biomodels-qc 0.0.3

Utility functions to assist biomodels curation.

BioModels-QC

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.

Local installation

Requirements

• Python 3.9.0+
• pip >= 19.3
• Systems Biology Format Converter
  • Java
• Octave
  • Mac OS installer
  • Ubuntu: apt-get install octave
  • Windows installer
• Scilab
  • Mac OS installer
  • Ubuntu: apt-get install scilab
  • Windows installer
• SVGLint
  • Node.js
    • Mac OS installer
    • Ubuntu instructions
    • Windows installer
• 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) 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.

License

This package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai and the Center for Reproducible Biomedical Modeling.

Contributing to BioModels-QC

We enthusiastically welcome contributions! 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 BioSimulations Team with any questions or comments.