Adams model on ketamine

examples/Adam_NMDA_MWE.jl

@@ -0,0 +1,40 @@
+using Neuroblox
+using DifferentialEquations
+using Graphs
+using MetaGraphs
+using Plots
+
+@named n1=HHNeuronExci_pyr_Adam_Blox(σ=0,I_bg=-1.25;N_nmda=1,namespace=:g)
+@named n2=HHNeuronExci_pyr_Adam_Blox(σ=3;N_nmda=1,namespace=:g)
+#this parameter set reproduces figure 3C    DO NOT CHANGE
+@named n3=HHNeuronInh_inter_Adam_Blox(σ=1,I_bg=-1.8;N_nmda=1,k_unblock=5.4,namespace=:g)
+
+@named glu1= Glutamate_puff()
+@named glu2= Steady_Glutamate()
+
+assembly = [n1,n2]
+#assembly = [glu1,n1]
+g = MetaDiGraph()
+add_blox!.(Ref(g), assembly)
+add_edge!(g,1,2,Dict(:weight=>0,:nmda=>true,:nmda_weight=>2))
+
+@named neuron_net = system_from_graph(g)
+sys = structural_simplify(neuron_net)
+prob = SDEProblem(sys, [], (0.0, 2000), [])
+sol = solve(prob, ImplicitEM(),saveat = 0.01)
+ss=convert(Array,sol)
+st=unknowns(sys)
+vlist=Int64[]
+for ii = 1:length(st)
+    if contains(string(st[ii]), "V(t)")
+            push!(vlist,ii)
+    end
+end
+V = ss[vlist,:]
+
+VV=zeros(length(vlist),length(sol.t))
+for ii = 1:length(vlist)
+    VV[ii,:] .= V[ii,:] .+ 200*(ii-1)
+
+end
+plot(sol.t,VV[:,:]',color= "blue",label=false)

examples/Adam_NMDA_full_working_example.jl

@@ -0,0 +1,54 @@
+using Neuroblox
+using DifferentialEquations
+using Graphs
+using MetaGraphs
+using Plots
+
+#Number of neurons in each block
+N_pyr=30
+N_in_phasic=20
+N_in_tonic=10
+
+#number of connections between each block pair
+prj_pyr_phasic = 10
+prj_phasic_pyr = 10
+prj_tonic_pyr = 5
+prj_tonic_phasic = 5
+
+@named cb_pyr = Cortical_Pyramidal_Assembly_Adam(N_exci=N_pyr,namespace=:g)
+@named cb_in_phasic = Cortical_Interneuron_Assembly_Phasic_Adam(namespace=:g,N_inhib=N_in_phasic)
+@named cb_in_tonic = Cortical_Interneuron_Assembly_Tonic_Adam(namespace=:g,N_inhib=N_in_tonic)
+@named glu= Steady_Glutamate()
+assembly = [cb_pyr,cb_in_phasic,cb_in_tonic,glu];
+g = MetaDiGraph()
+add_blox!.(Ref(g), assembly)
+
+add_edge!(g,1,2,Dict(:weight=>0.2/prj_pyr_phasic,:density=>prj_pyr_phasic/N_pyr,:nmda=>true,:nmda_weight=>9.5/prj_pyr_phasic))
+add_edge!(g,2,1,Dict(:weight=>0.8/prj_phasic_pyr,:density=>prj_phasic_pyr/N_in_phasic))
+add_edge!(g,3,1,Dict(:weight=>5/prj_tonic_pyr,:density=>prj_tonic_pyr/N_in_tonic))
+add_edge!(g,3,2,Dict(:weight=>5/prj_tonic_phasic,:density=>prj_tonic_phasic/N_in_tonic))
+add_edge!(g,4,3,Dict(:nmda=>true,:nmda_weight=>9.5))
+
+@named neuron_net = system_from_graph(g)
+sys = structural_simplify(neuron_net)
+prob = SDEProblem(sys, [], (0.0, 2000), [])
+sol = solve(prob,saveat = 0.01)
+#sol = solve(prob, ImplicitEM(),saveat = 0.01)
+ss=convert(Array,sol)
+st=unknowns(sys)
+vlist=Int64[]
+for ii = 1:length(st)
+    if contains(string(st[ii]), "V(t)")
+            push!(vlist,ii)
+    end
+end
+V = ss[vlist,:]
+
+VV=zeros(length(vlist),length(sol.t))
+for ii = 1:length(vlist)
+    VV[ii,:] .= V[ii,:] .+ 200*(ii-1)
+
+end
+plot(sol.t,VV[:,:]',color= "blue",label=false)
+
+

examples/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+Neuroblox = "769b91e5-4c60-41ee-bfae-153c84203cb2"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"

src/Neuroblox.jl

@@ -70,6 +70,7 @@ abstract type NeuralMassBlox <: AbstractBlox end
 abstract type CompositeBlox <: AbstractBlox end
 abstract type StimulusBlox <: AbstractBlox end
 abstract type ObserverBlox end # not AbstractBlox since it should not show up in the GUI
+abstract type AbstractReceptorBlox end # not shown in the GUI
 
 # we define these in neural_mass.jl
 # abstract type HarmonicOscillatorBlox <: NeuralMassBlox end
@@ -108,6 +109,7 @@ include("blox/cortical.jl")
 include("blox/canonicalmicrocircuit.jl")
 include("blox/neuron_models.jl")
 include("blox/DBS_Model_Blox_Adam_Brown.jl")
+include("blox/Ketamine_Cortical_Model_Blox_Adam_Brown.jl")
 include("blox/van_der_pol.jl")
 include("blox/ts_outputs.jl")
 include("blox/sources.jl")
@@ -221,7 +223,8 @@ export JansenRitSPM12, next_generation, qif_neuron, if_neuron, hh_neuron_excitat
     hh_neuron_inhibitory, van_der_pol, Generic2dOscillator
 export HHNeuronExciBlox, HHNeuronInhibBlox, IFNeuron, LIFNeuron, QIFNeuron, IzhikevichNeuron, LIFExciNeuron, LIFInhNeuron,
     CanonicalMicroCircuitBlox, WinnerTakeAllBlox, CorticalBlox, SuperCortical, HHNeuronInhib_MSN_Adam_Blox, HHNeuronInhib_FSI_Adam_Blox, HHNeuronExci_STN_Adam_Blox,
-    HHNeuronInhib_GPe_Adam_Blox, Striatum_MSN_Adam, Striatum_FSI_Adam, GPe_Adam, STN_Adam, LIFExciCircuitBlox, LIFInhCircuitBlox
+    HHNeuronInhib_GPe_Adam_Blox, Striatum_MSN_Adam, Striatum_FSI_Adam, GPe_Adam, STN_Adam, LIFExciCircuitBlox, LIFInhCircuitBlox, HHNeuronExci_pyr_Adam_Blox, HHNeuronInh_inter_Adam_Blox
+export Cortical_Pyramidal_Assembly_Adam, Cortical_Interneuron_Assembly_Phasic_Adam, Cortical_Interneuron_Assembly_Tonic_Adam, NMDA_receptor, Steady_Glutamate, Glutamate_puff
 export LinearNeuralMass, HarmonicOscillator, JansenRit, WilsonCowan, LarterBreakspear, NextGenerationBlox, NextGenerationResolvedBlox, NextGenerationEIBlox, KuramotoOscillator
 export Matrisome, Striosome, Striatum, GPi, GPe, Thalamus, STN, TAN, SNc
 export HebbianPlasticity, HebbianModulationPlasticity