Package: biomodels-qc
BioModels-QCCommand-line application for quality controlling entries in theBioModels databaseand 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 recommendedhere.Local installationRequirementsPython3.9.0+pip>= 19.3Systems Biology Format
ConverterJavaOctaveMac OS
installerUbuntu:apt-getinstall octaveWindows
installerScilabMac OS installerUbuntu:apt-getinstall scilabWindows installerSVGLintNode.jsMac OS installerUbuntu
instructionsWindows installerXPPMac OS
instructionsUbuntu:apt-getinstall xppautWindows
instructionsAfter installing the packages above, the following must be added to your
system path:sbfConverter.sh(Linux/Mac OS) orsbfConverter.bat(Windows)svglintxppautInstallationRun the following command to install the package.pip install biomodels-qcDocker imageRun the following command to pull the Docker imagedocker pull ghcr.io/biosimulations/biomodels_qcTutorialConvert the files for an entry to additional formatsRun 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 "$ENTRY_DIR"Validate an entryRun the following command to validate an entry of the BioModels
database:ENTRY_DIR=/path/to/directory-for-entry
biomodels-qc validate "$ENTRY_DIR"Using the Docker imageRun 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 formatsENTRY_DIR=/path/to/directory-for-entry\
docker run \
    --mount type=bind,source="$ENTRY_DIR",target=/biomodels-entry \
    --interactive \
    --tty \
    --rm \
    ghcr.io/biosimulations/biomodels_qc \
        convert \
            /biomodels-entryValidate an entryENTRY_DIR=/path/to/directory-for-entry
CONTAINER_TEMP_DIR=$(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-entryDocumentationDocumentation for the command-line program is available inline.Run the following command to obtain the help.biomodels-qc --helpUsing the Docker imageRun the following command to use the BioModels-QC Docker image to obtain
the help.docker run \
    --interactive \
    --tty \
    --rm \
    ghcr.io/biosimulations/biomodels_qc \
        --helpAPI documentationAPI documentation is availablehere.LicenseThis package is released under theMIT license.Development teamThis package was developed by theKarr Labat
the Icahn School of Medicine at Mount Sinai and theCenter for
Reproducible Biomedical Modeling.Contributing to BioModels-QCWe enthusiastically welcome contributions! Please see theguide to
contributingand thedeveloper’s code of
conduct.AcknowledgementsThis work was supported by National Institutes of Health award
P41EB023912.Questions and commentsPlease contact theBioSimulations
Teamwith any questions or comments.