodels_qc \
convert \
/biomodels-entry
ENTRY_DIR=/path/to/directory-for-entry
CONTAINER_TEMP_DIR=$(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 for the command-line program is available inline.
Run the following command to obtain the help.
biomodels-qc --help
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 is available here.
This package is released under the MIT license.
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai and the Center for Reproducible Biomedical Modeling.
We enthusiastically welcome contributions! Please see the guide to contributing and the developer's code of conduct.
This work was supported by National Institutes of Health award P41EB023912.
Please contact the BioSimulations Team with any questions or comments.