amici.ode_model

Objects for AMICI’s internal ODE model representation

Classes

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.