Objects for AMICI’s internal ODE model representation


ConservationLaw(identifier, name, value, ...)

A conservation law defines the absolute the total amount of a (weighted) sum of states

Constant(identifier, name, value)

A Constant is a fixed variable in the model with respect to which sensitivities cannot be computed, abbreviated by k.

Event(identifier, name, value, state_update)

An Event defines either a SBML event or a root of the argument of a Heaviside function.

EventObservable(identifier, name, value, event)

An Event Observable links model simulations to event related experimental measurements, abbreviated by z.

Expression(identifier, name, value)

An Expression is a recurring elements in symbolic formulas.

LogLikelihood(identifier, name, value)

A LogLikelihood defines the distance between measurements and experiments for a particular observable.

LogLikelihoodRZ(identifier, name, value)

Loglikelihood for event observables regularization

LogLikelihoodY(identifier, name, value)

Loglikelihood for observables

LogLikelihoodZ(identifier, name, value)

Loglikelihood for event observables

ModelQuantity(identifier, name, value)

Base class for model components

Observable(identifier, name, value[, ...])

An Observable links model simulations to experimental measurements, abbreviated by y.

Parameter(identifier, name, value)

A Parameter is a free variable in the model with respect to which sensitivities may be computed, abbreviated by p.

Sigma(identifier, name, value)

A Standard Deviation Sigma rescales the distance between simulations and measurements when computing residuals or objective functions, abbreviated by sigma{y,z}.

SigmaY(identifier, name, value)

Standard deviation for observables

SigmaZ(identifier, name, value)

Standard deviation for event observables

State(identifier, name, init, dt)

A State variable defines an entity that evolves with time according to the provided time derivative, abbreviated by x.