biosimulators_utils.model_lang package

Subpackages

• biosimulators_utils.model_lang.bngl package
  • Submodules
  • biosimulators_utils.model_lang.bngl.utils module
    • get_parameters_variables_outputs_for_simulation()
  • biosimulators_utils.model_lang.bngl.validation module
    • read_model()
    • validate_model()
• biosimulators_utils.model_lang.cellml package
  • Submodules
  • biosimulators_utils.model_lang.cellml.utils module
    • get_parameters_variables_outputs_for_simulation()
  • biosimulators_utils.model_lang.cellml.validation module
    • validate_model()
    • validate_model_version_1_0()
    • validate_model_version_1_1()
    • validate_model_version_2()
• biosimulators_utils.model_lang.lems package
  • Submodules
  • biosimulators_utils.model_lang.lems.validation module
    • validate_model()
    • validate_neuroml2_lems_file()
• biosimulators_utils.model_lang.neuroml package
  • Submodules
  • biosimulators_utils.model_lang.neuroml.validation module
    • validate_model()
    • validate_model_l1()
    • validate_model_l2()
• biosimulators_utils.model_lang.rba package
  • Submodules
  • biosimulators_utils.model_lang.rba.utils module
  • biosimulators_utils.model_lang.rba.validation module
• biosimulators_utils.model_lang.sbml package
  • Submodules
  • biosimulators_utils.model_lang.sbml.utils module
    • get_package_namespace()
    • get_parameters_variables_outputs_for_simulation()
  • biosimulators_utils.model_lang.sbml.validation module
    • validate_model()
• biosimulators_utils.model_lang.smoldyn package
  • Submodules
  • biosimulators_utils.model_lang.smoldyn.simularium_converter module
    • BiosimulatorsDataConverter
      • BiosimulatorsDataConverter.generate_camera_data_object()
      • BiosimulatorsDataConverter.generate_display_data_object()
      • BiosimulatorsDataConverter.generate_display_data_object_dict()
      • BiosimulatorsDataConverter.generate_input_file_data_object()
      • BiosimulatorsDataConverter.generate_metadata_object()
      • BiosimulatorsDataConverter.generate_output_data_object()
      • BiosimulatorsDataConverter.generate_simularium_file()
      • BiosimulatorsDataConverter.prepare_agent_data()
      • BiosimulatorsDataConverter.prepare_simularium_fp()
      • BiosimulatorsDataConverter.save_simularium_file()
      • BiosimulatorsDataConverter.translate_data_object()
    • SmoldynCombineArchive
      • SmoldynCombineArchive.get_manifest_filepath()
      • SmoldynCombineArchive.set_model_filepath()
      • SmoldynCombineArchive.verify_smoldyn_in_manifest()
    • SmoldynDataConverter
      • SmoldynDataConverter.generate_output_data_object()
      • SmoldynDataConverter.generate_simularium_file()
      • SmoldynDataConverter.read_model_output_dataframe()
      • SmoldynDataConverter.translate_data_object()
      • SmoldynDataConverter.write_model_output_dataframe_to_csv()
  • biosimulators_utils.model_lang.smoldyn.utils module
    • generate_new_simularium_file()
    • get_parameters_variables_outputs_for_simulation()
  • biosimulators_utils.model_lang.smoldyn.validation module
    • ModelValidation
    • generate_model_validation_object()
    • validate_model()
• biosimulators_utils.model_lang.xpp package
  • Submodules
  • biosimulators_utils.model_lang.xpp.data_model module
  • biosimulators_utils.model_lang.xpp.utils module
    • get_parameters_variables_outputs_for_simulation()
  • biosimulators_utils.model_lang.xpp.validation module
    • get_xpp_input_configuration_from_directory()
    • sanitize_model()
    • validate_model()