Add connections for PING neurons

Neuroblox · Aug 9, 2024 · 0282417 · 0282417
1 parent d2a1766
commit 0282417
Showing 1 changed file with 66 additions and 13 deletions.
diff --git a/src/blox/ping_neuron_examples.jl b/src/blox/ping_neuron_examples.jl
@@ -1,9 +1,12 @@
+# First, create an abstract neuron that we'll extend to create the neurons for this tutorial.
 abstract type AbstractPINGNeuron <: AbstractNeuronBlox end
 
+# Create an excitatory neuron that inherits from this neuron blox.
 struct PINGNeuronExci <: AbstractPINGNeuron
     params
     output
     jcn
+    voltage
     odesystem
     namespace
     function PINGNeuronExci(;name,
@@ -15,10 +18,12 @@ struct PINGNeuronExci <: AbstractPINGNeuron
                              V_K=-100.0,
                              g_L=0.1,
                              V_L=-67.0,
-                             I_ext=0.0)
-        p = paramscoping(C=C, g_Na=g_Na, V_Na=V_Na, g_K=g_K, V_K=V_K, g_L=g_L, V_L=V_L, I_ext=I_ext)
-        C, g_Na, V_Na, g_K, V_K, g_L, V_L, I_ext = p
-        sts = @variables V(t)=0.0 [output=true] n(t)=0.0 h(t)=0.0 jcn(t)=0.0 [input=true]
+                             I_ext=0.0,
+                             τ_R=0.2,
+                             τ_D=2.0)
+        p = paramscoping(C=C, g_Na=g_Na, V_Na=V_Na, g_K=g_K, V_K=V_K, g_L=g_L, V_L=V_L, I_ext=I_ext, τ_R=τ_R, τ_D=τ_D)
+        C, g_Na, V_Na, g_K, V_K, g_L, V_L, I_ext, τ_R, τ_D = p
+        sts = @variables V(t)=0.0 [output=true] n(t)=0.0 h(t)=0.0 s(t)=0.0 jcn(t)=0.0 [input=true]
 
         a_m(v) = 0.32*(v+54.0)/(1.0 - exp(-(v+54.0)/4.0))
         b_m(v) = 0.28*(v+27.0)/(exp((v+27.0)/5.0) - 1.0)
@@ -28,19 +33,22 @@ struct PINGNeuronExci <: AbstractPINGNeuron
         b_h(v) = 4.0/(1.0 + exp(-(v+27.0)/5.0))
 
         m∞(v) = a_m(v)/(a_m(v) + b_m(v))
-        eqs = [D(V) ~ g_Na*m∞(V)^3*h*(V_Na - V) + g_K*(n^4)*(V_K - V) + g_L*(V_L - V) + I_ext,
+        eqs = [D(V) ~ g_Na*m∞(V)^3*h*(V_Na - V) + g_K*(n^4)*(V_K - V) + g_L*(V_L - V) + I_ext + jcn,
                D(n) ~ (a_n(V)*(1.0 - n) - b_n(V)*n),
-               D(h) ~ (a_h(V)*(1.0 - h) - b_h(V)*h)
+               D(h) ~ (a_h(V)*(1.0 - h) - b_h(V)*h),
+               D(s) ~ ((1+tanh(V/10.0))/2.0)*((1.0 - s)/τ_R) - s/τ_D
         ]
         sys = ODESystem(eqs, t, sts, p; name=name)
-        new(p, sts[1], sts[4], sys, namespace)
+        new(p, sts[4], sts[5], sts[1], sys, namespace)
     end
 end
 
+# Create an inhibitory neuron that inherits from the same neuron blox.
 struct PINGNeuronInhib <: AbstractPINGNeuron
     params
     output
     jcn
+    voltage
     odesystem
     namespace
     function PINGNeuronInhib(;name,
@@ -52,10 +60,12 @@ struct PINGNeuronInhib <: AbstractPINGNeuron
                              V_K=-90.0,
                              g_L=0.1,
                              V_L=-65.0,
-                             I_ext=0.0)
-        p = paramscoping(C=C, g_Na=g_Na, V_Na=V_Na, g_K=g_K, V_K=V_K, g_L=g_L, V_L=V_L, I_ext=I_ext)
-        C, g_Na, V_Na, g_K, V_K, g_L, V_L, I_ext = p
-        sts = @variables V(t)=0.0 [output=true] n(t)=0.0 h(t)=0.0 jcn(t)=0.0 [input=true]
+                             I_ext=0.0,
+                             τ_R=0.5,
+                             τ_D=10.0)
+        p = paramscoping(C=C, g_Na=g_Na, V_Na=V_Na, g_K=g_K, V_K=V_K, g_L=g_L, V_L=V_L, I_ext=I_ext, τ_R=τ_R, τ_D=τ_D)
+        C, g_Na, V_Na, g_K, V_K, g_L, V_L, I_ext, τ_R, τ_D = p
+        sts = @variables V(t)=0.0 [output=true] n(t)=0.0 h(t)=0.0 s(t)=0.0 jcn(t)=0.0 [input=true]
 
         a_m(v) = 0.1*(v+35.0)/(1.0 - exp(-(v+35.0)/10.0))
         b_m(v) = 4*exp(-(v+60.0)/18.0)
@@ -67,9 +77,52 @@ struct PINGNeuronInhib <: AbstractPINGNeuron
         m∞(v) = a_m(v)/(a_m(v) + b_m(v))
         eqs = [D(V) ~ g_Na*m∞(V)^3*h*(V_Na - V) + g_K*(n^4)*(V_K - V) + g_L*(V_L - V) + I_ext,
                D(n) ~ (a_n(V)*(1.0 - n) - b_n(V)*n),
-               D(h) ~ (a_h(V)*(1.0 - h) - b_h(V)*h)
+               D(h) ~ (a_h(V)*(1.0 - h) - b_h(V)*h),
+               D(s) ~ ((1+tanh(V/10.0))/2.0)*((1.0 - s)/τ_R) - s/τ_D
         ]
         sys = ODESystem(eqs, t, sts, p; name=name)
-        new(p, sts[1], sts[4], sys, namespace)
+        new(p, sts[4], sts[5], sts[1], sys, namespace)
         end
+end
+
+# Create excitatory -> inhibitory AMPA receptor conenction
+function (bc::BloxConnector)(
+    bloxout::PINGNeuronExci, 
+    bloxin::PINGNeuronInhib; 
+    kwargs...
+)
+    sys_out = get_namespaced_sys(bloxout)
+    sys_in = get_namespaced_sys(bloxin)
+
+    w = generate_weight_param(bloxout, bloxin; kwargs...)
+    push!(bc.weights, w)
+
+    V_E = haskey(kwargs, :V_E) ? kwargs[:V_E] : 0.0
+
+    s    = namespace_expr(bloxout.output, sys_out)
+    v_in = namespace_expr(bloxin.voltage, sys_in)
+    eq = sys_in.jcn ~ w*s*(V_E-v_in)
+
+    accumulate_equation!(bc, eq)
+end
+
+# Create inhibitory -> inhibitory/excitatory GABA_A receptor connection
+function (bc::BloxConnector)(
+    bloxout::PINGNeuronInhib, 
+    bloxin::AbstractPINGNeuron; 
+    kwargs...
+)
+    sys_out = get_namespaced_sys(bloxout)
+    sys_in = get_namespaced_sys(bloxin)
+
+    w = generate_weight_param(bloxout, bloxin; kwargs...)
+    push!(bc.weights, w)
+
+    V_I = haskey(kwargs, :V_I) ? kwargs[:V_I] : -80.0    
+
+    s    = namespace_expr(bloxout.output, sys_out)
+    v_in = namespace_expr(bloxin.voltage, sys_in)
+    eq = sys_in.jcn ~ w*s*(V_I-v_in)
+
+    accumulate_equation!(bc, eq)
 end