Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __enter__() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.log.utils.StandardOutputErrorCapturer method) __exit__() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.log.utils.StandardOutputErrorCapturer method) __format__() (biosimulators_utils.combine.data_model.CombineArchiveContentFormat method) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern method) (biosimulators_utils.config.Colors method) (biosimulators_utils.data_model.ValueType method) (biosimulators_utils.log.data_model.StandardOutputErrorCapturerLevel method) (biosimulators_utils.log.data_model.Status method) (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat method) (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat method) (biosimulators_utils.omex_meta.data_model.OmexMetadataSchema method) (biosimulators_utils.report.data_model.ReportFormat method) (biosimulators_utils.sedml.data_model.AxisScale method) (biosimulators_utils.sedml.data_model.LineStyleType method) (biosimulators_utils.sedml.data_model.MarkerStyleType method) (biosimulators_utils.sedml.data_model.ModelLanguage method) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId method) (biosimulators_utils.sedml.data_model.ModelLanguagePattern method) (biosimulators_utils.sedml.data_model.Symbol method) (biosimulators_utils.simulator.data_model.SoftwareInterface method) (biosimulators_utils.simulator_registry.data_model.IssueLabel method) (biosimulators_utils.viz.data_model.VizFormat method) _captured (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) _doc_sed (biosimulators_utils.sedml.io.SedmlSimulationWriter attribute) _log (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) _num_meta_id (biosimulators_utils.sedml.io.SedmlSimulationWriter attribute) _obj_to_sed_obj_map (biosimulators_utils.sedml.io.SedmlSimulationWriter attribute) _stderr (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) _stdout (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) A AbstractTask (class in biosimulators_utils.sedml.data_model) action_error (biosimulators_utils.simulator_registry.data_model.IssueLabel attribute) ACTIONSCRIPT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) add_comment_to_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) add_error_comment_to_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) add_labels_to_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) add_namespaces_to_xml_node() (in module biosimulators_utils.sedml.utils) AddElementModelChange (class in biosimulators_utils.sedml.data_model) ADOBE_FLASH (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) AI (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) algorithm (biosimulators_utils.log.data_model.TaskLog attribute) (biosimulators_utils.sedml.data_model.OneStepSimulation attribute) (biosimulators_utils.sedml.data_model.Simulation attribute) (biosimulators_utils.sedml.data_model.SteadyStateSimulation attribute) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) Algorithm (class in biosimulators_utils.sedml.data_model) ALGORITHM_SUBSTITUTION_POLICY (biosimulators_utils.config.Config attribute) AlgorithmDoesNotSupportModelFeatureException AlgorithmParameterChange (class in biosimulators_utils.sedml.data_model) any (biosimulators_utils.data_model.ValueType attribute) append_all_nested_children_to_doc() (in module biosimulators_utils.sedml.utils) append_report_id() (biosimulators_utils.report.io.ReportReader static method) apply_changes_to_xml_model() (in module biosimulators_utils.sedml.utils) approved (biosimulators_utils.simulator_registry.data_model.IssueLabel attribute) Archive (class in biosimulators_utils.archive.data_model) archive_path (biosimulators_utils.archive.data_model.ArchiveFile attribute) ArchiveFile (class in biosimulators_utils.archive.data_model) ArchiveReader (class in biosimulators_utils.archive.io) ArchiveWriter (class in biosimulators_utils.archive.io) are_lists_equal() (in module biosimulators_utils.utils.core) assert_exception() (in module biosimulators_utils.utils.core) assign_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) authors (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.biosimulations.data_model.Metadata attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] AxisScale (class in biosimulators_utils.sedml.data_model) B base (biosimulators_utils.sedml.data_model.Style attribute) BioPAX (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) biosimulations (biosimulators_utils.omex_meta.data_model.OmexMetadataSchema attribute) BIOSIMULATIONS_API_AUDIENCE (biosimulators_utils.config.Config attribute) BIOSIMULATIONS_API_AUTH_ENDPOINT (biosimulators_utils.config.Config attribute) BIOSIMULATIONS_API_ENDPOINT (biosimulators_utils.config.Config attribute) BiosimulationsOmexMetaReader (class in biosimulators_utils.omex_meta.io) BiosimulationsOmexMetaWriter (class in biosimulators_utils.omex_meta.io) BIOSIMULATORS_API_ENDPOINT (biosimulators_utils.config.Config attribute) biosimulators_docker_image (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) biosimulators_utils module biosimulators_utils.archive module biosimulators_utils.archive.data_model module biosimulators_utils.archive.io module biosimulators_utils.archive.utils module biosimulators_utils.biosimulations module biosimulators_utils.biosimulations.data_model module biosimulators_utils.biosimulations.utils module biosimulators_utils.combine module biosimulators_utils.combine.data_model module biosimulators_utils.combine.exceptions module biosimulators_utils.combine.exec module biosimulators_utils.combine.io module biosimulators_utils.combine.utils module biosimulators_utils.combine.validation module biosimulators_utils.config module biosimulators_utils.data_model module biosimulators_utils.exceptions module biosimulators_utils.gh_action module biosimulators_utils.gh_action.core module biosimulators_utils.gh_action.data_model module biosimulators_utils.globals module biosimulators_utils.image module biosimulators_utils.kisao module biosimulators_utils.kisao.utils module biosimulators_utils.licensing module biosimulators_utils.licensing.core module biosimulators_utils.licensing.gurobi module biosimulators_utils.log module biosimulators_utils.log.data_model module biosimulators_utils.log.utils module biosimulators_utils.log.warnings module biosimulators_utils.model_lang module biosimulators_utils.model_lang.bngl module biosimulators_utils.model_lang.cellml module biosimulators_utils.model_lang.cellml.utils module biosimulators_utils.model_lang.cellml.validation module biosimulators_utils.model_lang.lems module biosimulators_utils.model_lang.lems.validation module biosimulators_utils.model_lang.neuroml module biosimulators_utils.model_lang.neuroml.validation module biosimulators_utils.model_lang.rba module biosimulators_utils.model_lang.sbml module biosimulators_utils.model_lang.sbml.utils module biosimulators_utils.model_lang.sbml.validation module biosimulators_utils.model_lang.smoldyn module biosimulators_utils.model_lang.smoldyn.simularium_converter module biosimulators_utils.model_lang.xpp module biosimulators_utils.model_lang.xpp.data_model module biosimulators_utils.model_lang.xpp.utils module biosimulators_utils.model_lang.xpp.validation module biosimulators_utils.omex_meta module biosimulators_utils.omex_meta.data_model module biosimulators_utils.omex_meta.io module biosimulators_utils.omex_meta.utils module biosimulators_utils.omex_meta.validation module biosimulators_utils.ref module biosimulators_utils.ref.data_model module biosimulators_utils.ref.utils module biosimulators_utils.report module biosimulators_utils.report.data_model module biosimulators_utils.report.io module biosimulators_utils.report.warnings module biosimulators_utils.sedml module biosimulators_utils.sedml.data_model module biosimulators_utils.sedml.exceptions module biosimulators_utils.sedml.exec module biosimulators_utils.sedml.io module biosimulators_utils.sedml.math module biosimulators_utils.sedml.model_utils module biosimulators_utils.sedml.utils module biosimulators_utils.sedml.validation module biosimulators_utils.sedml.warnings module biosimulators_utils.simulator module biosimulators_utils.simulator.cli module biosimulators_utils.simulator.data_model module biosimulators_utils.simulator.environ module biosimulators_utils.simulator.exceptions module biosimulators_utils.simulator.exec module biosimulators_utils.simulator.io module biosimulators_utils.simulator.specs module biosimulators_utils.simulator.utils module biosimulators_utils.simulator_registry module biosimulators_utils.simulator_registry.data_model module biosimulators_utils.simulator_registry.process_submission module biosimulators_utils.simulator_registry.query module biosimulators_utils.simulator_registry.submit module biosimulators_utils.utils module biosimulators_utils.utils.core module biosimulators_utils.utils.identifiers_org module biosimulators_utils.utils.logging module biosimulators_utils.viz module biosimulators_utils.viz.data_model module biosimulators_utils.viz.io module biosimulators_utils.viz.utils module biosimulators_utils.viz.vega module biosimulators_utils.viz.vega.escher module biosimulators_utils.viz.vega.escher.core module biosimulators_utils.viz.vega.ginml module biosimulators_utils.viz.vega.ginml.core module biosimulators_utils.viz.vega.sbgn module biosimulators_utils.viz.vega.sbgn.core module biosimulators_utils.viz.vega.utils module biosimulators_utils.viz.warnings module biosimulators_utils.warnings module biosimulators_utils.xml module biosimulators_utils.xml.utils module BiosimulatorsDataConverter (class in biosimulators_utils.model_lang.smoldyn.simularium_converter) BioSimulatorsException BioSimulatorsWarning BMP (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) BNGL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) boolean (biosimulators_utils.data_model.ValueType attribute) BOURNE_SHELL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) build_archive_from_paths() (in module biosimulators_utils.archive.utils) build_cli() (in module biosimulators_utils.simulator.cli) build_combine_archive_for_model() (in module biosimulators_utils.sedml.model_utils) build_gh_issue_body() (in module biosimulators_utils.simulator_registry.submit) build_omex_meta_file_for_model() (in module biosimulators_utils.omex_meta.utils) BUNDLE_OUTPUTS (biosimulators_utils.config.Config attribute) C C (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) c (biosimulators_utils.log.data_model.StandardOutputErrorCapturerLevel attribute) calc_compute_model_change_new_value() (in module biosimulators_utils.sedml.utils) calc_data_generator_results() (in module biosimulators_utils.sedml.utils) calc_data_generators_results() (in module biosimulators_utils.sedml.utils) CannotExportMultidimensionalTableWarning caption (biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic attribute), [1] catch_errors() (biosimulators_utils.gh_action.core.GitHubActionErrorHandling class method) CellML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) changes (biosimulators_utils.sedml.data_model.Algorithm attribute) (biosimulators_utils.sedml.data_model.Model attribute) (biosimulators_utils.sedml.data_model.RepeatedTask attribute) circle (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) Citation (class in biosimulators_utils.biosimulations.data_model) citations (biosimulators_utils.biosimulations.data_model.ExternalReferences attribute) close_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) code (biosimulators_utils.utils.identifiers_org.IdentifiersOrgCountry attribute) COLLECT_COMBINE_ARCHIVE_RESULTS (biosimulators_utils.config.Config attribute) COLLECT_SED_DOCUMENT_RESULTS (biosimulators_utils.config.Config attribute) color (biosimulators_utils.sedml.data_model.FillStyle attribute) (biosimulators_utils.sedml.data_model.LineStyle attribute) Color (class in biosimulators_utils.sedml.data_model) Colors (class in biosimulators_utils.config) CombineArchive (class in biosimulators_utils.combine.data_model) CombineArchiveBase (class in biosimulators_utils.combine.data_model) CombineArchiveContent (class in biosimulators_utils.combine.data_model) CombineArchiveContentFormat (class in biosimulators_utils.combine.data_model) CombineArchiveContentFormatPattern (class in biosimulators_utils.combine.data_model) CombineArchiveExecutionError CombineArchiveLog (class in biosimulators_utils.log.data_model) CombineArchiveReader (class in biosimulators_utils.combine.io) CombineArchiveWriter (class in biosimulators_utils.combine.io) CombineArchiveZipReader (class in biosimulators_utils.combine.io) command_line (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) Comment (class in biosimulators_utils.gh_action.data_model) commit_simulator (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) compile_math() (in module biosimulators_utils.sedml.math) ComputeModelChange (class in biosimulators_utils.sedml.data_model) Config (class in biosimulators_utils.config) contents (biosimulators_utils.combine.data_model.CombineArchive attribute) convert_docker_image_to_singularity() (in module biosimulators_utils.image) convert_xml_node_to_string() (in module biosimulators_utils.sedml.utils) CopasiML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) country (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) CPP_HEADER (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) CPP_SOURCE (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) created (biosimulators_utils.biosimulations.data_model.Metadata attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) CSS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) CSV (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) csv (biosimulators_utils.report.data_model.ReportFormat attribute) cubic_bezier_angle() (in module biosimulators_utils.viz.utils) cubic_bezier_point() (in module biosimulators_utils.viz.utils) Curve (class in biosimulators_utils.sedml.data_model) curves (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.sedml.data_model.Plot2D attribute) D dash (biosimulators_utils.sedml.data_model.LineStyleType attribute) dashDot (biosimulators_utils.sedml.data_model.LineStyleType attribute) dashDotDot (biosimulators_utils.sedml.data_model.LineStyleType attribute) data_generator (biosimulators_utils.sedml.data_model.DataSet attribute) data_generators (biosimulators_utils.sedml.data_model.SedDocument attribute) data_sets (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.sedml.data_model.Report attribute) DataGenerator (class in biosimulators_utils.sedml.data_model) DataGeneratorResults (class in biosimulators_utils.report.data_model) DataSet (class in biosimulators_utils.sedml.data_model) DataSetResults (class in biosimulators_utils.report.data_model) date (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] DEBUG (biosimulators_utils.config.Config attribute) deprecated (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) deprecated_date (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) description (biosimulators_utils.biosimulations.data_model.Metadata attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) desktop_application (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) diamond (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) dict_to_vega_dataset() (in module biosimulators_utils.viz.vega.utils) disabled (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) DLL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) DOC (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) DOCX (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) does_algorithm_implementation_have_capabilities_to_execute_parameter() (in module biosimulators_utils.simulator.specs) does_algorithm_implementation_have_capabilities_to_execute_sed_model_language() (in module biosimulators_utils.simulator.specs) does_algorithm_implementation_have_capabilities_to_execute_sed_task() (in module biosimulators_utils.simulator.specs) does_model_language_use_xpath_variable_targets() (in module biosimulators_utils.sedml.utils) does_simulator_have_capabilities_to_execute_sed_document() (in module biosimulators_utils.simulator.specs) does_simulator_have_capabilities_to_execute_sed_task() (in module biosimulators_utils.simulator.specs) doi (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] dot (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) (biosimulators_utils.sedml.data_model.LineStyleType attribute) download_identifiers_org_namespaces() (in module biosimulators_utils.utils.identifiers_org) duration (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) E embedded_in_lui (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) end (biosimulators_utils.sedml.data_model.UniformRange attribute) end() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method) ENV_VAR_PREFIX (biosimulators_utils.licensing.core.LicenseManager property) (biosimulators_utils.licensing.gurobi.GurobiLicenseManager attribute) EnvironmentVariable (class in biosimulators_utils.simulator.data_model) EPS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) error (biosimulators_utils.gh_action.data_model.Comment attribute) errors (biosimulators_utils.combine.io.CombineArchiveReader attribute) (biosimulators_utils.combine.io.CombineArchiveWriter attribute) (biosimulators_utils.sedml.io.SedmlSimulationReader attribute) Escher (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) escher_to_vega() (in module biosimulators_utils.viz.vega.escher.core) eval_math() (in module biosimulators_utils.sedml.math) eval_xpath() (in module biosimulators_utils.xml.utils) exception (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) exec_plot_2d() (in module biosimulators_utils.sedml.exec) exec_plot_3d() (in module biosimulators_utils.sedml.exec) exec_repeated_task() (in module biosimulators_utils.sedml.exec) exec_report() (in module biosimulators_utils.sedml.exec) exec_sed_doc() (in module biosimulators_utils.sedml.exec) exec_sedml_docs_in_archive() (in module biosimulators_utils.combine.exec) exec_sedml_docs_in_archive_with_containerized_simulator() (in module biosimulators_utils.simulator.exec) exec_sedml_docs_in_archive_with_simulator_cli() (in module biosimulators_utils.simulator.exec) exec_task() (in module biosimulators_utils.sedml.exec) export() (biosimulators_utils.log.data_model.Log method) ExternalReferences (class in biosimulators_utils.biosimulations.data_model) ExtraDataWarning F failed (biosimulators_utils.config.Colors attribute) FAILED (biosimulators_utils.log.data_model.Status attribute) failure (biosimulators_utils.config.Colors attribute) family_name (biosimulators_utils.data_model.Person attribute) filename (biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic attribute), [1] files (biosimulators_utils.archive.data_model.Archive attribute) fill (biosimulators_utils.sedml.data_model.Style attribute) fill_color (biosimulators_utils.sedml.data_model.MarkerStyle attribute) FillStyle (class in biosimulators_utils.sedml.data_model) finalize() (biosimulators_utils.log.data_model.CombineArchiveLog method) (biosimulators_utils.log.data_model.Log method) (biosimulators_utils.log.data_model.Plot2DLog method) (biosimulators_utils.log.data_model.Plot3DLog method) (biosimulators_utils.log.data_model.ReportLog method) (biosimulators_utils.log.data_model.SedDocumentLog method) flatten_nested_list_of_strings() (in module biosimulators_utils.utils.core) float (biosimulators_utils.data_model.ValueType attribute) flush() (biosimulators_utils.log.utils.StandardOutputErrorCapturer method) format (biosimulators_utils.combine.data_model.CombineArchiveContent attribute) format_error_comment() (biosimulators_utils.gh_action.core.GitHubAction class method) format_float() (in module biosimulators_utils.utils.core) format_value() (in module biosimulators_utils.utils.core) FunctionalRange (class in biosimulators_utils.sedml.data_model) G gen_algorithms_from_specs() (in module biosimulators_utils.simulator.specs) generate_camera_data_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter static method) generate_display_data_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter static method) generate_display_data_object_dict() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) generate_input_file_data_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) generate_metadata_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter static method) generate_output_data_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method) generate_simularium_file() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method) GENESIS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) get_algorithm_substitution_policy() (in module biosimulators_utils.simulator.utils) get_api_session() (in module biosimulators_utils.biosimulations.utils) get_app_dirs() (in module biosimulators_utils.config) get_attributes_of_xpaths() (in module biosimulators_utils.xml.utils) get_authorization_for_client() (in module biosimulators_utils.biosimulations.utils) get_citation() (biosimulators_utils.ref.data_model.JournalArticle method) (biosimulators_utils.ref.data_model.Reference method) get_combine_archive_uri() (biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaReader class method) get_config() (in module biosimulators_utils.config) get_data_generators_for_output() (in module biosimulators_utils.sedml.utils) get_data_in_issue() (biosimulators_utils.gh_action.core.GitHubAction static method) get_docker_image() (in module biosimulators_utils.image) get_file_extension_combine_uri_map() (in module biosimulators_utils.biosimulations.utils) get_first_last_models_executed_by_task() (in module biosimulators_utils.sedml.utils) get_formats() (in module biosimulators_utils.biosimulations.utils) get_gh_action_run_id() (biosimulators_utils.gh_action.core.GitHubAction static method) get_gh_action_run_url() (biosimulators_utils.gh_action.core.GitHubAction class method) get_gh_auth() (biosimulators_utils.gh_action.core.GitHubAction static method) get_gh_repo() (biosimulators_utils.gh_action.core.GitHubAction static method) get_global_combine_archive_content_uri() (in module biosimulators_utils.omex_meta.utils) get_identifiers_org_namespace() (in module biosimulators_utils.utils.identifiers_org) get_identifiers_org_namespaces() (in module biosimulators_utils.utils.identifiers_org) get_ids() (biosimulators_utils.report.io.ReportReader method) get_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) get_issue_number() (biosimulators_utils.gh_action.core.GitHubAction static method) get_keys_from_env_vars() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method) get_labels_for_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) get_local_combine_archive_content_uri() (in module biosimulators_utils.omex_meta.utils) get_logger() (in module biosimulators_utils.utils.logging) get_manifest_filepath() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive method) get_master_content() (biosimulators_utils.combine.data_model.CombineArchive method) get_model_changes_for_task() (in module biosimulators_utils.sedml.utils) get_models_referenced_by_model_change() (in module biosimulators_utils.sedml.utils) get_models_referenced_by_range() (in module biosimulators_utils.sedml.utils) get_models_referenced_by_task() (in module biosimulators_utils.sedml.utils) get_namespaces_for_sed_object() (in module biosimulators_utils.sedml.utils) get_namespaces_for_xml_doc() (in module biosimulators_utils.xml.utils) get_namespaces_for_xml_element() (in module biosimulators_utils.xml.utils) get_namespaces_with_prefixes() (in module biosimulators_utils.xml.utils) get_ontology_terms() (in module biosimulators_utils.biosimulations.utils) get_package_namespace() (in module biosimulators_utils.model_lang.sbml.utils) get_parameters_variables_outputs_for_simulation() (in module biosimulators_utils.model_lang.cellml.utils) (in module biosimulators_utils.model_lang.sbml.utils) (in module biosimulators_utils.model_lang.xpp.utils) (in module biosimulators_utils.sedml.model_utils) get_published_project() (in module biosimulators_utils.biosimulations.utils) get_pubmed_central_open_access_graphics() (in module biosimulators_utils.ref.utils) get_range_len() (in module biosimulators_utils.sedml.utils) get_reference() (in module biosimulators_utils.ref.utils) get_report_for_plot2d() (in module biosimulators_utils.sedml.exec) get_report_for_plot3d() (in module biosimulators_utils.sedml.exec) get_sedml_contents() (in module biosimulators_utils.combine.utils) get_simulator_specs() (in module biosimulators_utils.simulator.specs) get_simulator_submission_from_gh_issue_body() (in module biosimulators_utils.simulator_registry.process_submission) get_simulator_version_specs() (in module biosimulators_utils.simulator_registry.query) get_summary_combine_archive_log() (in module biosimulators_utils.log.utils) get_summary_sedml_contents() (in module biosimulators_utils.combine.utils) get_task_results_shape() (in module biosimulators_utils.sedml.utils) get_term() (in module biosimulators_utils.kisao.utils) get_term_type() (in module biosimulators_utils.kisao.utils) get_text() (biosimulators_utils.log.utils.StandardOutputErrorCapturer method) get_uncaught_exception_msg() (biosimulators_utils.gh_action.core.GitHubActionErrorHandling method) get_uri() (biosimulators_utils.ref.data_model.JournalArticle method) get_value_of_variable_model_xml_targets() (in module biosimulators_utils.sedml.utils) get_values_of_variable_model_xml_targets_of_model_change() (in module biosimulators_utils.sedml.utils) get_variables_for_data_generators() (in module biosimulators_utils.sedml.utils) get_variables_for_task() (in module biosimulators_utils.sedml.utils) get_xml_node_namespace_tag_target() (in module biosimulators_utils.sedml.utils) get_xpp_input_configuration_from_directory() (in module biosimulators_utils.model_lang.xpp.validation) GH_ACTION_RUN_URL (biosimulators_utils.gh_action.core.GitHubAction attribute) gh_auth (biosimulators_utils.gh_action.core.GitHubAction attribute) gh_repo (biosimulators_utils.gh_action.core.GitHubAction attribute) GIF (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) GINML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) ginml_to_vega() (in module biosimulators_utils.viz.vega.ginml.core) GitHubAction (class in biosimulators_utils.gh_action.core) GitHubActionCaughtError GitHubActionErrorHandling (class in biosimulators_utils.gh_action.core) given_name (biosimulators_utils.data_model.Person attribute) GMSH_MESH (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) GRAPHML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) GurobiLicenseManager (class in biosimulators_utils.licensing.gurobi) H h5 (biosimulators_utils.report.data_model.ReportFormat attribute) H5_REPORTS_PATH (biosimulators_utils.config.Config attribute) has_structural_changes() (biosimulators_utils.sedml.data_model.Model method) hDash (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) hdf (biosimulators_utils.report.data_model.ReportFormat attribute) HDF5 (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) hdf5 (biosimulators_utils.report.data_model.ReportFormat attribute) HOC (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) home_url (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) HTML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) html (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) I ICO (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) id (biosimulators_utils.data_model.Identifier attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) (biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic attribute), [1] (biosimulators_utils.sedml.data_model.AbstractTask attribute) (biosimulators_utils.sedml.data_model.AddElementModelChange attribute) (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.DataGenerator attribute) (biosimulators_utils.sedml.data_model.DataSet attribute) (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.Model attribute) (biosimulators_utils.sedml.data_model.ModelAttributeChange attribute) (biosimulators_utils.sedml.data_model.ModelChange attribute) (biosimulators_utils.sedml.data_model.OneStepSimulation attribute) (biosimulators_utils.sedml.data_model.Output attribute) (biosimulators_utils.sedml.data_model.Parameter attribute) (biosimulators_utils.sedml.data_model.Plot attribute) (biosimulators_utils.sedml.data_model.Plot2D attribute) (biosimulators_utils.sedml.data_model.Plot3D attribute) (biosimulators_utils.sedml.data_model.Range attribute) (biosimulators_utils.sedml.data_model.RemoveElementModelChange attribute) (biosimulators_utils.sedml.data_model.RepeatedTask attribute) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange attribute) (biosimulators_utils.sedml.data_model.Report attribute) (biosimulators_utils.sedml.data_model.SedIdGroupMixin attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Simulation attribute) (biosimulators_utils.sedml.data_model.SteadyStateSimulation attribute) (biosimulators_utils.sedml.data_model.Style attribute) (biosimulators_utils.sedml.data_model.Surface attribute) (biosimulators_utils.sedml.data_model.Task attribute) (biosimulators_utils.sedml.data_model.UniformRange attribute) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) (biosimulators_utils.sedml.data_model.Variable attribute) (biosimulators_utils.sedml.data_model.VectorRange attribute) (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) Identifier (class in biosimulators_utils.data_model) identifiers (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.biosimulations.data_model.ExternalReferences attribute) IdentifiersOrgCountry (class in biosimulators_utils.utils.identifiers_org) IdentifiersOrgInstitution (class in biosimulators_utils.utils.identifiers_org) IdentifiersOrgNamespace (class in biosimulators_utils.utils.identifiers_org) IdentifiersOrgNamespaceResource (class in biosimulators_utils.utils.identifiers_org) IllogicalSedmlWarning IllogicalVizWarning InconsistentVariableShapesWarning INI (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) init_combine_archive_log() (in module biosimulators_utils.log.utils) init_output_log() (in module biosimulators_utils.log.utils) init_plot2d_log() (in module biosimulators_utils.log.utils) init_plot3d_log() (in module biosimulators_utils.log.utils) init_report_log() (in module biosimulators_utils.log.utils) init_sed_document_log() (in module biosimulators_utils.log.utils) init_task_log() (in module biosimulators_utils.log.utils) initial_time (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) institution (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) integer (biosimulators_utils.data_model.ValueType attribute) invalid (biosimulators_utils.simulator_registry.data_model.IssueLabel attribute) InvalidIdentifiersOrgUri IPython_Notebook (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) is_equal() (biosimulators_utils.archive.data_model.Archive method) (biosimulators_utils.archive.data_model.ArchiveFile method) (biosimulators_utils.biosimulations.data_model.Citation method) (biosimulators_utils.biosimulations.data_model.ExternalReferences method) (biosimulators_utils.biosimulations.data_model.Metadata method) (biosimulators_utils.combine.data_model.CombineArchive method) (biosimulators_utils.combine.data_model.CombineArchiveContent method) (biosimulators_utils.data_model.Identifier method) (biosimulators_utils.data_model.Person method) (biosimulators_utils.sedml.data_model.AbstractTask method) (biosimulators_utils.sedml.data_model.AddElementModelChange method) (biosimulators_utils.sedml.data_model.Algorithm method) (biosimulators_utils.sedml.data_model.AlgorithmParameterChange method) (biosimulators_utils.sedml.data_model.ComputeModelChange method) (biosimulators_utils.sedml.data_model.Curve method) (biosimulators_utils.sedml.data_model.DataGenerator method) (biosimulators_utils.sedml.data_model.DataSet method) (biosimulators_utils.sedml.data_model.FillStyle method) (biosimulators_utils.sedml.data_model.FunctionalRange method) (biosimulators_utils.sedml.data_model.LineStyle method) (biosimulators_utils.sedml.data_model.MarkerStyle method) (biosimulators_utils.sedml.data_model.Model method) (biosimulators_utils.sedml.data_model.ModelAttributeChange method) (biosimulators_utils.sedml.data_model.ModelChange method) (biosimulators_utils.sedml.data_model.OneStepSimulation method) (biosimulators_utils.sedml.data_model.Output method) (biosimulators_utils.sedml.data_model.Parameter method) (biosimulators_utils.sedml.data_model.Plot2D method) (biosimulators_utils.sedml.data_model.Plot3D method) (biosimulators_utils.sedml.data_model.Range method) (biosimulators_utils.sedml.data_model.RepeatedTask method) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange method) (biosimulators_utils.sedml.data_model.Report method) (biosimulators_utils.sedml.data_model.SedBase method) (biosimulators_utils.sedml.data_model.SedDocument method) (biosimulators_utils.sedml.data_model.SedIdGroupMixin method) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange method) (biosimulators_utils.sedml.data_model.Simulation method) (biosimulators_utils.sedml.data_model.Style method) (biosimulators_utils.sedml.data_model.SubTask method) (biosimulators_utils.sedml.data_model.Surface method) (biosimulators_utils.sedml.data_model.TargetGroupMixin method) (biosimulators_utils.sedml.data_model.Task method) (biosimulators_utils.sedml.data_model.UniformRange method) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation method) (biosimulators_utils.sedml.data_model.Variable method) (biosimulators_utils.sedml.data_model.VectorRange method) (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission method) is_executable_task() (in module biosimulators_utils.sedml.utils) is_model_language_encoded_in_xml() (in module biosimulators_utils.sedml.utils) is_package_available() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method) issue (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] ISSUE_ASIGNEES_ENDPOINT (biosimulators_utils.gh_action.core.GitHubAction attribute) ISSUE_COMMENTS_ENDPOINT (biosimulators_utils.gh_action.core.GitHubAction attribute) ISSUE_ENDPOINT (biosimulators_utils.gh_action.core.GitHubAction attribute) ISSUE_LABELS_ENDPOINT (biosimulators_utils.gh_action.core.GitHubAction attribute) IssueLabel (class in biosimulators_utils.simulator_registry.data_model) J JAVA_ARCHIVE (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) JAVA_CLASS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) JAVA_SOURCE (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) JAVASCRIPT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) journal (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] JournalArticle (class in biosimulators_utils.ref.data_model) JPEG (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) jpg (biosimulators_utils.viz.data_model.VizFormat attribute) JSON (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) json (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) json_triples (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) K Kappa (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) KEEP_INDIVIDUAL_OUTPUTS (biosimulators_utils.config.Config attribute) kisao_id (biosimulators_utils.data_model.ValueType attribute) (biosimulators_utils.sedml.data_model.Algorithm attribute) (biosimulators_utils.sedml.data_model.AlgorithmParameterChange attribute) L label (biosimulators_utils.ref.data_model.PubMedCentralOpenAccesGraphic attribute), [1] (biosimulators_utils.sedml.data_model.DataSet attribute) language (biosimulators_utils.sedml.data_model.Model attribute) LEMS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) level (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) (biosimulators_utils.sedml.data_model.SedDocument attribute) library (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) license (biosimulators_utils.biosimulations.data_model.Metadata attribute) LicenseManager (class in biosimulators_utils.licensing.core) line (biosimulators_utils.sedml.data_model.Style attribute) line_color (biosimulators_utils.sedml.data_model.MarkerStyle attribute) line_thickness (biosimulators_utils.sedml.data_model.MarkerStyle attribute) linear (biosimulators_utils.sedml.data_model.AxisScale attribute) LineStyle (class in biosimulators_utils.sedml.data_model) LineStyleType (class in biosimulators_utils.sedml.data_model) list (biosimulators_utils.data_model.ValueType attribute) local_path (biosimulators_utils.archive.data_model.ArchiveFile attribute) location (biosimulators_utils.combine.data_model.CombineArchiveContent attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) LOG (biosimulators_utils.config.Config attribute) log (biosimulators_utils.sedml.data_model.AxisScale attribute) Log (class in biosimulators_utils.log.data_model) log() (in module biosimulators_utils.sedml.math) LOG_PATH (biosimulators_utils.config.Config attribute) login_to_docker_registry() (in module biosimulators_utils.image) M MAPLE_WORKSHEET (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) MARKDOWN (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) marker (biosimulators_utils.sedml.data_model.Style attribute) MarkerStyle (class in biosimulators_utils.sedml.data_model) MarkerStyleType (class in biosimulators_utils.sedml.data_model) MASS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) master (biosimulators_utils.combine.data_model.CombineArchiveContent attribute) math (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.DataGenerator attribute) (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) MATHEMATICA_NOTEBOOK (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) MATLAB (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) MATLAB_DATA (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) MATLAB_FIGURE (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) metadata (biosimulators_utils.sedml.data_model.SedDocument attribute) Metadata (class in biosimulators_utils.biosimulations.data_model) mir_id (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) MissingDataWarning MissingReportMetadataWarning mobile_application (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) model (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Task attribute) (biosimulators_utils.sedml.data_model.Variable attribute) Model (class in biosimulators_utils.sedml.data_model) ModelAttributeChange (class in biosimulators_utils.sedml.data_model) ModelChange (class in biosimulators_utils.sedml.data_model) ModelLanguage (class in biosimulators_utils.sedml.data_model) ModelLanguageEdamId (class in biosimulators_utils.sedml.data_model) ModelLanguagePattern (class in biosimulators_utils.sedml.data_model) models (biosimulators_utils.sedml.data_model.SedDocument attribute) modified (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) module biosimulators_utils biosimulators_utils.archive biosimulators_utils.archive.data_model biosimulators_utils.archive.io biosimulators_utils.archive.utils biosimulators_utils.biosimulations biosimulators_utils.biosimulations.data_model biosimulators_utils.biosimulations.utils biosimulators_utils.combine biosimulators_utils.combine.data_model biosimulators_utils.combine.exceptions biosimulators_utils.combine.exec biosimulators_utils.combine.io biosimulators_utils.combine.utils biosimulators_utils.combine.validation biosimulators_utils.config biosimulators_utils.data_model biosimulators_utils.exceptions biosimulators_utils.gh_action biosimulators_utils.gh_action.core biosimulators_utils.gh_action.data_model biosimulators_utils.globals biosimulators_utils.image biosimulators_utils.kisao biosimulators_utils.kisao.utils biosimulators_utils.licensing biosimulators_utils.licensing.core biosimulators_utils.licensing.gurobi biosimulators_utils.log biosimulators_utils.log.data_model biosimulators_utils.log.utils biosimulators_utils.log.warnings biosimulators_utils.model_lang biosimulators_utils.model_lang.bngl biosimulators_utils.model_lang.cellml biosimulators_utils.model_lang.cellml.utils biosimulators_utils.model_lang.cellml.validation biosimulators_utils.model_lang.lems biosimulators_utils.model_lang.lems.validation biosimulators_utils.model_lang.neuroml biosimulators_utils.model_lang.neuroml.validation biosimulators_utils.model_lang.rba biosimulators_utils.model_lang.sbml biosimulators_utils.model_lang.sbml.utils biosimulators_utils.model_lang.sbml.validation biosimulators_utils.model_lang.smoldyn biosimulators_utils.model_lang.smoldyn.simularium_converter biosimulators_utils.model_lang.xpp biosimulators_utils.model_lang.xpp.data_model biosimulators_utils.model_lang.xpp.utils biosimulators_utils.model_lang.xpp.validation biosimulators_utils.omex_meta biosimulators_utils.omex_meta.data_model biosimulators_utils.omex_meta.io biosimulators_utils.omex_meta.utils biosimulators_utils.omex_meta.validation biosimulators_utils.ref biosimulators_utils.ref.data_model biosimulators_utils.ref.utils biosimulators_utils.report biosimulators_utils.report.data_model biosimulators_utils.report.io biosimulators_utils.report.warnings biosimulators_utils.sedml biosimulators_utils.sedml.data_model biosimulators_utils.sedml.exceptions biosimulators_utils.sedml.exec biosimulators_utils.sedml.io biosimulators_utils.sedml.math biosimulators_utils.sedml.model_utils biosimulators_utils.sedml.utils biosimulators_utils.sedml.validation biosimulators_utils.sedml.warnings biosimulators_utils.simulator biosimulators_utils.simulator.cli biosimulators_utils.simulator.data_model biosimulators_utils.simulator.environ biosimulators_utils.simulator.exceptions biosimulators_utils.simulator.exec biosimulators_utils.simulator.io biosimulators_utils.simulator.specs biosimulators_utils.simulator.utils biosimulators_utils.simulator_registry biosimulators_utils.simulator_registry.data_model biosimulators_utils.simulator_registry.process_submission biosimulators_utils.simulator_registry.query biosimulators_utils.simulator_registry.submit biosimulators_utils.utils biosimulators_utils.utils.core biosimulators_utils.utils.identifiers_org biosimulators_utils.utils.logging biosimulators_utils.viz biosimulators_utils.viz.data_model biosimulators_utils.viz.io biosimulators_utils.viz.utils biosimulators_utils.viz.vega biosimulators_utils.viz.vega.escher biosimulators_utils.viz.vega.escher.core biosimulators_utils.viz.vega.ginml biosimulators_utils.viz.vega.ginml.core biosimulators_utils.viz.vega.sbgn biosimulators_utils.viz.vega.sbgn.core biosimulators_utils.viz.vega.utils biosimulators_utils.viz.warnings biosimulators_utils.warnings biosimulators_utils.xml biosimulators_utils.xml.utils MorpheusML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) N name (biosimulators_utils.sedml.data_model.AbstractTask attribute) (biosimulators_utils.sedml.data_model.AddElementModelChange attribute) (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.DataGenerator attribute) (biosimulators_utils.sedml.data_model.DataSet attribute) (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.Model attribute) (biosimulators_utils.sedml.data_model.ModelAttributeChange attribute) (biosimulators_utils.sedml.data_model.ModelChange attribute) (biosimulators_utils.sedml.data_model.OneStepSimulation attribute) (biosimulators_utils.sedml.data_model.Output attribute) (biosimulators_utils.sedml.data_model.Parameter attribute) (biosimulators_utils.sedml.data_model.Plot attribute) (biosimulators_utils.sedml.data_model.Plot2D attribute) (biosimulators_utils.sedml.data_model.Plot3D attribute) (biosimulators_utils.sedml.data_model.Range attribute) (biosimulators_utils.sedml.data_model.RemoveElementModelChange attribute) (biosimulators_utils.sedml.data_model.RepeatedTask attribute) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange attribute) (biosimulators_utils.sedml.data_model.Report attribute) (biosimulators_utils.sedml.data_model.SedIdGroupMixin attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Simulation attribute) (biosimulators_utils.sedml.data_model.SteadyStateSimulation attribute) (biosimulators_utils.sedml.data_model.Style attribute) (biosimulators_utils.sedml.data_model.Surface attribute) (biosimulators_utils.sedml.data_model.Task attribute) (biosimulators_utils.sedml.data_model.UniformRange attribute) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) (biosimulators_utils.sedml.data_model.Variable attribute) (biosimulators_utils.sedml.data_model.VectorRange attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgCountry attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) namespace (biosimulators_utils.data_model.Identifier attribute) NCS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) NeuroML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) NEURON_SESSION (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) new_elements (biosimulators_utils.sedml.data_model.AddElementModelChange attribute) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange attribute) new_value (biosimulators_utils.sedml.data_model.AlgorithmParameterChange attribute) (biosimulators_utils.sedml.data_model.ModelAttributeChange attribute) NMODL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) NoCurvesWarning NoDataSetsWarning none (biosimulators_utils.sedml.data_model.LineStyleType attribute) (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) NONE_DATETIME (biosimulators_utils.combine.io.CombineArchiveReader attribute) none_sorted() (in module biosimulators_utils.utils.core) NoOutputsWarning NoSedmlError NoSurfacesWarning NoTasksWarning nquads (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat attribute) (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) ntriples (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat attribute) (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) number_of_points (biosimulators_utils.sedml.data_model.UniformRange property) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation property) number_of_steps (biosimulators_utils.sedml.data_model.UniformRange attribute) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) NuML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) O object (biosimulators_utils.data_model.ValueType attribute) (biosimulators_utils.omex_meta.data_model.Triple attribute) ODE (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) ODT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) official (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) OMEX (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) OMEX_MANIFEST (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) OMEX_METADATA (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) OMEX_METADATA_INPUT_FORMAT (biosimulators_utils.config.Config attribute) OMEX_METADATA_OUTPUT_FORMAT (biosimulators_utils.config.Config attribute) OMEX_METADATA_SCHEMA (biosimulators_utils.config.Config attribute) OmexMetadataInputFormat (class in biosimulators_utils.omex_meta.data_model) OmexMetadataOutputFormat (class in biosimulators_utils.omex_meta.data_model) OmexMetadataSchema (class in biosimulators_utils.omex_meta.data_model) OneStepSimulation (class in biosimulators_utils.sedml.data_model) OntologyTerm (class in biosimulators_utils.data_model) order (biosimulators_utils.sedml.data_model.SubTask attribute) OTHER (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) other_name (biosimulators_utils.data_model.Person attribute) out_dir (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) output (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) Output (class in biosimulators_utils.sedml.data_model) output_end_time (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) output_start_time (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation attribute) OutputLog (class in biosimulators_utils.log.data_model) outputs (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.sedml.data_model.SedDocument attribute) OWL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) P pad_arrays_to_consistent_shapes() (in module biosimulators_utils.utils.core) pages (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] Parameter (class in biosimulators_utils.sedml.data_model) parameters (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.DataGenerator attribute) (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) parent (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) parse_dataset_str_list_values() (biosimulators_utils.report.io.ReportReader static method) parse_dataset_str_value() (biosimulators_utils.report.io.ReportReader static method) parse_triples_to_schema() (biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaReader class method) parse_value() (in module biosimulators_utils.utils.core) pass (biosimulators_utils.config.Colors attribute) passed (biosimulators_utils.config.Colors attribute) patch_dict() (in module biosimulators_utils.utils.core) pattern (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) PDF (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) pdf (biosimulators_utils.viz.data_model.VizFormat attribute) PERL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) Person (class in biosimulators_utils.data_model) pharmML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) PHP (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) piecewise() (in module biosimulators_utils.sedml.math) Plot (class in biosimulators_utils.sedml.data_model) Plot2D (class in biosimulators_utils.sedml.data_model) Plot2DLog (class in biosimulators_utils.log.data_model) Plot3D (class in biosimulators_utils.sedml.data_model) Plot3DLog (class in biosimulators_utils.log.data_model) PLOTS_PATH (biosimulators_utils.config.Config attribute) plus (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) PNG (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) png (biosimulators_utils.viz.data_model.VizFormat attribute) POSTSCRIPT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) PPT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) PPTX (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) predicate (biosimulators_utils.omex_meta.data_model.Triple attribute) prefix (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) prepare_agent_data() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) prepare_simularium_fp() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter static method) provider_code (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) PSD (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) publish_simulation_project() (in module biosimulators_utils.biosimulations.utils) pubmed_central_id (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] pubmed_id (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] PubMedCentralOpenAccesGraphic (class in biosimulators_utils.ref.data_model) pull_docker_image() (in module biosimulators_utils.image) Python (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) python (biosimulators_utils.log.data_model.StandardOutputErrorCapturerLevel attribute) Q queued (biosimulators_utils.config.Colors attribute) QUEUED (biosimulators_utils.log.data_model.Status attribute) QUICKTIME (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) R R (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) R_Project (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) raise_errors_warnings() (in module biosimulators_utils.utils.core) range (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.RepeatedTask attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) Range (class in biosimulators_utils.sedml.data_model) ranges (biosimulators_utils.sedml.data_model.RepeatedTask attribute) RBA (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) rdf_triples (biosimulators_utils.omex_meta.data_model.OmexMetadataSchema attribute) RDF_XML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) rdfa (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat attribute) rdfxml (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat attribute) (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) rdfxml_abbrev (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) rdfxml_xmp (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) read_escher_map_config() (in module biosimulators_utils.viz.vega.escher.core) read_manifest() (biosimulators_utils.combine.io.CombineArchiveReader method) read_model_output_dataframe() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method) read_omex_meta_file() (in module biosimulators_utils.omex_meta.io) read_omex_meta_files_for_archive() (in module biosimulators_utils.omex_meta.io) read_simulator_specs() (in module biosimulators_utils.simulator.io) Reference (class in biosimulators_utils.ref.data_model) references (biosimulators_utils.biosimulations.data_model.Metadata attribute) relay (biosimulators_utils.log.utils.StandardOutputErrorCapturer attribute) remove_algorithm_parameter_changes() (in module biosimulators_utils.sedml.utils) remove_label_from_issue() (biosimulators_utils.gh_action.core.GitHubAction class method) remove_model_changes() (in module biosimulators_utils.sedml.utils) remove_plots() (in module biosimulators_utils.sedml.utils) RemoveElementModelChange (class in biosimulators_utils.sedml.data_model) RepeatDataSetLabelsWarning RepeatedTask (class in biosimulators_utils.sedml.data_model) replace_complex_data_generators_with_generators_for_individual_variables() (in module biosimulators_utils.sedml.utils) ReplaceElementModelChange (class in biosimulators_utils.sedml.data_model) Report (class in biosimulators_utils.sedml.data_model) REPORT_FORMATS (biosimulators_utils.config.Config attribute) ReportFormat (class in biosimulators_utils.report.data_model) ReportLog (class in biosimulators_utils.log.data_model) ReportReader (class in biosimulators_utils.report.io) ReportResults (class in biosimulators_utils.report.data_model) REPORTS_PATH (biosimulators_utils.config.Config attribute) ReportWriter (class in biosimulators_utils.report.io) reset_issue_labels() (biosimulators_utils.gh_action.core.GitHubAction class method) reset_model_for_each_iteration (biosimulators_utils.sedml.data_model.RepeatedTask attribute) resolve_model() (in module biosimulators_utils.sedml.utils) resolve_model_and_apply_xml_changes() (in module biosimulators_utils.sedml.utils) resolve_range() (in module biosimulators_utils.sedml.utils) resources (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) ror_id (biosimulators_utils.utils.identifiers_org.IdentifiersOrgInstitution attribute) RST (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) RUBY (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) run() (biosimulators_utils.archive.io.ArchiveReader method) (biosimulators_utils.archive.io.ArchiveWriter method) (biosimulators_utils.combine.io.CombineArchiveReader method) (biosimulators_utils.combine.io.CombineArchiveWriter method) (biosimulators_utils.combine.io.CombineArchiveZipReader class method) (biosimulators_utils.gh_action.core.GitHubAction method) (biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaReader method) (biosimulators_utils.omex_meta.io.BiosimulationsOmexMetaWriter method) (biosimulators_utils.omex_meta.io.TriplesOmexMetaReader method) (biosimulators_utils.omex_meta.io.TriplesOmexMetaWriter method) (biosimulators_utils.report.io.ReportReader method) (biosimulators_utils.report.io.ReportWriter method) (biosimulators_utils.sedml.io.SedmlSimulationReader method) (biosimulators_utils.sedml.io.SedmlSimulationWriter method) run_simulation_project() (in module biosimulators_utils.biosimulations.utils) running (biosimulators_utils.config.Colors attribute) RUNNING (biosimulators_utils.log.data_model.Status attribute) S sample_id (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespace attribute) (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) sanitize_model() (in module biosimulators_utils.model_lang.xpp.validation) save_keys_to_license_file() (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method) SAVE_PLOT_DATA (biosimulators_utils.config.Config attribute) save_simularium_file() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter static method) SBGN (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) sbgn_pd_map_to_vega() (in module biosimulators_utils.viz.vega.sbgn.core) SBML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) SBOL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) SBOL_VISUAL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) Scilab (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) sed_documents (biosimulators_utils.log.data_model.CombineArchiveLog attribute) SED_ML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) SedBase (class in biosimulators_utils.sedml.data_model) SedDocument (class in biosimulators_utils.sedml.data_model) SedDocumentLog (class in biosimulators_utils.log.data_model) SedDocumentResults (class in biosimulators_utils.report.data_model) SedIdGroupMixin (class in biosimulators_utils.sedml.data_model) SedmlExecutionError SedmlFeatureNotSupportedWarning SedmlSimulationReader (class in biosimulators_utils.sedml.io) SedmlSimulationWriter (class in biosimulators_utils.sedml.io) set_model_filepath() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive method) SetValueComputeModelChange (class in biosimulators_utils.sedml.data_model) SHOCKWAVE_FLASH (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) SimBiology_Project (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) simulation (biosimulators_utils.sedml.data_model.Task attribute) Simulation (class in biosimulators_utils.sedml.data_model) simulations (biosimulators_utils.sedml.data_model.SedDocument attribute) simulator_details (biosimulators_utils.log.data_model.TaskLog attribute) SimulatorSubmission (class in biosimulators_utils.simulator_registry.data_model) size (biosimulators_utils.sedml.data_model.MarkerStyle attribute) skip (biosimulators_utils.config.Colors attribute) skip_reason (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) skipped (biosimulators_utils.config.Colors attribute) SKIPPED (biosimulators_utils.log.data_model.Status attribute) SLI (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) Smoldyn (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) SmoldynCombineArchive (class in biosimulators_utils.model_lang.smoldyn.simularium_converter) SmoldynDataConverter (class in biosimulators_utils.model_lang.smoldyn.simularium_converter) SO (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) SoftwareInterface (class in biosimulators_utils.simulator.data_model) solid (biosimulators_utils.sedml.data_model.LineStyleType attribute) source (biosimulators_utils.sedml.data_model.Model attribute) specifications_patch (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) specifications_url (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) SQL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) square (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) StandardOutputErrorCapturer (class in biosimulators_utils.log.utils) StandardOutputErrorCapturerLevel (class in biosimulators_utils.log.data_model) StandardOutputNotLoggedWarning star (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) start (biosimulators_utils.sedml.data_model.UniformRange attribute) start() (biosimulators_utils.licensing.core.LicenseManager method) (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method) status (biosimulators_utils.log.data_model.CombineArchiveLog attribute) (biosimulators_utils.log.data_model.Log attribute) (biosimulators_utils.log.data_model.OutputLog attribute) (biosimulators_utils.log.data_model.Plot2DLog attribute) (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.log.data_model.ReportLog attribute) (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.log.data_model.TaskLog attribute) Status (class in biosimulators_utils.log.data_model) SteadyStateSimulation (class in biosimulators_utils.sedml.data_model) step (biosimulators_utils.sedml.data_model.OneStepSimulation attribute) string (biosimulators_utils.data_model.ValueType attribute) style (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.Surface attribute) Style (class in biosimulators_utils.sedml.data_model) sub_tasks (biosimulators_utils.sedml.data_model.RepeatedTask attribute) subject (biosimulators_utils.omex_meta.data_model.Triple attribute) submit_simulator_to_biosimulators_registry() (in module biosimulators_utils.simulator_registry.submit) SubTask (class in biosimulators_utils.sedml.data_model) succeeded (biosimulators_utils.config.Colors attribute) SUCCEEDED (biosimulators_utils.log.data_model.Status attribute) success (biosimulators_utils.config.Colors attribute) Surface (class in biosimulators_utils.sedml.data_model) surfaces (biosimulators_utils.log.data_model.Plot3DLog attribute) (biosimulators_utils.sedml.data_model.Plot3D attribute) SVG (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) svg (biosimulators_utils.viz.data_model.VizFormat attribute) SVGZ (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) symbol (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.Variable attribute) Symbol (class in biosimulators_utils.sedml.data_model) T tag_and_push_docker_image() (in module biosimulators_utils.image) tags (biosimulators_utils.biosimulations.data_model.Metadata attribute) target (biosimulators_utils.sedml.data_model.AddElementModelChange attribute) (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.ModelAttributeChange attribute) (biosimulators_utils.sedml.data_model.ModelChange attribute) (biosimulators_utils.sedml.data_model.RemoveElementModelChange attribute) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.TargetGroupMixin attribute) (biosimulators_utils.sedml.data_model.Variable attribute) target_namespaces (biosimulators_utils.sedml.data_model.AddElementModelChange attribute) (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.ModelAttributeChange attribute) (biosimulators_utils.sedml.data_model.ModelChange attribute) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) (biosimulators_utils.sedml.data_model.TargetGroupMixin attribute) (biosimulators_utils.sedml.data_model.Variable attribute) TargetGroupMixin (class in biosimulators_utils.sedml.data_model) task (biosimulators_utils.sedml.data_model.SubTask attribute) (biosimulators_utils.sedml.data_model.Variable attribute) Task (class in biosimulators_utils.sedml.data_model) TaskLog (class in biosimulators_utils.log.data_model) tasks (biosimulators_utils.log.data_model.SedDocumentLog attribute) (biosimulators_utils.sedml.data_model.SedDocument attribute) TEXT (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) text (biosimulators_utils.gh_action.data_model.Comment attribute) thickness (biosimulators_utils.sedml.data_model.LineStyle attribute) TIFF (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) time (biosimulators_utils.sedml.data_model.Symbol attribute) title (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] to_json() (biosimulators_utils.log.data_model.CombineArchiveLog method) (biosimulators_utils.log.data_model.Log method) (biosimulators_utils.log.data_model.OutputLog method) (biosimulators_utils.log.data_model.Plot2DLog method) (biosimulators_utils.log.data_model.Plot3DLog method) (biosimulators_utils.log.data_model.ReportLog method) (biosimulators_utils.log.data_model.SedDocumentLog method) (biosimulators_utils.log.data_model.TaskLog method) to_tuple() (biosimulators_utils.archive.data_model.Archive method) (biosimulators_utils.archive.data_model.ArchiveFile method) (biosimulators_utils.biosimulations.data_model.Citation method) (biosimulators_utils.biosimulations.data_model.ExternalReferences method) (biosimulators_utils.biosimulations.data_model.Metadata method) (biosimulators_utils.combine.data_model.CombineArchive method) (biosimulators_utils.combine.data_model.CombineArchiveContent method) (biosimulators_utils.data_model.Identifier method) (biosimulators_utils.data_model.Person method) (biosimulators_utils.sedml.data_model.AddElementModelChange method) (biosimulators_utils.sedml.data_model.Algorithm method) (biosimulators_utils.sedml.data_model.AlgorithmParameterChange method) (biosimulators_utils.sedml.data_model.ComputeModelChange method) (biosimulators_utils.sedml.data_model.Curve method) (biosimulators_utils.sedml.data_model.DataGenerator method) (biosimulators_utils.sedml.data_model.DataSet method) (biosimulators_utils.sedml.data_model.FillStyle method) (biosimulators_utils.sedml.data_model.FunctionalRange method) (biosimulators_utils.sedml.data_model.LineStyle method) (biosimulators_utils.sedml.data_model.MarkerStyle method) (biosimulators_utils.sedml.data_model.Model method) (biosimulators_utils.sedml.data_model.ModelAttributeChange method) (biosimulators_utils.sedml.data_model.OneStepSimulation method) (biosimulators_utils.sedml.data_model.Parameter method) (biosimulators_utils.sedml.data_model.Plot2D method) (biosimulators_utils.sedml.data_model.Plot3D method) (biosimulators_utils.sedml.data_model.RemoveElementModelChange method) (biosimulators_utils.sedml.data_model.RepeatedTask method) (biosimulators_utils.sedml.data_model.ReplaceElementModelChange method) (biosimulators_utils.sedml.data_model.Report method) (biosimulators_utils.sedml.data_model.SedBase method) (biosimulators_utils.sedml.data_model.SedDocument method) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange method) (biosimulators_utils.sedml.data_model.SteadyStateSimulation method) (biosimulators_utils.sedml.data_model.Style method) (biosimulators_utils.sedml.data_model.SubTask method) (biosimulators_utils.sedml.data_model.Surface method) (biosimulators_utils.sedml.data_model.Task method) (biosimulators_utils.sedml.data_model.UniformRange method) (biosimulators_utils.sedml.data_model.UniformTimeCourseSimulation method) (biosimulators_utils.sedml.data_model.Variable method) (biosimulators_utils.sedml.data_model.VectorRange method) (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission method) translate_data_object() (biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter method) (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method) triangleDown (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) triangleLeft (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) triangleRight (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) triangleUp (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) Triple (class in biosimulators_utils.omex_meta.data_model) TriplesOmexMetaReader (class in biosimulators_utils.omex_meta.io) TriplesOmexMetaWriter (class in biosimulators_utils.omex_meta.io) TSV (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) tsv (biosimulators_utils.report.data_model.ReportFormat attribute) turtle (biosimulators_utils.omex_meta.data_model.OmexMetadataInputFormat attribute) (biosimulators_utils.omex_meta.data_model.OmexMetadataOutputFormat attribute) type (biosimulators_utils.sedml.data_model.LineStyle attribute) (biosimulators_utils.sedml.data_model.MarkerStyle attribute) (biosimulators_utils.sedml.data_model.UniformRange attribute) U UniformRange (class in biosimulators_utils.sedml.data_model) UniformTimeCourseSimulation (class in biosimulators_utils.sedml.data_model) UnsupportedModelLanguageError updated (biosimulators_utils.biosimulations.data_model.Metadata attribute) url (biosimulators_utils.data_model.Identifier attribute) url_pattern (biosimulators_utils.utils.identifiers_org.IdentifiersOrgNamespaceResource attribute) V validate() (in module biosimulators_utils.combine.validation) validate_algorithm() (in module biosimulators_utils.sedml.validation) validate_biosimulations_api_response() (in module biosimulators_utils.biosimulations.utils) validate_biosimulations_metadata() (in module biosimulators_utils.omex_meta.validation) validate_biosimulations_metadata_for_uri() (in module biosimulators_utils.omex_meta.validation) validate_calculation() (in module biosimulators_utils.sedml.validation) validate_content() (in module biosimulators_utils.combine.validation) validate_data_generator() (in module biosimulators_utils.sedml.validation) validate_data_generator_variables() (in module biosimulators_utils.sedml.validation) validate_doc() (in module biosimulators_utils.sedml.validation) validate_format() (in module biosimulators_utils.combine.validation) validate_identifiers_org_uri() (in module biosimulators_utils.utils.identifiers_org) validate_image (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) VALIDATE_IMAGES (biosimulators_utils.config.Config attribute) VALIDATE_IMPORTED_MODEL_FILES (biosimulators_utils.config.Config attribute) validate_model() (in module biosimulators_utils.model_lang.cellml.validation) (in module biosimulators_utils.model_lang.lems.validation) (in module biosimulators_utils.model_lang.neuroml.validation) (in module biosimulators_utils.model_lang.sbml.validation) (in module biosimulators_utils.model_lang.xpp.validation) (in module biosimulators_utils.sedml.validation) validate_model_change_types() (in module biosimulators_utils.sedml.validation) validate_model_changes() (in module biosimulators_utils.sedml.validation) validate_model_l1() (in module biosimulators_utils.model_lang.neuroml.validation) validate_model_l2() (in module biosimulators_utils.model_lang.neuroml.validation) validate_model_language() (in module biosimulators_utils.sedml.validation) validate_model_source() (in module biosimulators_utils.sedml.validation) validate_model_version_1_0() (in module biosimulators_utils.model_lang.cellml.validation) validate_model_version_1_1() (in module biosimulators_utils.model_lang.cellml.validation) validate_model_version_2() (in module biosimulators_utils.model_lang.cellml.validation) validate_model_with_language() (in module biosimulators_utils.sedml.validation) validate_neuroml2_lems_file() (in module biosimulators_utils.model_lang.lems.validation) VALIDATE_OMEX_MANIFESTS (biosimulators_utils.config.Config attribute) VALIDATE_OMEX_METADATA (biosimulators_utils.config.Config attribute) validate_output() (in module biosimulators_utils.sedml.validation) validate_reference() (in module biosimulators_utils.sedml.validation) validate_repeated_task_has_one_model() (in module biosimulators_utils.sedml.validation) VALIDATE_RESULTS (biosimulators_utils.config.Config attribute) VALIDATE_SEDML (biosimulators_utils.config.Config attribute) VALIDATE_SEDML_MODELS (biosimulators_utils.config.Config attribute) validate_simulation() (in module biosimulators_utils.sedml.validation) validate_simulation_type() (in module biosimulators_utils.sedml.validation) validate_str_value() (in module biosimulators_utils.utils.core) validate_target() (in module biosimulators_utils.sedml.validation) validate_target_xpaths() (in module biosimulators_utils.sedml.validation) validate_task() (in module biosimulators_utils.sedml.validation) validate_uniform_range() (in module biosimulators_utils.sedml.validation) validate_value() (in module biosimulators_utils.utils.core) validate_xpaths_ref_to_unique_objects() (in module biosimulators_utils.xml.utils) validated (biosimulators_utils.simulator_registry.data_model.IssueLabel attribute) value (biosimulators_utils.sedml.data_model.Parameter attribute) values (biosimulators_utils.sedml.data_model.VectorRange attribute) ValueType (class in biosimulators_utils.data_model) Variable (class in biosimulators_utils.sedml.data_model) VariableResults (class in biosimulators_utils.report.data_model) variables (biosimulators_utils.sedml.data_model.ComputeModelChange attribute) (biosimulators_utils.sedml.data_model.DataGenerator attribute) (biosimulators_utils.sedml.data_model.FunctionalRange attribute) (biosimulators_utils.sedml.data_model.SetValueComputeModelChange attribute) VCML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) vDash (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) VectorRange (class in biosimulators_utils.sedml.data_model) Vega (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) Vega_Lite (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) VERBOSE (biosimulators_utils.config.Config attribute) verify_smoldyn_in_manifest() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive method) version (biosimulators_utils.sedml.data_model.SedDocument attribute) (biosimulators_utils.simulator_registry.data_model.SimulatorSubmission attribute) VIZ_FORMATS (biosimulators_utils.config.Config attribute) VizFormat (class in biosimulators_utils.viz.data_model) volume (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] W warn() (in module biosimulators_utils.warnings) warned (biosimulators_utils.config.Colors attribute) warning (biosimulators_utils.config.Colors attribute) warnings (biosimulators_utils.combine.io.CombineArchiveReader attribute) (biosimulators_utils.combine.io.CombineArchiveWriter attribute) (biosimulators_utils.sedml.io.SedmlSimulationReader attribute) web_application (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) web_service (biosimulators_utils.simulator.data_model.SoftwareInterface attribute) WEBP (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) write() (biosimulators_utils.log.utils.StandardOutputErrorCapturer method) write_manifest() (biosimulators_utils.combine.io.CombineArchiveWriter method) write_model_output_dataframe_to_csv() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method) write_omex_meta_file() (in module biosimulators_utils.omex_meta.io) write_plot_2d() (in module biosimulators_utils.viz.io) write_plot_3d() (in module biosimulators_utils.viz.io) X x_data_generator (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.Surface attribute) x_scale (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.Surface attribute) xCross (biosimulators_utils.sedml.data_model.MarkerStyleType attribute) XLS (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XLSX (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) xlsx (biosimulators_utils.report.data_model.ReportFormat attribute) XML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XPP (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) XPP_AUTO (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XPP_SET (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XSL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XUL (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) XYZ (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) Y y_data_generator (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.Surface attribute) y_scale (biosimulators_utils.sedml.data_model.Curve attribute) (biosimulators_utils.sedml.data_model.Surface attribute) YAML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) year (biosimulators_utils.biosimulations.data_model.Citation attribute) (biosimulators_utils.ref.data_model.JournalArticle attribute), [1] Z z_data_generator (biosimulators_utils.sedml.data_model.Surface attribute) z_scale (biosimulators_utils.sedml.data_model.Surface attribute) ZGINML (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute) (biosimulators_utils.sedml.data_model.ModelLanguage attribute) (biosimulators_utils.sedml.data_model.ModelLanguageEdamId attribute) (biosimulators_utils.sedml.data_model.ModelLanguagePattern attribute) ZIP (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute) (biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute)
