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BioSimulators utils documentation¶

Command-line application and high-level utilities for reading, writing, validating, and executing COMBINE/OMEX format files that contain descriptions of simulations in Simulation Experiment Description Markup Language (SED-ML) format with models in formats such as the BioNetGen Language (BNGL) and the Systems Biology Markup Language (SBML).

Contents¶

  • Installation instructions
    • Requirements
    • Optional requirements
    • Installing the latest release from PyPI
    • Installing the latest revision from GitHub
    • Installing the optional features
  • Tutorial for the command-line application
    • Convert an Escher metabolic map to a Vega data visualization
    • Convert a GINML activity flow diagram to a Vega data visualization
    • Convert a SBGN process description map to a Vega data visualization
    • Validate a modeling project
    • Execute a modeling project with a standardized simulation tool from the BioSimulators registry
    • Additional documentation
  • API documentation
    • Subpackages
    • Submodules
    • biosimulators_utils.config module
    • biosimulators_utils.data_model module
    • biosimulators_utils.exceptions module
    • biosimulators_utils.image module
    • biosimulators_utils.warnings module
  • About BioSimulators utils
    • License
    • Development team
    • Contributing to BioSimulators utils
    • Acknowledgements
    • Questions and comments
  • Index

© Copyright 2021, BioSimulators Team.