mira
fix-docs
MIRA
Sources of model content
Meta-model
Modeling
Domain Knowledge Graph
Metaregistry
Terarium Client
mira
Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
add_controller() (ControlledDegradation method)
(ControlledProduction method)
(GroupedControlledDegradation method)
(GroupedControlledProduction method)
add_resource() (in module mira.dkg)
add_template() (TemplateModel method)
add_transition() (TemplateModel method)
aggregate_parameters() (in module mira.metamodel.ops)
alts (Entity attribute)
(NodeInfo attribute)
annotations (TemplateModel attribute)
as_askem_entity() (Entity method)
AskeNetPetriNetModel (class in mira.modeling.askenet.petrinet)
AskeNetRegNetModel (class in mira.modeling.askenet.regnet)
associate() (in module mira.terarium_client)
authors (Annotations attribute)
B
BilayerModel (class in mira.modeling.bilayer)
C
collections (Config attribute)
compare_models() (TemplateModelComparison method)
concept (Initial attribute)
concept_keys (ControlledDegradation attribute)
(ControlledProduction attribute)
(GroupedControlledDegradation attribute)
(GroupedControlledProduction attribute)
concept_nodes (ModelComparisonGraphdata attribute)
context_refinement() (in module mira.metamodel.templates)
controller (ControlledDegradation attribute)
(ControlledProduction attribute)
controllers (GroupedControlledDegradation attribute)
(GroupedControlledProduction attribute)
counts_to_dimensionless() (in module mira.metamodel.ops)
curie (NodeInfo attribute)
D
deactivate_templates() (in module mira.metamodel.ops)
definition (NodeInfo attribute)
deprecated (NodeInfo attribute)
description (Annotations attribute)
(Entity attribute)
(Term attribute)
dimensionality (Term attribute)
diseases (Annotations attribute)
distribution (Parameter attribute)
DKG_REFINER_RELS (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)
EQUIVALENCE_TYPES (in module mira.dkg.askemo.api)
expression (Observable attribute)
(Unit attribute)
expression_to_mathml() (in module mira.metamodel.io)
extend() (TemplateModel method)
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() (Initial class method)
(TemplateModel class method)
(Unit class method)
from_template_model() (GraphicalModel class method)
from_template_models() (ModelComparisonGraphdata class method)
G
generate_model_graph() (TemplateModel method)
get_all_used_parameters() (TemplateModel method)
get_app() (in module mira.dkg.metaregistry.utils)
get_askemo_terms() (in module mira.dkg.askemo.api)
get_askemosw_terms() (in module mira.dkg.askemo.api)
get_common_parents() (Neo4jClient method)
get_concept() (TemplateModel method)
get_concepts() (GroupedControlledDegradation method)
(GroupedControlledProduction method)
get_concepts_by_name() (TemplateModel method)
get_concepts_map() (TemplateModel method)
get_concepts_name_map() (TemplateModel method)
get_dkg_refinement_closure() (in module mira.metamodel.comparison)
get_entity() (Neo4jClient method)
get_entity_web() (in module mira.dkg.web_client)
get_json_schema() (in module mira.metamodel.schema)
get_key() (ControlledDegradation method)
(ControlledProduction method)
(GroupedControlledDegradation method)
(GroupedControlledProduction method)
get_lexical() (Neo4jClient method)
get_lexical_web() (in module mira.dkg.web_client)
get_node_counter() (Neo4jClient method)
get_parameter_names() (Observable 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_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)
H
hosts (Annotations attribute)
I
id (Entity attribute)
(Term attribute)
(Xref attribute)
initials (TemplateModel attribute)
inter_model_edges (ModelComparisonGraphdata attribute)
intra_model_edges (ModelComparisonGraphdata attribute)
is_ontological_child_web() (in module mira.dkg.web_client)
L
label (NodeInfo attribute)
labels (Entity attribute)
license (Annotations attribute)
link (Entity attribute)
locations (Annotations attribute)
M
main() (in module mira.sources.biomodels)
make_bilayer() (BilayerModel static method)
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.metamodel
module
mira.metamodel.comparison
module
mira.metamodel.io
module
mira.metamodel.ops
module
mira.metamodel.schema
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.askenet.petrinet
module
mira.modeling.askenet.regnet
module
mira.modeling.bilayer
module
mira.modeling.ode
module
mira.modeling.petri
module
mira.modeling.viz
module
mira.sources
module
mira.sources.askenet
module
mira.sources.askenet.flux_span
module
mira.sources.askenet.petrinet
module
mira.sources.bilayer
module
mira.sources.biomodels
module
mira.sources.petri
module
mira.sources.sbml.api
module
mira.terarium_client
module
MiraState (class in mira.dkg.utils)
model_from_json_file() (in module mira.metamodel.io)
(in module mira.sources.askenet)
(in module mira.sources.askenet.petrinet)
model_from_url() (in module mira.sources.askenet)
(in module mira.sources.askenet.petrinet)
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)
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.metamodel
mira.metamodel.comparison
mira.metamodel.io
mira.metamodel.ops
mira.metamodel.schema
mira.metamodel.search
mira.metamodel.template_model
mira.metamodel.templates
mira.metamodel.units
mira.metamodel.utils
mira.modeling
mira.modeling.askenet.petrinet
mira.modeling.askenet.regnet
mira.modeling.bilayer
mira.modeling.ode
mira.modeling.petri
mira.modeling.viz
mira.sources
mira.sources.askenet
mira.sources.askenet.flux_span
mira.sources.askenet.petrinet
mira.sources.bilayer
mira.sources.biomodels
mira.sources.petri
mira.sources.sbml.api
mira.terarium_client
N
name (Annotations attribute)
(Entity attribute)
(Term attribute)
(Time attribute)
Neo4jClient (class in mira.dkg.client)
NodeInfo (class in mira.dkg.construct)
NON_COVID_EPI_MODELS (in module mira.sources.biomodels)
O
observables (TemplateModel attribute)
obsolete (Entity attribute)
(Term attribute)
OdeModel (class in mira.modeling.ode)
outcome (ControlledProduction attribute)
(GroupedControlledProduction attribute)
P
parameters (Distribution attribute)
(TemplateModel attribute)
parents (Term attribute)
pathogens (Annotations attribute)
PetriNetModel (class in mira.modeling.petri)
physical_max (Term attribute)
physical_min (Term attribute)
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)
properties (Entity attribute)
property_predicates (NodeInfo attribute)
property_values (NodeInfo attribute)
provenance (ControlledDegradation attribute)
(ControlledProduction attribute)
(GroupedControlledDegradation attribute)
(GroupedControlledProduction attribute)
Q
query_biomodels() (in module mira.sources.biomodels)
query_nodes() (Neo4jClient method)
query_wikidata() (in module mira.dkg.units)
R
references (Annotations attribute)
RefinementClosure (class in mira.metamodel.comparison)
registry (Config attribute)
reproduce_ode_semantics() (in module mira.sources.askenet.flux_span)
reset_base_names() (TemplateModel method)
revert_parseable_expression() (in module mira.metamodel.utils)
S
safe_parse_expr() (in module mira.metamodel.utils)
sanity_check_tm() (in module mira.metamodel.utils)
save_bilayer() (BilayerModel method)
sbml_model_from_file() (in module mira.sources.sbml.api)
search() (Neo4jClient method)
search_web() (in module mira.dkg.web_client)
set_initials() (TemplateModel method)
set_link() (Entity class method)
set_parameters() (OdeModel method)
(TemplateModel method)
simplify_rate_laws() (in module mira.metamodel.ops)
simulate_ode_model() (in module mira.modeling.ode)
stratify() (in module mira.metamodel.ops)
subject (ControlledDegradation attribute)
(GroupedControlledDegradation attribute)
substitute_parameter() (Observable method)
(TemplateModel method)
suggested_data_type (Term attribute)
suggested_unit (Term attribute)
SympyExprStr (class in mira.metamodel.utils)
SYNONYM_TYPES (in module mira.dkg.askemo.api)
synonym_types (NodeInfo attribute)
synonyms (Entity attribute)
(NodeInfo attribute)
(Term attribute)
T
template_model_from_askenet_json() (in module mira.sources.askenet.petrinet)
template_model_from_bilayer() (in module mira.sources.bilayer)
template_model_from_bilayer_file() (in module mira.sources.bilayer)
template_model_from_petri_json() (in module mira.sources.petri)
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_string() (in module mira.sources.sbml.api)
template_models (ModelComparisonGraphdata attribute)
template_nodes (ModelComparisonGraphdata attribute)
TemplateModelComparison (class in mira.metamodel.comparison)
TemplateModelDelta (class in mira.metamodel.comparison)
templates (TemplateModel attribute)
templates_equal() (in module mira.metamodel.templates)
time (TemplateModel attribute)
time_end (Annotations attribute)
time_scale (Annotations attribute)
time_start (Annotations attribute)
to_json() (AskeNetPetriNetModel method)
(AskeNetRegNetModel method)
(PetriNetModel method)
to_json_file() (AskeNetPetriNetModel method)
(AskeNetRegNetModel method)
(PetriNetModel method)
to_json_str() (AskeNetPetriNetModel method)
(AskeNetRegNetModel method)
(PetriNetModel method)
type (ControlledDegradation attribute)
(ControlledProduction attribute)
(Distribution attribute)
(Entity attribute)
(GroupedControlledDegradation attribute)
(GroupedControlledProduction attribute)
(NodeInfo attribute)
(Synonym attribute)
(Term attribute)
(Xref attribute)
typical_max (Term attribute)
typical_min (Term attribute)
U
units (Time attribute)
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 (Initial attribute)
(Parameter attribute)
(Synonym attribute)
version (NodeInfo attribute)
W
web (Config attribute)
web_client() (in module mira.dkg.web_client)
with_context() (ControlledDegradation method)
(ControlledProduction method)
(GroupedControlledDegradation method)
(GroupedControlledProduction method)
with_controller() (ControlledDegradation method)
(ControlledProduction method)
with_controllers() (GroupedControlledDegradation method)
(GroupedControlledProduction method)
write() (GraphicalModel method)
X
xref_types (NodeInfo attribute)
xrefs (Entity attribute)
(NodeInfo attribute)
(Term attribute)
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