### A Pluto.jl notebook ###
# v0.17.3

using Markdown
using InteractiveUtils

# ╔═╡ 7c456c0c-aa2b-45a2-aa74-d50acf9b3e27
begin
	using DiffEqJump
	using Catalyst
end

# ╔═╡ 218c3506-6717-11ec-1529-71383cd2f400
md"# Modelisation of the ICEclc element"

# ╔═╡ 6297e440-3720-4ed4-a076-217efbce9422
md"## Packages"

# ╔═╡ 13119b26-15ec-4925-9766-98fdf840f6dc
md"## No loop"

# ╔═╡ 7bbabeae-90ca-4807-91d2-fba7916de0dc
let
	ice_model = @reaction_network ICE begin
	    A4, BisCD --> ∅
	    B1, 4BisR + PalpA_0 --> PalpA_BisR
	    B2, PalpA_BisR --> PalpA_0 + 4BisR
	    B3, PalpA_BisR --> PalpA_BisR + BisCD
	    B4,  ∅ --> BisR
	    B5, BisR --> ∅
	    end A4 B1 B2 B3 B4 B5
	
	A4 = 0.17;
	B1 = 1.0;
	B2 = 1.0;
	B3 = 1.0;
	B4 = 0.1;
	B5 = 0.17;
	
	p = (A4,B1,B2,B3,B4,B5);
	prob = DiscreteProblem([0,10,1,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

# ╔═╡ 548c3582-d0af-4bee-bf94-fbbf931bcc35
md"## Self loop only"

# ╔═╡ 55478f82-6b7e-483c-83c0-b3ebef70a1a7
let
	ice_model = @reaction_network begin
	    A1, 2BisCD + PalpA_0 --> PalpA_BisCD
	    A2, PalpA_BisCD --> PalpA_0 + 2BisCD
	    A3, PalpA_BisCD --> PalpA_BisCD + BisCD
	    A4, BisCD --> ∅
	    end A1 A2 A3 A4
	
	A1 = 1.0;
	A2 = 1.0;
	A3 = 1.0;
	A4 = 0.17;
	
	p = (A1,A2,A3,A4);
	prob = DiscreteProblem([10,1,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

# ╔═╡ 4121bd95-b06d-4343-97bf-23072127ea34
md"## Self loop with BisR"

# ╔═╡ c08ea54a-41db-4f9f-bcff-30451ae12ba4
let
	ice_model = @reaction_network begin
	    A1, 2BisCD + PalpA_0 --> PalpA_BisCD
	    A2, PalpA_BisCD --> PalpA_0 + 2BisCD
	    A3, PalpA_BisCD --> PalpA_BisCD + BisCD
	    A4, BisCD --> ∅
	    B1, 4BisR + PalpA_0 --> PalpA_BisR
	    B2, PalpA_BisR --> PalpA_0 + 4BisR
	    B3, PalpA_BisR --> PalpA_BisR + BisCD
	    B4,  ∅ --> BisR
	    B5, BisR --> ∅
	    end A1 A2 A3 A4 B1 B2 B3 B4 B5
	
	A1 = 1.0;
	A2 = 1.0;
	A3 = 1.0;
	A4 = 0.17;
	B1 = 1.0;
	B2 = 1.0;
	B3 = 1.0;
	B4 = 0.1;
	B5 = 0.17;
	
	p = (A1,A2,A3,A4,B1,B2,B3,B4,B5);
	prob = DiscreteProblem([0,1,0,10,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

# ╔═╡ 193af49a-c365-4344-83fa-17fee8842b59
md"## Self loop with BisR and late promoter activation"

# ╔═╡ ff1eae8a-c77b-411b-baaf-bcbd334a10f0
let
	ice_model = @reaction_network begin
	    A1, 2BisCD + PalpA_0 --> PalpA_BisCD
	    A2, PalpA_BisCD --> PalpA_0 + 2BisCD
	    A3, PalpA_BisCD --> PalpA_BisCD + BisCD
	    A4, BisCD --> ∅
	    B1, 4BisR + PalpA_0 --> PalpA_BisR
	    B2, PalpA_BisR --> PalpA_0 + 4BisR
	    B3, PalpA_BisR --> PalpA_BisR + BisCD
	    B4,  ∅ --> BisR
	    B5, BisR --> ∅
		D1, 2BisCD + Late_0 --> Late_1
	    D2, Late_1 --> 2BisCD + Late_0
	    end A1 A2 A3 A4 B1 B2 B3 B4 B5 D1 D2
	
	A1 = 1.0;
	A2 = 1.0;
	A3 = 1.0;
	A4 = 0.17;
	B1 = 1.0;
	B2 = 1.0;
	B3 = 1.0;
	B4 = 0.1;
	B5 = 0.17;
	D1 = 1.0;
	D2 = 1.0;

	p = (A1,A2,A3,A4,B1,B2,B3,B4,B5,D1,D2);
	prob = DiscreteProblem([0,1,0,10,0,1,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

# ╔═╡ 434e6385-61c4-4b3d-8aab-1574d7921f50
md"## Self loop with BisR, TciR induction and late promoter activation"

# ╔═╡ 878f2448-b239-4597-8769-58d5bbe36df0
let
	ice_model = @reaction_network begin
	    A1, 2BisCD + PalpA_0 --> PalpA_BisCD
	    A2, PalpA_BisCD --> PalpA_0 + 2BisCD
	    A3, PalpA_BisCD --> PalpA_BisCD + BisCD
	    A4, BisCD --> ∅
	    B1, 4BisR + PalpA_0 --> PalpA_BisR
	    B2, PalpA_BisR --> PalpA_0 + 4BisR
	    B3, PalpA_BisR --> PalpA_BisR + BisCD
	    B4,  ∅ --> BisR
	    B5, BisR --> ∅
	    C1, ∅ --> TciR
	    C2, TciR --> ∅
	    C3, 4TciR + PbisR_0 --> PbisR_1
	    C4, PbisR_1 --> 4TciR
	    C5, PbisR_1 --> PbisR_1 + 10BisR
	    D1, 2BisCD + Late_0 --> Late_1
		D2, Late_1 --> 2BisCD + Late_0
	    end A1 A2 A3 A4 B1 B2 B3 B4 B5 C1 C2 C3 C4 C5 D1 D2 
	
	A1 = 1.0;
	A2 = 1.0;
	A3 = 1.0;
	A4 = 0.17;
	B1 = 1.0;
	B2 = 1.0;
	B3 = 1.0;
	B4 = 0.0;
	B5 = 0.17;
	C1 = 0.35;
	C2 = 0.17;
	C3 = 1.0;
	C4 = 1.0;
	C5 = 1.0;
	D1 = 1.0;
	D2 = 1.0;
	
	p = (A1,A2,A3,A4,B1,B2,B3,B4,B5,C1,C2,C3,C4,C5,D1,D2);
	prob = DiscreteProblem([0,1,0,0,0,0,1,0,1,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

# ╔═╡ dc770cfe-fb45-453a-8857-ac0089a8c174
md"## Ptac modulation"

# ╔═╡ 83e3e47a-2deb-41e6-83e1-4bed6a6c1b77
let
	ice_model = @reaction_network begin
	    A1, 2BisCD + PalpA_0 --> PalpA_BisCD
	    A2, PalpA_BisCD --> PalpA_0 + 2BisCD
	    A3, PalpA_BisCD --> PalpA_BisCD + BisCD
	    A4, BisCD --> ∅
	    B1, 4BisR + PalpA_0 --> PalpA_BisR
	    B2, PalpA_BisR --> PalpA_0 + 4BisR
	    B3, PalpA_BisR --> PalpA_BisR + BisCD
	    B4,  ∅ --> BisR
	    B5, BisR --> ∅
	    E1, 2BisCD + PGFP_0 --> PGFP_1
	    E2, PGFP_1 --> 2BisCD + PGFP_0
	    E3, PGFP_1 --> PGFP_1 + GFP
		E4, GFP --> ∅
	    end A1 A2 A3 A4 B1 B2 B3 B4 B5 E1 E2 E3
	
	
	A1 = 1.0;
	A2 = 1.0;
	A3 = 1.0;
	A4 = 0.17;
	B1 = 1.0;
	B2 = 1.0;
	B3 = 1.0;
	B4 = 1.0; # vary between 0.0 and 1.0
	B5 = 0.17;
	E1 = 1.0;
	E2 = 1.0;
	E3 = 1.0;
	
	
	p = (A1,A2,A3,A4,B1,B2,B3,B4,B5,E1,E2,E3);
	prob = DiscreteProblem([0,1,0,0,0,1,0,0],(0.0,100.0),p);
	
	jump_prob = JumpProblem(ice_model,prob,Direct());
	sol = solve(jump_prob,SSAStepper());
end;

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"""

# ╔═╡ Cell order:
# ╟─218c3506-6717-11ec-1529-71383cd2f400
# ╟─6297e440-3720-4ed4-a076-217efbce9422
# ╠═7c456c0c-aa2b-45a2-aa74-d50acf9b3e27
# ╟─13119b26-15ec-4925-9766-98fdf840f6dc
# ╠═7bbabeae-90ca-4807-91d2-fba7916de0dc
# ╟─548c3582-d0af-4bee-bf94-fbbf931bcc35
# ╠═55478f82-6b7e-483c-83c0-b3ebef70a1a7
# ╟─4121bd95-b06d-4343-97bf-23072127ea34
# ╠═c08ea54a-41db-4f9f-bcff-30451ae12ba4
# ╟─193af49a-c365-4344-83fa-17fee8842b59
# ╠═ff1eae8a-c77b-411b-baaf-bcbd334a10f0
# ╟─434e6385-61c4-4b3d-8aab-1574d7921f50
# ╠═878f2448-b239-4597-8769-58d5bbe36df0
# ╟─dc770cfe-fb45-453a-8857-ac0089a8c174
# ╠═83e3e47a-2deb-41e6-83e1-4bed6a6c1b77
# ╟─00000000-0000-0000-0000-000000000001
# ╟─00000000-0000-0000-0000-000000000002
