Finite State Projection [1] algorithms for chemical reaction networks based on Catalyst.jl and ModelingToolkit.jl. Converts descriptions of reaction networks into ODEProblems and SteadyStateProblems for use with DifferentialEquations.jl.
- Built on top of Catalyst.jl
- FSP equations are generated as
ODEFunction/ODEProblems and can be solved with DifferentialEquations.jl, with on-the-fly generation of targeted functions for improved performance - The Chemical Master Equation can be represented as a
SparseMatrixCSC
More information is available in the documentation. Please feel free to open issues and submit pull requests!
using FiniteStateProjection
using OrdinaryDiffEq
rn = @reaction_network begin
σ, 0 --> A
d, A --> 0
end
sys = FSPSystem(rn)
# Parameters for our system
ps = [ :σ => 10.0, :d => 1.0 ]
# Initial distribution (over 1 species)
# Here we start with 0 copies of A
u0 = zeros(50)
u0[1] = 1.0
prob = ODEProblem(sys, u0, (0, 10.0), ps)
sol = solve(prob, Vern7())
using FiniteStateProjection
using OrdinaryDiffEq
rn = @reaction_network begin
σ_on * (1 - G_on), 0 --> G_on
σ_off, G_on --> 0
ρ, G_on --> G_on + M
d, M --> 0
end
sys = FSPSystem(rn)
# Parameters for our system
ps = [ :σ_on => 0.25, :σ_off => 0.15, :ρ => 15.0, :d => 1.0 ]
# Initial distribution (over two species)
# Here we start with 0 copies of G_on and M
u0 = zeros(2, 50)
u0[1,1] = 1.0
prob = ODEProblem(sys, u0, (0, 10.0), ps)
sol = solve(prob, Vern7())
[1] B. Munsky and M. Khammash, "The Finite State Projection algorithm for the solution of the Chemical Master Equation", Journal of Chemical Physics 124, 044104 (2006). https://doi.org/10.1063/1.2145882