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__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)
_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
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.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.bngl.utils
module
biosimulators_utils.model_lang.bngl.validation
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.rba.utils
module
biosimulators_utils.model_lang.rba.validation
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.utils
module
biosimulators_utils.model_lang.smoldyn.validation
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
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)
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)
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
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)
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)
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)
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)
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_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.bngl.utils)
(in module biosimulators_utils.model_lang.cellml.utils)
(in module biosimulators_utils.model_lang.rba.utils)
(in module biosimulators_utils.model_lang.sbml.utils)
(in module biosimulators_utils.model_lang.smoldyn.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_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)
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.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.FunctionalRange 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.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_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)
linear (biosimulators_utils.sedml.data_model.AxisScale attribute)
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)
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.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.bngl.utils
biosimulators_utils.model_lang.bngl.validation
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.rba.utils
biosimulators_utils.model_lang.rba.validation
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.utils
biosimulators_utils.model_lang.smoldyn.validation
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.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_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)
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_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)
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)
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() (in module biosimulators_utils.model_lang.bngl.validation)
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)
save_keys_to_license_file() (biosimulators_utils.licensing.gurobi.GurobiLicenseManager method)
SAVE_PLOT_DATA (biosimulators_utils.config.Config attribute)
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)
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)
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)
SO (biosimulators_utils.combine.data_model.CombineArchiveContentFormat attribute)
(biosimulators_utils.combine.data_model.CombineArchiveContentFormatPattern attribute)
SoftwareInterface (class in biosimulators_utils.simulator.data_model)
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)
StandardOutputErrorCapturer (class in biosimulators_utils.log.utils)
StandardOutputErrorCapturerLevel (class in biosimulators_utils.log.data_model)
StandardOutputNotLoggedWarning
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)
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)
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.FunctionalRange 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.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)
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.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.bngl.validation)
(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.rba.validation)
(in module biosimulators_utils.model_lang.sbml.validation)
(in module biosimulators_utils.model_lang.smoldyn.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)
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)
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_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)
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)