fit.petab_v2.observables¶

Observables of a PEtab problem which are formulas.

An observable of PEtab is a math expression over the entities of a model, e.g. the fraction

(100 * pApB + 200 * pApA * specC17) / (pApB + STAT5A * specC17 + ...)

of a phosphorylated protein, while sbmlsim observes what roadrunner selects, i.e. an entity of the model. The formulas of a problem therefore become entities: a copy of the model gets a parameter per formula observable and an assignment rule which is the formula, and the fit selects the parameter.

The math of PEtab is the math of the model, i.e. the identifier of a species is its amount or its concentration exactly as the model means it, so the formula is the rule without translating it.

observable_id ¶

observable_id(petab_id)

Get the identifier of the model entity of an observable.

Parameters:

Name	Type	Description	Default
`petab_id`	`str`	id of the observable in the PEtab problem.	required

Returns:

Type	Description
`str`	The identifier of the parameter which the assignment rule sets.

add_observables ¶

add_observables(sbml_path, formulas, output_path)

Write a copy of a model which has the observables of a problem.

Parameters:

Name	Type	Description	Default
`sbml_path`	`Path`	path of the model of the PEtab problem.	required
`formulas`	`dict[str, str]`	math expression per observable, i.e. `observableFormula`.	required
`output_path`	`Path`	path the model with the observables is written to.	required

Returns:

Type	Description
`Path`	The path of the model which was written.

Raises:

Type	Description
`ValueError`	if the model cannot be read, if a formula is not valid math or if the model with the observables is not valid SBML.

is_entity ¶

is_entity(formula, sbml_model)

Check whether a formula is an entity of the model rather than math.

Parameters:

Name	Type	Description	Default
`formula`	`str`	the `observableFormula` of an observable.	required
`sbml_model`	`Any`	`libsbml.Model` of the problem.	required

Returns:

Type	Description
`bool`	Whether the formula is the identifier of an entity, i.e. whether the
`bool`	fit can select it without adding it to the model.