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Update jump problems to Catalyst 13 #113

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merged 1 commit into from
Sep 1, 2023
Merged

Update jump problems to Catalyst 13 #113

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4 changes: 2 additions & 2 deletions lib/JumpProblemLibrary/Project.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
name = "JumpProblemLibrary"
uuid = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e"
version = "0.1.3"
version = "0.1.4"

[deps]
Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
Expand All @@ -9,7 +9,7 @@ RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"

[compat]
Aqua = "0.5"
Catalyst = "11, 12"
Catalyst = "13"
DiffEqBase = "6"
RuntimeGeneratedFunctions = "0.5"
julia = "1.6"
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20 changes: 11 additions & 9 deletions lib/JumpProblemLibrary/src/JumpProblemLibrary.jl
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Expand Up @@ -38,7 +38,7 @@
k4, P --> 0
k5, DNA + P --> DNAR
k6, DNAR --> DNA + P
end k1 k2 k3 k4 k5 k6
end
rates = [0.5, (20 * log(2.0) / 120.0), (log(2.0) / 120.0), (log(2.0) / 600.0), 0.025, 1.0]
tf = 1000.0
u0 = [1, 0, 0, 0]
Expand All @@ -54,7 +54,7 @@
bd_rs = @reaction_network begin
k1, 0 --> A
k2, A --> 0
end k1 k2
end
rates = [1000.0, 10.0]
tf = 1.0
u0 = [0]
Expand All @@ -73,7 +73,7 @@
k3, A + B --> C
k4, C --> A + B
k5, 3C --> 3A
end k1 k2 k3 k4 k5
end
rates = [1.0, 2.0, 0.5, 0.75, 0.25]
tf = 0.01
u0 = [200, 100, 150]
Expand Down Expand Up @@ -137,7 +137,7 @@
kAoff, S8 --> S1 + S9
kAdp, S8 --> S5
kAdp, S9 --> S3
end kon kAon koff kAoff kAp kAdp
end
rsi = rates_sym_to_idx
rates = params[[rsi[:kon], rsi[:kAon], rsi[:koff], rsi[:kAoff], rsi[:kAp], rsi[:kAdp]]]
u0 = zeros(Int, 9)
Expand All @@ -160,8 +160,8 @@

# generate the network
N = 10 # number of genes
@parameters t
@variables G[1:(2N)](t) M[1:(2N)](t) P[1:(2N)](t) G_ind[1:(2N)](t)
@variables t
@species (G(t))[1:(2N)] (M(t))[1:(2N)] (P(t))[1:(2N)] (G_ind(t))[1:(2N)]

function construct_genenetwork(N)
genenetwork = make_empty_network()
Expand Down Expand Up @@ -209,6 +209,7 @@
end
tf = 2000.0
prob = DiscreteProblem(rs, u0, (0.0, tf), eval_module = @__MODULE__)

"""
Twenty-gene model from McCollum et al,
"The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior"
Expand All @@ -225,7 +226,7 @@
c6, P2 --> 2P
c7, P2 + G --> P2G
c8, P2G --> P2 + G
end c1 c2 c3 c4 c5 c6 c7 c8
end
rnpar = [0.09, 0.05, 0.001, 0.0009, 0.00001, 0.0005, 0.005, 0.9]
varlabels = ["G", "M", "P", "P2", "P2G"]
u0 = [1000, 0, 0, 0, 0]
Expand All @@ -243,8 +244,9 @@
# diffusion model
function getDiffNetwork(N)
diffnetwork = make_empty_network()
@parameters t K
@variables X[1:N](t)
@parameters K
@variables t
@species (X(t))[1:N]

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lib/JumpProblemLibrary/src/JumpProblemLibrary.jl#L247-L249 

Added lines #L247 - L249 were not covered by tests
for i in 1:N
addspecies!(diffnetwork, X[i])
end
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