Package: biosimulators-utils
BioSimulators utilsCommand-line application and high-level utilities for reading, writing, validating, and executingCOMBINE/OMEX formatfiles that contain descriptions of simulations inSimulation Experiment Description Markup Language(SED-ML) format with models in formats such as theBioNetGen Language(BNGL) and theSystems Biology Markup Language(SBML).InstallationRequirementsPython >= 3.7pip (latest)Optional requirementsDocker: required to execute containerized simulation toolsJava: required to parse and validate NeuroML/LEMS filesPerl: required to parse and validate BioNetGen filesRBApy: required to parse and validate RBA filesXPP: required to parse and validate XPP filesInstall latest release from PyPIpip install biosimulators-utilsInstall latest revision from GitHubpip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimulators_utilsInstallation optional featuresTo use BioSimulators utils to validate BNGL models, install BioSimulators utils with thebgnloption:pip install biosimulators-utils[bgnl]To use BioSimulators utils to validate CellML models, install BioSimulators utils with thecellmloption:pip install biosimulators-utils[cellml]To use BioSimulators utils to validate LEMS models, installJavaand then install BioSimulators utils with thelemsoption:pip install biosimulators-utils[lems]To use BioSimulators utils to validate NeuroML models, install BioSimulators utils with theneuromloption:pip install biosimulators-utils[neuroml]To use BioSimulators utils to validate SBML models, install BioSimulators utils with thesbmloption:pip install biosimulators-utils[sbml]To use BioSimulators utils to validate SBML models, install BioSimulators utils with thesmoldynoption:pip install biosimulators-utils[smoldyn]To use BioSimulators utils to convert Escher metabolic maps to Vega flux data visualizations, install BioSimulators utils with theescheroption:pip install biosimulators-utils[escher]To use BioSimulators utils to execute containerized simulation tools, install BioSimulators utils with thecontainersoption:pip install biosimulators-utils[containers]To use BioSimulators utils to log the standard output and error produced by simulation tools, install BioSimulators utils with theloggingoption:pip install biosimulators-utils[logging]Dockerfile and Docker imageThis package is available in theghcr.io/biosimulators/biosimulatorsDocker image. This image includes all of the optional dependencies and installation options.To install and run this image, run the following commands:docker pull ghcr.io/biosimulators/biosimulators
docker run -it --rm ghcr.io/biosimulators/biosimulatorsThis image includes this package, as well as standardized Python APIs for the simulation tools validated by BioSimulators. Because this image aims to incorporate as many simulation tools as possible within a single Python environment, this image may sometimes lag behind the latest version of this package.The Dockerfile for this image is availablehere.TutorialsCommand-line interfaceA tutorial for the command-line interface is availablehere.Python APIInteractive tutorials for using BioSimulators-utils and Python APIs for simulation tools to execute simulations are available online from Binderhere. The Jupyter notebooks for these tutorials are also availablehere.API 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 in New York and theCenter for Reproducible Biomedical Modelingwith assistance from the contributors listedhere.Contributing to BioSimulators utilsWe enthusiastically welcome contributions to BioSimulators utils! Please see theguide to contributingand thedeveloper's code of conduct.FundingThis work was supported by National Institutes of Health award P41EB023912.Questions and commentsPlease contact theBioSimulators Teamwith any questions or comments.