Index

A

ACSetsStockFlowModel (class in mira.modeling.acsets.stockflow) add_controller() (ControlledConversion method) (ControlledDegradation method) (ControlledProduction method) (GroupedControlledConversion method) (GroupedControlledDegradation method) (GroupedControlledProduction method) add_node() (Neo4jClient method) add_observable() (in module mira.modeling.amr.ops) add_observable_pattern() (in module mira.metamodel.ops) add_parameter() (in module mira.modeling.amr.ops) (TemplateModel method) add_relation() (Neo4jClient method) add_resource() (in module mira.dkg) add_state() (in module mira.modeling.amr.ops) add_template() (TemplateModel method)

add_transition() (in module mira.modeling.amr.ops) (TemplateModel method) aggregate_parameters() (in module mira.metamodel.ops) (in module mira.modeling.amr.ops) alts (NodeInfo attribute) AMRPetriNetModel (class in mira.modeling.amr.petrinet) AMRRegNetModel (class in mira.modeling.amr.regnet) AMRStockFlowModel (class in mira.modeling.amr.stockflow) Annotations (class in mira.metamodel.template_model) annotations (TemplateModel attribute) as_askem_entity() (Entity method) assemble_parameter() (Model method) assemble_variable() (Model method) associate() (in module mira.terarium_client) Author (class in mira.metamodel.template_model) authors (Annotations attribute)

B

BilayerModel (class in mira.modeling.bilayer)

C

check_simplify_rate_laws() (in module mira.metamodel.ops) clean_response() (in module mira.sources.sympy_ode.llm_util) CodeExecutionError compare_models() (TemplateModelComparison method) compose() (in module mira.metamodel.composition) compose_two_models() (in module mira.metamodel.composition) Concept (class in mira.metamodel.template_model) concept (Initial attribute) (ModelParameter attribute) (Variable attribute) concept_nodes (ModelComparisonGraphdata attribute) Config (class in mira.dkg.models) consumed (Transition attribute) context (Concept attribute) (Observable attribute) (Parameter attribute) context_refinement() (in module mira.metamodel.templates) control (Transition attribute)

ControlledConversion (class in mira.metamodel.templates) ControlledDegradation (class in mira.metamodel.templates) ControlledProduction (class in mira.metamodel.templates) ControlledReplication (class in mira.metamodel.templates) controller (ControlledConversion attribute) (ControlledDegradation attribute) (ControlledProduction attribute) (ControlledReplication attribute) controllers (GroupedControlledConversion attribute) (GroupedControlledDegradation attribute) (GroupedControlledProduction attribute) conversion_to_deg_prod() (in module mira.metamodel.templates) counts_to_dimensionless() (in module mira.metamodel.ops) (in module mira.modeling.amr.ops) create_edge() (AMRRegNetModel method) create_single_property_node_index() (Neo4jClient method) create_tx() (Neo4jClient method) curie (NodeInfo attribute)

D

data (Variable attribute) deactivate() (Template method) deactivate_templates() (in module mira.metamodel.ops) Decapode (class in mira.metamodel.decapodes) definition (NodeInfo attribute) deprecated (NodeInfo attribute) description (Annotations attribute) (Concept attribute) (ModelParameter attribute) (Observable attribute) (Parameter attribute) diseases (Annotations attribute)

display_name (Concept attribute) (ModelParameter attribute) (Observable attribute) (Parameter attribute) (Template attribute) Distribution (class in mira.metamodel.template_model) distribution (ModelParameter attribute) (Parameter attribute) DKGConfig (class in mira.dkg.construct) DOCKER_FILES_ROOT (in module mira.dkg.utils) draw_graph() (TemplateModel method) (TemplateModelDelta method) draw_jupyter() (TemplateModel method)

E

eliminate_duplicate_parameter() (TemplateModel method) eliminate_parameter() (TemplateModel method) eliminate_unused_parameters() (TemplateModel method) Entity (class in mira.dkg.client) EQUIVALENCE_TYPES (in module mira.dkg.askemo.api) expression (Initial attribute) (Observable attribute) (RootVariable attribute) (Unit attribute) (Variable attribute)

expression_to_mathml() (in module mira.metamodel.io) extend() (TemplateModel method) extract_ode_str_from_base64_image() (in module mira.sources.sympy_ode.llm_util) extract_ode_str_from_base64_pdf() (in module mira.sources.sympy_ode.llm_util) extract_ontology_subtree() (in module mira.dkg.construct)

F

find_models_with_grounding() (in module mira.metamodel.search) for_jupyter() (GraphicalModel class method) (TemplateModelDelta class method) from_data() (Entity class method) from_json() (Annotations class method) (Concept class method) (Initial class method) (Parameter class method) (Template class method) (TemplateModel class method)

from_template_model() (GraphicalModel class method) from_template_models() (ModelComparisonGraphdata class method) function_str (Op1 attribute) (Op2 attribute)

G

generate_model_graph() (TemplateModel method) get_all_used_parameters() (TemplateModel method) get_app() (in module mira.dkg.metaregistry.utils) get_askem_climate_ontology_terms() (in module mira.dkg.askemo.api) get_askemo_terms() (in module mira.dkg.askemo.api) get_askemosw_terms() (in module mira.dkg.askemo.api) get_binding_templates() (in module mira.metamodel.templates) get_budyko_seller_decapode_json() (in module mira.examples.decapodes.decapodes_examples) get_budyko_sellers_example() (in module mira.examples.decapodes.decapodes_examples) get_common_parents() (Neo4jClient method) get_concept() (TemplateModel method) get_concept_comparison_table() (in module mira.metamodel.comparison) get_concept_names() (Template method) get_concepts() (GroupedControlledConversion method) (GroupedControlledDegradation method) (GroupedControlledProduction method) (MultiConversion method) (ReversibleFlux method) (StaticConcept method) (Template method) get_concepts_by_name() (TemplateModel method) get_concepts_by_role() (Template method) get_concepts_flat() (Template method) get_concepts_from_odes() (in module mira.sources.sympy_ode.llm_util) get_concepts_map() (TemplateModel method) get_concepts_name_map() (TemplateModel method) get_controllers() (Template method) get_curie() (Concept method) get_curie_str() (Concept method) get_dkg_refinement_closure() (in module mira.metamodel.comparison) get_entities_web() (in module mira.dkg.web_client) get_entity() (Neo4jClient method) get_entity_web() (in module mira.dkg.web_client) get_expression_parameter_names() (Distribution method) get_friction_decaexpr() (in module mira.examples.decapodes.decapodes_examples) get_friction_decapode() (in module mira.examples.decapodes.decapodes_examples) get_friction_decapode_json() (in module mira.examples.decapodes.decapodes_examples) get_ice_decapode_json() (in module mira.examples.decapodes.decapodes_examples) get_ice_dynamics_example() (in module mira.examples.decapodes.decapodes_examples) get_included_identifiers() (Concept method) get_independent_mass_action_rate_law() (Template method) get_interactor_rate_law() (Template method) get_interactors() (Template method) get_key() (Concept method) (ControlledConversion method) (ControlledDegradation method) (ControlledProduction method) (ControlledReplication method) (GroupedControlledConversion method) (GroupedControlledDegradation method) (GroupedControlledProduction method) (MultiConversion method) (NaturalConversion method) (NaturalDegradation method) (NaturalProduction method) (NaturalReplication method) (ReversibleFlux method) (StaticConcept method) (Template method)

get_lexical() (Neo4jClient method) get_lexical_web() (in module mira.dkg.web_client) get_mass_action_rate_law() (Template method) get_mass_action_symbol() (Template method) get_node_counter() (Neo4jClient method) get_oscillator_decaexpr() (in module mira.examples.decapodes.decapodes_examples) get_oscillator_decapode() (in module mira.examples.decapodes.decapodes_examples) get_oscillator_decapode_json() (in module mira.examples.decapodes.decapodes_examples) get_parameter_names() (Initial method) (Observable method) (Template method) get_parameters_from_expression() (TemplateModel method) get_parameters_from_rate_law() (TemplateModel method) get_parseable_expression() (in module mira.metamodel.utils) get_prefixes() (in module mira.dkg.construct_registry) get_relations_web() (in module mira.dkg.web_client) get_rhs() (OdeModel method) get_sbml_model() (in module mira.sources.biomodels) get_similarity_score() (ModelComparisonGraphdata method) get_similarity_scores() (ModelComparisonGraphdata method) get_sympy() (in module mira.sources.util) get_template_model() (in module mira.sources.biomodels) (in module mira.terarium_client) get_term_roles() (in module mira.metamodel.ops) get_transitive_closure() (Neo4jClient method) get_transitive_closure_web() (in module mira.dkg.web_client) get_unit_terms() (in module mira.dkg.units) graph_as_json() (TemplateModel method) (TemplateModelDelta method) GraphicalModel (class in mira.modeling.viz) ground_web() (in module mira.dkg.web_client) GroupedControlledConversion (class in mira.metamodel.templates) GroupedControlledDegradation (class in mira.metamodel.templates) GroupedControlledProduction (class in mira.metamodel.templates)

H

has_controller() (in module mira.metamodel.templates) has_outcome() (in module mira.metamodel.templates)

has_subject() (in module mira.metamodel.templates) hosts (Annotations attribute)

I

id (Op1 attribute) (Op2 attribute) (Summation attribute) (TangentVariable attribute) (Variable attribute) identifiers (Concept attribute) (Observable attribute) (Parameter attribute) (Variable attribute) image_file_to_odes_str() (in module mira.sources.sympy_ode.llm_util) image_to_odes_str() (in module mira.sources.sympy_ode.llm_util) incl_var (TangentVariable attribute)

Initial (class in mira.metamodel.template_model) initials (TemplateModel attribute) inter_model_edges (ModelComparisonGraphdata attribute) intra_model_edges (ModelComparisonGraphdata attribute) is_conversion() (in module mira.metamodel.templates) is_degradation() (in module mira.metamodel.templates) is_equal_to() (Concept method) (Template method) is_ontological_child() (RefinementClosure method) is_ontological_child_web() (in module mira.dkg.web_client) is_production() (in module mira.metamodel.templates) is_replication() (in module mira.metamodel.templates) is_reversible() (in module mira.metamodel.templates)

K

key (ModelParameter attribute) (Transition attribute) (Variable attribute)

L

label (NodeInfo attribute) left (ReversibleFlux attribute)

license (Annotations attribute) locations (Annotations attribute)

M

make_bilayer() (BilayerModel static method) make_model() (Model method) match_concepts() (in module mira.metamodel.templates) mathml_to_expression() (in module mira.metamodel.io) mira.dkg module mira.dkg.askemo.api module mira.dkg.client module mira.dkg.construct module mira.dkg.construct_registry module mira.dkg.metaregistry module mira.dkg.metaregistry.utils module mira.dkg.models module mira.dkg.units module mira.dkg.utils module mira.dkg.web_client module mira.examples.decapodes.decapodes_examples module mira.metamodel module mira.metamodel.comparison module mira.metamodel.composition module mira.metamodel.decapodes module mira.metamodel.io module mira.metamodel.ops module mira.metamodel.search module mira.metamodel.template_model module mira.metamodel.templates module mira.metamodel.units module mira.metamodel.utils module mira.modeling module mira.modeling.acsets.petri module mira.modeling.acsets.stockflow module mira.modeling.amr.ops module mira.modeling.amr.petrinet module mira.modeling.amr.regnet module mira.modeling.amr.stockflow module mira.modeling.bilayer module mira.modeling.ode module mira.modeling.sbml module mira.modeling.sbml.export module mira.modeling.viz module mira.sources module mira.sources.acsets.decapodes.deca_expr module mira.sources.acsets.decapodes.decapodes module mira.sources.acsets.petri module mira.sources.acsets.stockflow module mira.sources.amr module mira.sources.amr.flux_span module mira.sources.amr.petrinet module mira.sources.amr.regnet module mira.sources.amr.stockflow module mira.sources.bilayer module mira.sources.biomodels module mira.sources.sbml.api module

mira.sources.sbml.qual_api module mira.sources.sif module mira.sources.sympy_ode module mira.sources.sympy_ode.llm_util module mira.sources.system_dynamics.pysd module mira.sources.system_dynamics.stella module mira.sources.system_dynamics.vensim module mira.sources.util module mira.terarium_client module MiraState (class in mira.dkg.utils) MissingBaseUrlError Model (class in mira.modeling) model_config (Config attribute) (DKGConfig attribute) (Entity attribute) (Synonym attribute) (Term attribute) (Xref attribute) model_from_json() (in module mira.sources.amr) model_from_json_file() (in module mira.metamodel.io) (in module mira.sources.amr) (in module mira.sources.amr.petrinet) (in module mira.sources.amr.regnet) model_from_url() (in module mira.sources.amr) (in module mira.sources.amr.petrinet) (in module mira.sources.amr.regnet) (in module mira.sources.amr.stockflow) model_has_grounding() (in module mira.metamodel.template_model) model_to_json_file() (in module mira.metamodel.io) MODEL_TO_PUBMED (in module mira.sources.biomodels) model_types (Annotations attribute) ModelComparisonGraphdata (class in mira.metamodel.comparison) ModelParameter (class in mira.modeling) module mira.dkg mira.dkg.askemo.api mira.dkg.client mira.dkg.construct mira.dkg.construct_registry mira.dkg.metaregistry mira.dkg.metaregistry.utils mira.dkg.models mira.dkg.units mira.dkg.utils mira.dkg.web_client mira.examples.decapodes.decapodes_examples mira.metamodel mira.metamodel.comparison mira.metamodel.composition mira.metamodel.decapodes mira.metamodel.io mira.metamodel.ops mira.metamodel.search mira.metamodel.template_model mira.metamodel.templates mira.metamodel.units mira.metamodel.utils mira.modeling mira.modeling.acsets.petri mira.modeling.acsets.stockflow mira.modeling.amr.ops mira.modeling.amr.petrinet mira.modeling.amr.regnet mira.modeling.amr.stockflow mira.modeling.bilayer mira.modeling.ode mira.modeling.sbml mira.modeling.sbml.export mira.modeling.viz mira.sources mira.sources.acsets.decapodes.deca_expr mira.sources.acsets.decapodes.decapodes mira.sources.acsets.petri mira.sources.acsets.stockflow mira.sources.amr mira.sources.amr.flux_span mira.sources.amr.petrinet mira.sources.amr.regnet mira.sources.amr.stockflow mira.sources.bilayer mira.sources.biomodels mira.sources.sbml.api mira.sources.sbml.qual_api mira.sources.sif mira.sources.sympy_ode mira.sources.sympy_ode.llm_util mira.sources.system_dynamics.pysd mira.sources.system_dynamics.stella mira.sources.system_dynamics.vensim mira.sources.util mira.terarium_client MultiConversion (class in mira.metamodel.templates)

N

name (Annotations attribute) (Author attribute) (Concept attribute) (Observable attribute) (Parameter attribute) (Template attribute) (Time attribute) (Variable attribute)

NaturalConversion (class in mira.metamodel.templates) NaturalDegradation (class in mira.metamodel.templates) NaturalProduction (class in mira.metamodel.templates) NaturalReplication (class in mira.metamodel.templates) Neo4jClient (class in mira.dkg.client) NodeInfo (class in mira.dkg.construct) NON_COVID_EPI_MODELS (in module mira.sources.biomodels) num_controllers() (in module mira.metamodel.templates)

O

Observable (class in mira.metamodel.template_model) observables (Model attribute) (TemplateModel attribute) OdeModel (class in mira.modeling.ode) Op1 (class in mira.metamodel.decapodes) Op2 (class in mira.metamodel.decapodes)

outcome (ControlledConversion attribute) (ControlledProduction attribute) (GroupedControlledConversion attribute) (GroupedControlledProduction attribute) (NaturalConversion attribute) (NaturalProduction attribute) outcomes (MultiConversion attribute)

P

Parameter (class in mira.metamodel.template_model) parameter_to_mira() (in module mira.sources.util) parameters (Distribution attribute) (Model attribute) (TemplateModel attribute) pathogens (Annotations attribute) pdf_file_to_odes_str() (in module mira.sources.sympy_ode.llm_util) pdf_to_odes_str() (in module mira.sources.sympy_ode.llm_util) PetriNetModel (class in mira.modeling.acsets.petri) placeholder (ModelParameter attribute) plot_simulation_results() (OdeModel method) post_amr() (in module mira.terarium_client) post_amr_remote() (in module mira.terarium_client) post_template_model() (in module mira.terarium_client) prefix (Entity property) (NodeInfo attribute) (Term property) PREFIXES (in module mira.dkg.utils) print_params_table() (TemplateModel method) process_decaexpr() (in module mira.sources.acsets.decapodes.deca_expr)

process_decapode() (in module mira.sources.acsets.decapodes.decapodes) produced (Transition attribute) proj1 (Op2 attribute) proj2 (Op2 attribute) property_predicates (NodeInfo attribute) property_values (NodeInfo attribute) provenance (ControlledConversion attribute) (ControlledDegradation attribute) (ControlledProduction attribute) (ControlledReplication attribute) (GroupedControlledConversion attribute) (GroupedControlledDegradation attribute) (GroupedControlledProduction attribute) (MultiConversion attribute) (NaturalConversion attribute) (NaturalDegradation attribute) (NaturalProduction attribute) (NaturalReplication attribute) (ReversibleFlux attribute) (StaticConcept attribute)

Q

query_biomodels() (in module mira.sources.biomodels)

query_nodes() (Neo4jClient method) query_wikidata() (in module mira.dkg.units)

R

rate_law (Template attribute) references (Annotations attribute) refinement_of() (Concept method) (Template method) RefinementClosure (class in mira.metamodel.comparison) remove_observable() (in module mira.modeling.amr.ops) remove_parameter() (in module mira.modeling.amr.ops) remove_state() (in module mira.modeling.amr.ops) remove_transition() (in module mira.modeling.amr.ops) replace_initial_expression_mathml() (in module mira.modeling.amr.ops) replace_initial_expression_sympy() (in module mira.modeling.amr.ops) replace_initial_id() (in module mira.modeling.amr.ops) replace_observable_expression_mathml() (in module mira.modeling.amr.ops)

replace_observable_expression_sympy() (in module mira.modeling.amr.ops) replace_observable_id() (in module mira.modeling.amr.ops) replace_parameter_id() (in module mira.modeling.amr.ops) replace_rate_law_mathml() (in module mira.modeling.amr.ops) replace_rate_law_sympy() (in module mira.modeling.amr.ops) replace_state_id() (in module mira.modeling.amr.ops) replace_transition_id() (in module mira.modeling.amr.ops) reproduce_ode_semantics() (in module mira.sources.amr.flux_span) res (Op2 attribute) reset_base_names() (TemplateModel method) ReversibleFlux (class in mira.metamodel.templates) revert_parseable_expression() (in module mira.metamodel.utils) right (ReversibleFlux attribute) RootVariable (class in mira.metamodel.decapodes)

S

safe_parse_expr() (in module mira.metamodel.utils) sanity_check_amr() (in module mira.sources.amr) sanity_check_tm() (in module mira.metamodel.utils) save_bilayer() (BilayerModel method) sbml_model_from_file() (in module mira.sources.sbml.api) sbml_qual_model_from_file() (in module mira.sources.sbml.qual_api) SBMLModel (class in mira.modeling.sbml.export) search() (Neo4jClient method) search_web() (in module mira.dkg.web_client) set_initials() (TemplateModel method) set_link() (Entity class method) set_mass_action_rate_law() (Template method) set_parameters() (OdeModel method) (TemplateModel method) set_rate_law() (Template method) (TemplateModel method) simplify_rate_laws() (in module mira.metamodel.ops) (in module mira.modeling.amr.ops) simulate_model() (OdeModel method) simulate_ode_model() (in module mira.modeling.ode) src (Op1 attribute) StaticConcept (class in mira.metamodel.templates) stock_to_concept() (in module mira.sources.acsets.stockflow) (in module mira.sources.amr.stockflow)

stratify() (in module mira.metamodel.ops) (in module mira.modeling.amr.ops) subject (ControlledConversion attribute) (ControlledDegradation attribute) (ControlledReplication attribute) (GroupedControlledConversion attribute) (GroupedControlledDegradation attribute) (NaturalConversion attribute) (NaturalDegradation attribute) (NaturalReplication attribute) (StaticConcept attribute) subjects (MultiConversion attribute) substitute_parameter() (Distribution method) (Initial method) (Observable method) (Template method) (TemplateModel method) sum (Summation attribute) summands (Summation attribute) Summation (class in mira.metamodel.decapodes) Synonym (class in mira.dkg.models) SYNONYM_TYPES (in module mira.dkg.askemo.api) synonym_types (NodeInfo attribute) synonyms (NodeInfo attribute)

T

TangentVariable (class in mira.metamodel.decapodes) Template (class in mira.metamodel.templates) template_model (Model attribute) template_model_from_amr_json() (in module mira.sources.amr.petrinet) (in module mira.sources.amr.regnet) (in module mira.sources.amr.stockflow) template_model_from_bilayer() (in module mira.sources.bilayer) template_model_from_bilayer_file() (in module mira.sources.bilayer) template_model_from_mdl_file() (in module mira.sources.system_dynamics.vensim) template_model_from_mdl_url() (in module mira.sources.system_dynamics.vensim) template_model_from_petri_json() (in module mira.sources.acsets.petri) template_model_from_pysd_model() (in module mira.sources.system_dynamics.pysd) template_model_from_sbml_file() (in module mira.sources.sbml.api) template_model_from_sbml_file_obj() (in module mira.sources.sbml.api) template_model_from_sbml_model() (in module mira.sources.sbml.api) template_model_from_sbml_qual_file() (in module mira.sources.sbml.qual_api) template_model_from_sbml_qual_file_obj() (in module mira.sources.sbml.qual_api) template_model_from_sbml_qual_model() (in module mira.sources.sbml.qual_api) template_model_from_sbml_qual_string() (in module mira.sources.sbml.qual_api) template_model_from_sbml_string() (in module mira.sources.sbml.api) template_model_from_sif_edges() (in module mira.sources.sif) template_model_from_sif_file() (in module mira.sources.sif) template_model_from_sif_url() (in module mira.sources.sif) template_model_from_stella_model_file() (in module mira.sources.system_dynamics.stella) template_model_from_stella_model_url() (in module mira.sources.system_dynamics.stella) template_model_from_stockflow_ascet_json() (in module mira.sources.acsets.stockflow) template_model_from_sympy_odes() (in module mira.sources.sympy_ode) template_model_stella_model_string() (in module mira.sources.system_dynamics.stella) template_model_to_petrinet_json() (in module mira.modeling.amr.petrinet) template_model_to_regnet_json() (in module mira.modeling.amr.regnet) template_model_to_sbml_file() (in module mira.modeling.sbml.export) template_model_to_sbml_string() (in module mira.modeling.sbml.export) template_model_to_stockflow_ascet_json() (in module mira.modeling.acsets.stockflow) template_model_to_stockflow_json() (in module mira.modeling.amr.stockflow) template_models (ModelComparisonGraphdata attribute) template_nodes (ModelComparisonGraphdata attribute) TemplateModel (class in mira.metamodel.template_model) TemplateModelComparison (class in mira.metamodel.comparison) TemplateModelDelta (class in mira.metamodel.comparison) templates (TemplateModel attribute)

templates_equal() (in module mira.metamodel.templates) Term (class in mira.dkg.askemo.api) test_execution() (in module mira.sources.sympy_ode.llm_util) test_ode_model() (in module mira.sources.sympy_ode.llm_util) tgt (Op1 attribute) Time (class in mira.metamodel.template_model) time (TemplateModel attribute) time_end (Annotations attribute) time_scale (Annotations attribute) time_start (Annotations attribute) to_json() (ACSetsStockFlowModel method) (AMRPetriNetModel method) (AMRRegNetModel method) (AMRStockFlowModel method) (Annotations method) (Author method) (Concept method) (Distribution method) (Initial method) (ModelComparisonGraphdata method) (Observable method) (Parameter method) (PetriNetModel method) (Template method) (TemplateModel method) (Time method) to_json_file() (AMRPetriNetModel method) (AMRRegNetModel method) (PetriNetModel method) to_json_str() (AMRPetriNetModel method) (AMRRegNetModel method) (PetriNetModel method) to_xml() (SBMLModel method) to_xml_file() (SBMLModel method) Transition (class in mira.modeling) transition_to_templates() (in module mira.sources.util) transitions (Model attribute) type (Distribution attribute) (NodeInfo attribute) (Variable attribute)

U

Unit (class in mira.metamodel.units) units (Concept attribute) (Observable attribute) (Parameter attribute) (Time attribute)

update_parameter_name() (Template method) update_parameters() (TemplateModel method) update_unit_names_resource() (in module mira.dkg.units) upload_neo4j_s3() (in module mira.dkg.construct) upload_s3() (in module mira.dkg.construct) UseCasePaths (class in mira.dkg.construct)

V

value (ModelParameter attribute) (Parameter attribute) Variable (class in mira.metamodel.decapodes) (class in mira.modeling)

variables (Model attribute) version (NodeInfo attribute)

W

web_client() (in module mira.dkg.web_client) with_context() (Concept method) (ControlledConversion method) (ControlledDegradation method) (ControlledProduction method) (ControlledReplication method) (GroupedControlledConversion method) (GroupedControlledDegradation method) (GroupedControlledProduction method) (MultiConversion method) (NaturalConversion method) (NaturalDegradation method) (NaturalProduction method) (NaturalReplication method) (ReversibleFlux method) (StaticConcept method) (Template method)

with_controller() (ControlledConversion method) (ControlledDegradation method) (ControlledProduction method) (ControlledReplication method) with_controllers() (GroupedControlledConversion method) (GroupedControlledDegradation method) (GroupedControlledProduction method) with_mass_action_rate_law() (Template method) write() (GraphicalModel method)

X

Xref (class in mira.dkg.models)

xref_types (NodeInfo attribute) xrefs (NodeInfo attribute)