Merge pull request #296 from Neuroblox/adding-input-current-to-neurons

added I_bg (background current) as a parameter for neurons

src/blox/connections.jl

@@ -259,7 +259,7 @@ function (bc::BloxConnector)(
         sys_neuron = get_namespaced_sys(neuron)
         # Large negative current added to shut down the Striatum spiking neurons.
         # Value is hardcoded for now, as it's more of a hack, not user option. 
-        cb_neuron = [t_event] => [sys_neuron.I_in ~ IfElse.ifelse(sys_matr_out.ρ > sys_matr_in.ρ, -1000, 0)]
+        cb_neuron = [t_event] => [sys_neuron.I_bg ~ IfElse.ifelse(sys_matr_out.ρ > sys_matr_in.ρ, -2, 0)]
         push!(bc.events, cb_neuron)
     end
 end

src/blox/cortical_blox.jl

@@ -29,7 +29,7 @@ struct CorticalBlox{P} <: AbstractComponent
                 E_syn_inhib,
                 G_syn_exci,
                 G_syn_inhib,
-                I_in = rand(N_exci),
+                I_bg = rand(N_exci),
                 freq,
                 phase,
                 τ_exci,

src/blox/neuron_models.jl

@@ -159,7 +159,7 @@ struct HHNeuronExciBlox <: AbstractExciNeuronBlox
         θ_spike=0.0,
         E_syn=0.0, 
         G_syn=3, 
-        I_in=0,
+        I_bg=0,
         freq=0,
         phase=0,
         τ=5
@@ -171,8 +171,10 @@ struct HHNeuronExciBlox <: AbstractExciNeuronBlox
 			h(t)=0.59 
 			I_syn(t)=0.0 
 			[input=true] 
-            I_in(t)=I_in
+            I_in(t)=0.0
             [input=true]
+			I_asc(t)=0.0
+			[input=true]
 			G(t)=0.0 
 			z(t)=0.0
 			Gₛₜₚ(t)=0.0 
@@ -194,6 +196,7 @@ struct HHNeuronExciBlox <: AbstractExciNeuronBlox
 			τ₁ = 0.1 
 			τ₂ = τ 
 			τ₃ = 2000 
+			I_bg=I_bg
 			kₛₜₚ = 0.5
 			freq = freq 
 			phase = phase
@@ -209,7 +212,7 @@ struct HHNeuronExciBlox <: AbstractExciNeuronBlox
 		ϕ = 5 
 		G_asymp(v,G_syn) = (G_syn/(1 + exp(-4.394*((v-V_shift)/V_range))))
 	 	eqs = [ 
-			   D(V)~-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_in*(sin(t*freq*2*pi/1000)+1)+I_syn, 
+			   D(V)~-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)~ϕ*(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~ϕ*(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~ϕ*(αₕ(V)*(1-h)-βₕ(V)*h),
@@ -245,7 +248,7 @@ struct HHNeuronInhibBlox <: AbstractInhNeuronBlox
         θ_spike=0.0,
         E_syn=-70.0,
         G_syn=11.5,
-        I_in=0,
+        I_bg=0,
         freq=0,
         phase=0,
         τ=70
@@ -257,7 +260,11 @@ struct HHNeuronInhibBlox <: AbstractInhNeuronBlox
 			h(t)=0.59 
 			I_syn(t)=0.0 
 			[input=true] 
-			G(t)=0.0 
+			I_asc(t)=0.0
+			[input=true]
+			I_in(t)=0.0
+			[input=true]
+            G(t)=0.0 
 			[output = true] 
 			z(t)=0.0
             spikes_cumulative(t)=0.0
@@ -278,7 +285,7 @@ struct HHNeuronInhibBlox <: AbstractInhNeuronBlox
 			τ₁ = 0.1 
 			τ₂ = τ 
 			τ₃ = 2000 
-			I_in=I_in 
+			I_bg=I_bg 
 			freq = freq 
 			phase = phase
 		end
@@ -292,7 +299,7 @@ struct HHNeuronInhibBlox <: AbstractInhNeuronBlox
 		ϕ = 5 
 		G_asymp(v,G_syn) = (G_syn/(1 + exp(-4.394*((v-V_shift)/V_range))))
 	 	eqs = [ 
-			   D(V)~-G_Na*m^3*h*(V-E_Na)-G_K*n^4*(V-E_K)-G_L*(V-E_L)+I_in*(sin(t*freq*2*pi/1000)+1)+I_syn, 
+			   D(V)~-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)~ϕ*(αₙ(V)*(1-n)-βₙ(V)*n), 
 			   D(m)~ϕ*(αₘ(V)*(1-m)-βₘ(V)*m), 
 			   D(h)~ϕ*(αₕ(V)*(1-h)-βₕ(V)*h),

src/blox/subcortical_blox.jl

@@ -16,7 +16,7 @@ struct Striatum <: AbstractComponent
         N_inhib = 25,
         E_syn_inhib=-70,
         G_syn_inhib=1.2,
-        I_in=zeros(N_inhib),
+        I_bg=zeros(N_inhib),
         freq=zeros(N_inhib),
         phase=zeros(N_inhib),
         τ_inhib=70
@@ -28,7 +28,7 @@ struct Striatum <: AbstractComponent
                 E_syn = E_syn_inhib, 
                 G_syn = G_syn_inhib, 
                 τ = τ_inhib,
-                I_in = I_in[i],
+                I_bg = I_bg[i],
                 freq = freq[i],
                 phase = phase[i]
         ) 
@@ -94,7 +94,7 @@ struct GPi <: AbstractComponent
         N_inhib = 25,
         E_syn_inhib=-70,
         G_syn_inhib=8,
-        I_in=4*ones(N_inhib),
+        I_bg=4*ones(N_inhib),
         freq=zeros(N_inhib),
         phase=zeros(N_inhib),
         τ_inhib=70
@@ -106,7 +106,7 @@ struct GPi <: AbstractComponent
                     E_syn = E_syn_inhib, 
                     G_syn = G_syn_inhib, 
                     τ = τ_inhib,
-                    I_in = I_in[i],
+                    I_bg = I_bg[i],
                     freq = freq[i],
                     phase = phase[i]
             ) 
@@ -151,7 +151,7 @@ struct GPe <: AbstractComponent
         N_inhib = 15,
         E_syn_inhib=-70,
         G_syn_inhib=3,
-        I_in=2*ones(N_inhib),
+        I_bg=2*ones(N_inhib),
         freq=zeros(N_inhib),
         phase=zeros(N_inhib),
         τ_inhib=70
@@ -163,7 +163,7 @@ struct GPe <: AbstractComponent
                     E_syn = E_syn_inhib, 
                     G_syn = G_syn_inhib, 
                     τ = τ_inhib,
-                    I_in = I_in[i],
+                    I_bg = I_bg[i],
                     freq = freq[i],
                     phase = phase[i]
             ) 
@@ -209,7 +209,7 @@ struct Thalamus <: AbstractComponent
         N_exci = 25,
         E_syn_exci=0,
         G_syn_exci=3,
-        I_in=3*ones(N_exci),
+        I_bg=3*ones(N_exci),
         freq=zeros(N_exci),
         phase=zeros(N_exci),
         τ_exci=5
@@ -221,7 +221,7 @@ struct Thalamus <: AbstractComponent
                     E_syn = E_syn_exci, 
                     G_syn = G_syn_exci, 
                     τ = τ_exci,
-                    I_in = I_in[i],
+                    I_bg = I_bg[i],
                     freq = freq[i],
                     phase = phase[i]
             ) 
@@ -266,7 +266,7 @@ struct STN <: AbstractComponent
         N_exci = 25,
         E_syn_exci=0,
         G_syn_exci=3,
-        I_in=3*ones(N_exci),
+        I_bg=3*ones(N_exci),
         freq=zeros(N_exci),
         phase=zeros(N_exci),
         τ_exci=5
@@ -278,7 +278,7 @@ struct STN <: AbstractComponent
                 E_syn = E_syn_exci, 
                 G_syn = G_syn_exci, 
                 τ = τ_exci,
-                I_in = I_in[i],
+                I_bg = I_bg[i],
                 freq = freq[i],
                 phase = phase[i]
         ) 

src/blox/winnertakeall.jl

@@ -19,7 +19,7 @@ struct WinnerTakeAllBlox{P} <: AbstractComponent
         E_syn_inhib=-70,
         G_syn_exci=3.0,
         G_syn_inhib=3.0,
-        I_in=zeros(N_exci),
+        I_bg=zeros(N_exci),
         freq=zeros(N_exci),
         phase=zeros(N_exci),
         τ_exci=5,
@@ -39,7 +39,7 @@ struct WinnerTakeAllBlox{P} <: AbstractComponent
                     E_syn = E_syn_exci, 
                     G_syn = G_syn_exci, 
                     τ = τ_exci,
-                    I_in = I_in[i],
+                    I_bg = I_bg[i],
                     freq = freq[i],
                     phase = phase[i]
             ) 

test/components.jl

@@ -429,9 +429,9 @@ end
 end
 
 @testset "HH Neuron excitatory & inhibitory network" begin
-nn1 = HHNeuronExciBlox(name=Symbol("nrn1"), I_in=3, freq=4; t_spike_window=0.1)
-nn2 = HHNeuronExciBlox(name=Symbol("nrn2"), I_in=2, freq=6; t_spike_window=0.1)
-nn3 = HHNeuronInhibBlox(name=Symbol("nrn3"), I_in=2, freq=3)
+nn1 = HHNeuronExciBlox(name=Symbol("nrn1"), I_bg=3, freq=4; t_spike_window=0.1)
+nn2 = HHNeuronExciBlox(name=Symbol("nrn2"), I_bg=2, freq=6; t_spike_window=0.1)
+nn3 = HHNeuronInhibBlox(name=Symbol("nrn3"), I_bg=2, freq=3)
 assembly = [nn1, nn2, nn3]
 
 # Adjacency matrix : 
@@ -453,7 +453,7 @@ end
 
 @testset "WinnerTakeAll" begin
     N_exci = 5
-    @named wta= WinnerTakeAllBlox(;I_in=5*rand(N_exci), N_exci)
+    @named wta= WinnerTakeAllBlox(;I_bg=5*rand(N_exci), N_exci)
     sys = wta.odesystem
     wta_simp=structural_simplify(sys)
     prob = ODEProblem(wta_simp,[],(0,10))
@@ -466,8 +466,8 @@ end
 @testset "WinnerTakeAll network" begin
     global_ns = :g # global namespace
     N_exci = 5
-    @named wta1 = WinnerTakeAllBlox(;I_in=5*rand(N_exci), N_exci, namespace=global_ns)
-    @named wta2 = WinnerTakeAllBlox(;I_in=5*rand(N_exci), N_exci, namespace=global_ns)
+    @named wta1 = WinnerTakeAllBlox(;I_bg=5*rand(N_exci), N_exci, namespace=global_ns)
+    @named wta2 = WinnerTakeAllBlox(;I_bg=5*rand(N_exci), N_exci, namespace=global_ns)
     g = MetaDiGraph()
     add_blox!.(Ref(g), [wta1, wta2])
     add_edge!(g, 1, 2, Dict(:weight => 1, :density => 0.5))