Main API

Reaction Systems

This section describes the FSPSystem struct, a thin wrapper around Catalyst's ReactionSystem for use with this package.


Thin wrapper around Catalyst.ReactionSystem for use with this package.

Constructor: FSPSystem(rs::ReactionSystem[, ih=DefaultIndexHandler(); combinatoric_ratelaw::Bool=true])

Creating ODE systems

The following methods convert a reaction network into a system of ODEs representing the time-dependent FSP. This package provides a flexible way to represent the FSP in memory via index handlers, see [Index Handlers] for more information.

Base.convert(::Type{ODEFunction}, sys::FSPSystem)

Return an ODEFunction defining the right-hand side of the CME.

Creates an ODEFunction for use with DifferentialEquations. This is where most of the work in the package happens; for best performance it is suggested to build an ODEFunction once for a given reaction system and reuse it instead of directly converting a reaction system to an ODEProblem (which implicitly calls this function).

Base.convert(::Type{ODEProblem}, sys::FSPSystem, u0, tmax[, p])

Return an ODEProblem for use in DifferentialEquations. This function implicitly calls convert(ODEFunction, sys). It is usually more efficient to create an ODEFunction first and then use that to create ODEProblems.

Steady-State Problems

Computing steady-state distributions can be done using the SteadyStateDiffEq.jl package. At the moment FiniteStateProjection.jl adjusts the rate matrix so that reactions leaving the truncated state space have propensity 0.

Base.convert(::Type{ODEFunction}, sys::FSPSystem, ::SteadyState)

Return an ODEFunction defining the right-hand side of the CME, for use with SteadyStateProblems.

Base.convert(::Type{SteadyStateProblem}, sys::FSPSystem, u0[, p])

Return a SteadyStateProblem for use in `DifferentialEquations.