Merge branch 'Adam_ketamine' of https://github.com/Neuroblox/Neuroblo…

…x.jl into Adam_ketamine
Neuroblox · Jul 19, 2024 · ca1199f · ca1199f
2 parents 721cd16 + cb06d4c
commit ca1199f
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Showing 2 changed files with 80 additions and 37 deletions.
diff --git a/src/blox/discrete.jl b/src/blox/discrete.jl
@@ -60,8 +60,8 @@ struct TAN <: AbstractDiscrete
         @variables t 
         sts = @variables R(t)=κ 
         ps = @parameters κ=κ jcn=0.0 [input=true]
-        eqs = [
-                R ~ min(κ, κ/(λ*jcn + sqrt(eps())))
+        eqs = Equation[
+                # R ~ min(κ, κ/(λ*jcn + sqrt(eps()))) 
               ]
         sys = ODESystem(eqs, t, sts, ps; name)
 
@@ -98,4 +98,4 @@ end
 function get_modulator_state(s::SNc)
     sys = get_namespaced_sys(s)
     return sys.R_
-end
+end
diff --git a/src/blox/neuron_models.jl b/src/blox/neuron_models.jl
@@ -221,8 +221,6 @@ struct HHNeuronInhib_MSN_Adam_Blox <: AbstractInhNeuronBlox
 			T = T
 		end
 
-        @brownian χ
-
 		αₙ(v) = 0.032*(v+52)/(1-exp(-(v+52)/5))
 	    βₙ(v) = 0.5*exp(-(v+57)/40)
 	    αₘ(v) = 0.32*(v+54)/(1-exp(-(v+54)/4))
@@ -237,17 +235,25 @@ struct HHNeuronInhib_MSN_Adam_Blox <: AbstractInhNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)-G_M*mM*(V-E_K)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)-G_M*mM*(V-E_K)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in), 
 			   D(n)~(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~(αₕ(V)*(1-h)-βₕ(V)*h),
 			   D(mM)~(αₘₘ(V)*(1-mM)-βₘₘ(V)*mM),
 			   D(G)~(-1/τ)*G + G_asymp(V,a,b)*(1-G)
 
 		]
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+        ]
 
-		sys = System(
-            eqs, t, sts, ps; 
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 			)
 
@@ -312,8 +318,6 @@ struct HHNeuronInhib_FSI_Adam_Blox <: AbstractInhNeuronBlox
 			b = b
 			T = T
 		end
-
-        @brownian χ
 
 		n_inf(v) = 1/(1+exp(-(v+12.4)/6.8))
 	    τₙ(v) = (0.087+11.4/(1+exp((v+14.6)/8.6)))*(0.087+11.4/(1+exp(-(v-1.3)/18.7)))
@@ -327,7 +331,7 @@ struct HHNeuronInhib_FSI_Adam_Blox <: AbstractInhNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m_inf(V)^3*h*(V-E_Na)-G_K*n^2*(V-E_K)-G_L*(V-E_L)-G_D*mD^3*hD*(V-E_K)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_gap+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m_inf(V)^3*h*(V-E_Na)-G_K*n^2*(V-E_K)-G_L*(V-E_L)-G_D*mD^3*hD*(V-E_K)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_gap+I_asc+I_in), 
 			   D(n)~(n_inf(V)-n)/τₙ(V), 
 			   D(h)~(h_inf(V)-h)/τₕ(V),
 			   D(mD)~(mD_inf(V)-mD)/τₘD(V),
@@ -336,9 +340,18 @@ struct HHNeuronInhib_FSI_Adam_Blox <: AbstractInhNeuronBlox
 			   D(Gₛ)~(-1/τₛ)*Gₛ + G_asymp(V,a,b)*(1-Gₛ)
 
 		]
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+            0
+        ]
 
-		sys = System(
-            eqs, t, sts, ps; 
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 			)
 
@@ -395,8 +408,6 @@ struct HHNeuronExci_STN_Adam_Blox <: AbstractExciNeuronBlox
 			b = b
 		end
 
-        @brownian χ
-
 		αₙ(v) = 0.032*(v+52)/(1-exp(-(v+52)/5))
 	    βₙ(v) = 0.5*exp(-(v+57)/40)
 	    αₘ(v) = 0.32*(v+54)/(1-exp(-(v+54)/4))
@@ -407,16 +418,25 @@ struct HHNeuronExci_STN_Adam_Blox <: AbstractExciNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in), 
 			   D(n)~(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~(αₕ(V)*(1-h)-βₕ(V)*h),
 			   D(G)~(-1/τ)*G + G_asymp(V,a,b)*(1-G)
-
 		]
+
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+            0
+        ]
 
-		sys = System(
-            eqs, t, sts, ps; 
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 			)
 
@@ -476,8 +496,6 @@ struct HHNeuronInhib_GPe_Adam_Blox <: AbstractInhNeuronBlox
 			T = T
 		end
 
-        @brownian χ
-
 		αₙ(v) = 0.032*(v+52)/(1-exp(-(v+52)/5))
 	    βₙ(v) = 0.5*exp(-(v+57)/40)
 	    αₘ(v) = 0.32*(v+54)/(1-exp(-(v+54)/4))
@@ -489,15 +507,25 @@ struct HHNeuronInhib_GPe_Adam_Blox <: AbstractInhNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in), 
 			   D(n)~(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~(αₕ(V)*(1-h)-βₕ(V)*h),
 			   D(G)~(-1/τ)*G + G_asymp(V,a,b)*(1-G)			  
 		]
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+            0
+        ]
 
-		sys = System(
-            eqs, t, sts, ps; 
+
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 			)
 
@@ -561,8 +589,6 @@ mutable struct HHNeuronExci_pyr_Adam_Blox <: AbstractExciNeuronBlox
 			a = a
 			b = b
 		end
-
-        @brownian χ
 
 		αₙ(v) = 0.032*(v+52)/(1-exp(-(v+52)/5))
 	    βₙ(v) = 0.5*exp(-(v+57)/40)
@@ -574,17 +600,26 @@ mutable struct HHNeuronExci_pyr_Adam_Blox <: AbstractExciNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in), 
 			   D(n)~(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~(αₕ(V)*(1-h)-βₕ(V)*h),
 			   D(G)~(-1/τ)*G + G_asymp(V,a,b)*(1-G),
 			   D(Glu)~(-1/τ_glu)*Glu + G_asymp(V-20,2.35,0.01) #this approximates the glutamate dynamics in the model where every spike instantaneously raises glutamate to 1mM
 
 		]
-
-		sys = System(
-            eqs, t, sts, ps; 
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+            0
+        ]
+
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 		)
 		nmda_rec = map(Base.OneTo(N_nmda)) do i
@@ -654,8 +689,6 @@ mutable struct HHNeuronInh_inter_Adam_Blox <: AbstractInhNeuronBlox
 			a = a
 			b = b
 		end
-
-        @brownian χ
 
 		αₙ(v) = 0.032*(v+52)/(1-exp(-(v+52)/5))
 	    βₙ(v) = 0.5*exp(-(v+57)/40)
@@ -667,16 +700,26 @@ mutable struct HHNeuronInh_inter_Adam_Blox <: AbstractInhNeuronBlox
 		G_asymp(v,a,b) = a*(1+tanh(v/b))
 
 		eqs = [ 
-			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in+σ*χ), 
+			   D(V)~(1/Cₘ)*(-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_bg*(sin(t*freq*2*pi/1000)+1)+I_syn+I_asc+I_in), 
 			   D(n)~(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~(αₕ(V)*(1-h)-βₕ(V)*h),
 			   D(G)~(-1/τ)*G + G_asymp(V,a,b)*(1-G)
 
 		]
-
-		sys = System(
-            eqs, t, sts, ps; 
+
+        noise_eqs = [
+            σ/Cₘ
+            0
+            0
+            0
+            0
+            0
+            0
+        ]
+
+		sys = SDESystem(
+            eqs, noise_eqs, t, sts, ps; 
 			name = Symbol(name)
 			)
 
@@ -902,4 +945,4 @@ struct IzhikevichNeuron <: AbstractNeuronBlox
 		sys = ODESystem(eqs, t, sts, p, continuous_events=[ev]; name=name)
 		new(p, sts[2], sts[5], sts[1], sys, namespace)
 	end
-end
+end