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.

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.

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.

SigmaY(identifier, name, value)

A Standard Deviation SigmaY rescales the distance between simulations and measurements when computing residuals or objective functions, abbreviated by sigmay.

State(identifier, name, init, dt)

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