Sources of model content
Sources of models.
ASKEM AMR (mira.sources.amr)
- model_from_url(url)[source]
Return a model from a URL, handling multiple frameworks.
- Parameters:
url – The URL to the JSON file.
- Returns:
A TemplateModel object.
- model_from_json_file(fname)[source]
Return a model from a file, handling multiple frameworks.
- Parameters:
fname – The path to the JSON file.
- Returns:
A TemplateModel object.
- model_from_json(model_json)[source]
Return a model from a JSON object, handling multiple frameworks.
- Parameters:
model_json – The JSON object containing the model information.
- Returns:
A TemplateModel object.
- sanity_check_amr(amr_json)[source]
Check that the AMR is valid
- Parameters:
amr_json – The JSON object containing the AMR.
- Raises:
AssertionError – If the AMR doesn’t have a header or a schema.
jsonschema.exceptions.ValidationError – If the instance is invalid
jsonschema.exceptions.SchemaError – If the schema itself is invalid
ASKEM AMR Petri nets (mira.sources.amr.petrinet)
This module implements parsing Petri net models defined in https://github.com/DARPA-ASKEM/Model-Representations/tree/main/petrinet.
MIRA TemplateModel representation limitations to keep in mind:
Model version not supported
Model schema not supported
Initials only have a value, cannot be expressions so information on initial condition parameter relationship is lost
- model_from_url(url)[source]
Return a model from a URL
- Parameters:
url (
str) – The URL to the JSON file.- Return type:
- Returns:
A TemplateModel object.
- model_from_json_file(fname)[source]
Return a model from a JSON file.
- Parameters:
fname (
str) – The path to the JSON file.- Return type:
- Returns:
A TemplateModel object.
ASKEM AMR Stockflow (mira.sources.amr.stockflow)
This module implements parsing Stock and Flow models defined in https://github.com/DARPA-ASKEM/Model-Representations/tree/main/stockflow.
ASKEM AMR Regulatory nets (mira.sources.amr.regnet)
This module implements parsing RegNet models defined in https://github.com/DARPA-ASKEM/Model-Representations/tree/main/regnet.
- model_from_url(url)[source]
Return a model from a URL
- Parameters:
url (
str) – The URL to the JSON file.- Return type:
- Returns:
A TemplateModel object.
- model_from_json_file(fname)[source]
Return a model from a JSON file.
- Parameters:
fname (
str) – The path to the JSON file.- Return type:
- Returns:
A TemplateModel object.
Reconstruct ODE semantics (mira.sources.amr.flux_span)
This module implements handling flux span model representations that are the result of stratification and map back to original models before stratification.
SBML extraction (mira.sources.sbml)
- template_model_from_sbml_file(file_path, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a file containing SBML XML.
- Parameters:
- Return type:
- Returns:
The extracted MIRA template model.
- template_model_from_sbml_file_obj(file, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a file object containing SBML XML.
- Parameters:
- Return type:
- Returns:
The extracted MIRA template model.
- template_model_from_sbml_string(s, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a string representing SBML XML.
- Parameters:
- Return type:
- Returns:
The extracted TemplateModel.
SBML Qual extraction (mira.sources.sbml.qual_api)
- template_model_from_sbml_qual_file(file_path, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a file containing SBML Qual XML.
- Parameters:
- Return type:
- Returns:
The extracted MIRA template model.
- template_model_from_sbml_qual_file_obj(file, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a file object containing SBML Qual XML.
- Parameters:
file – The open file object containing the SBML Qual XML.
model_id (
Optional[str]) – The ID of the model to extract. (Optional) If not provided, an attempt will be made to extract an ID from the SBML Qual file if it’s a BIOMODELS model.reporter_ids (
Optional[Iterable[str]]) – An iterable of reporter IDs
- Return type:
- Returns:
The extracted MIRA template model.
- template_model_from_sbml_qual_string(s, *, model_id=None, reporter_ids=None)[source]
Extract a MIRA template model from a string representing SBML Qual XML.
- Parameters:
- Return type:
- Returns:
The extracted TemplateModel.
BioModels client (mira.sources.biomodels)
The BioModels database lists several high quality models at https://www.ebi.ac.uk/biomodels/covid-19.
- NON_COVID_EPI_MODELS = {'BIOMD0000000249', 'BIOMD0000000294', 'BIOMD0000000715', 'BIOMD0000000716', 'BIOMD0000000717', 'BIOMD0000000726', 'BIOMD0000000922', 'BIOMD0000000949', 'BIOMD0000000950', 'BIOMD0000001045', 'MODEL1008060000', 'MODEL1008060002', 'MODEL1805220001', 'MODEL1805230001', 'MODEL1808280006', 'MODEL1808280011', 'MODEL2212310001'}
Additional model identifiers for epidemiology models that do not appear in the BioModels curated list of COVID-19 models
- MODEL_TO_PUBMED = {'BIOMD0000000716': '30839942', 'BIOMD0000000717': '30839942'}
Annotation of missing pubmeds to model ids
- query_biomodels(query='submitter_keywords:COVID-19', limit=30)[source]
Query and paginate over results from the BioModels API.
- get_sbml_model(model_id)[source]
Return the SBML string content for a BioModels model from the web.
Bilayer extraction (mira.sources.bilayer)
This module implements an input processor for bilayer representations of models based on mass-action kinetics.
- template_model_from_bilayer_file(fname)[source]
Return a TemplateModel by processing a bilayer JSON file.
- Parameters:
fname (str) – The path to a bilayer JSON file.
- Return type:
- Returns:
A TemplateModel extracted from the bilayer.
ACSets Petri Net extraction (mira.sources.acsets.petri)
ACSets Stockflow extraction (mira.sources.acsets.stockflow)
This module implements parsing of a Stock and Flow acset model and turns it into a MIRA template models.
ACSets Decapodes extraction (mira.sources.acsets.decapodes.decapodes)
ACSets DecaExpr extraction (mira.sources.acsets.decapodes.deca_expr)
Vensim models (mira.sources.system_dynamics.vensim)
This module implements an API interface for retrieving Vensim models by Ventana Systems denoted by the .mdl extension through a locally downloaded file or URL. We then convert the Vensim model into a generic pysd model object that will be parsed and converted to an equivalent MIRA template model. We preprocess the vensim file to extract variable expressions.
Vensim model documentation:https://www.vensim.com/documentation/sample_models.html
Repository of sample Vensim models: https://github.com/SDXorg/test-models/tree/master/samples
- template_model_from_mdl_file(fname, *, grounding_map=None, initials=None, initials_from_integ=False)[source]
Return a template model from a local Vensim file
- Parameters:
fname (str or pathlib.Path) – The path to the local Vensim file
grounding_map (dict[str, Concept]) – A grounding map, a map from label to Concept
initials (dict[str, float]) – Explicit initial values to use for compartments in the model. Will overwrite model-internal definitions.
initials_from_integ (bool) – If true, gets initial values from INTEG expressions. If
initialsare given, they override anything from INTEG expressions
- Return type:
- Returns:
A MIRA template model
- template_model_from_mdl_url(url, *, grounding_map=None, initials=None, initials_from_integ=False)[source]
Return a template model from a Vensim file provided by an url
- Parameters:
url (str) – The url to the mdl file
grounding_map (dict[str, Concept]) – A grounding map, a map from label to Concept
initials (dict[str, float]) – Explicit initial values to use for compartments in the model. Will overwrite model-internal definitions.
initials_from_integ (bool) – If true, gets initial values from INTEG expressions. If
initialsare given, they override anything from INTEG expressions
- Return type:
- Returns:
A MIRA Template Model
Stella models (mira.sources.system_dynamics.stella)
This module implements an API interface for retrieving Stella models by ISEE Systems denoted by the .xmile, .xml, or .stmx extension through a locally downloaded file or URL. We cannot process stella models with the .itmx extension. Additionally, the PySD library depends on the parsimonious library which fails to parse a number of stella models with valid file extensions due to incompatible symbols and characters in equations for variables. We implemented preprocessing for stella models that fixes a number of these parsing errors when using PySD to ingest these models; however, a number of models still fail to be parsed by PySD’s “read_xmile” method. We extract the contents of the model as a string, perform expression preprocessing, and then convert the Stella model into a generic pysd model object that will be converted to an equivalent MIRA template model.
Landing page for Stella: https://www.iseesystems.com/store/products/stella-online.aspx
Website containing sample Stella models: https://www.vensim.com/documentation/sample_models.html
- template_model_from_stella_model_file(fname)[source]
Return a template model from a local Stella model file
- Parameters:
fname (str or pathlib.Path) – The path to the local Stella model file
- Return type:
- Returns:
A MIRA template model
- template_model_from_stella_model_url(url)[source]
Return a template model from a Stella model file provided by an url
- Parameters:
url (str) – The url to the Stella model file
- Return type:
- Returns:
A MIRA Template Model
PySD models (mira.sources.system_dynamics.pysd)
This module implements parsing of a generic pysd model irrespective of source and source type and extracting its contents to create an equivalent MIRA template model.
SIF networks (mira.sources.sif)
This module provides functions to create a MIRA TemplateModel from a Simple Interaction Format (SIF) file. The SIF format is a simple space-delimited format where each line represents a relationship between two entities. The first column is the source node, the second column is the relation, and the third column is the target node. The relation is a string that represents the type of interaction between the source and target nodes. SIF files are useful as a minimal representation of regulatory networks with positive/negative regulation.
- template_model_from_sif_edges(edges)[source]
Return TemplateModel from a list of SIF edges.
- Parameters:
edges (list) – A list of tuples of the form (source, rel, target) where source and target are strings representing the source and target nodes and rel is a string representing the relation between them.
- Returns:
A MIRA TemplateModel.
- Return type:
- template_model_from_sif_file(fname)[source]
Return TemplateModel from a SIF file.
- Parameters:
fname (str) – The path to the SIF file.
- Returns:
A MIRA TemplateModel.
- Return type:
Utility Methods (mira.sources.util)
- transition_to_templates(input_concepts, output_concepts, controller_concepts, transition_rate, transition_id, transition_name=None)[source]
Return a list of templates from a transition.
- Parameters:
input_concepts (list[Concept]) – A list of Concepts serving as input to a transition.
output_concepts (list[Concept]) – A list of Concepts serving as output to a transition.
controller_concepts (list[Concept]) – A list of Concepts serving as controllers towards a transition.
transition_rate (sympy.Expr) – The rate law associated with the transition.
transition_id (str) – The id of the transition.
transition_name (str) – The name of the transition.
- Returns:
A list containing Templates.
- Return type: