Updated README.md

README.md

@@ -25,7 +25,7 @@ end
 sys = FSPSystem(rn)
 
 # Parameters for our system
-ps = [ 10.0, 1.0 ]
+ps = [ :σ => 10.0, :d => 1.0 ]
 
 # Initial distribution (over 1 species)
 # Here we start with 0 copies of A
@@ -52,7 +52,7 @@ end
 sys = FSPSystem(rn)
 
 # Parameters for our system
-ps = [ 0.25, 0.15, 15.0, 1.0 ]
+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
@@ -64,10 +64,6 @@ sol = solve(prob, Vern7())
 ```
 ![Visualisation](docs/src/assets/telegraph.png)
 
-## TODO:
-- Add bursty reactions
-- Add support for sparse Jacobians
-
 ## References
 
 <a id="1">[1]</a> 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

demo/birth_death.jl

@@ -14,7 +14,7 @@ end
 sys = FSPSystem(rs)
 
 # Parameters for our system
-ps = [ 10.0, 1.0 ]
+ps = [ :r1 => 10.0, :r2 => 1.0 ]
 
 # Initial values
 u0 = zeros(50)

demo/telegraph.jl

@@ -16,7 +16,7 @@ end
 sys = FSPSystem(rs)
 
 # Parameters for our system
-ps = [ 0.25, 0.15, 15.0, 1.0 ]
+ps = [ :r1 => 0.25, :r2 => 0.15, :r3 => 15.0, :r4 => 1.0 ]
 
 # Initial values
 # Since G_on + G_off = const. we do not have to model the two