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Adams model on ketamine #358

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0339718
Adams model on ketamine
anandpathak31 Jul 10, 2024
26df492
adding connection types between neuron and receptor
anandpathak31 Jul 10, 2024
19dc4c6
composite neuron
anandpathak31 Jul 11, 2024
fb6e0c7
comments
anandpathak31 Jul 11, 2024
ace5277
add `Abstract` prefix to abstract types
harisorgn Jul 12, 2024
8660a31
add `namespaced_nameof` function and rename previous one to `inner_` …
harisorgn Jul 12, 2024
6cb96fd
update the new composite neuron structs (mutable + parts)
harisorgn Jul 12, 2024
8263767
glutamate source connection
anandpathak31 Jul 12, 2024
9f0faa5
add cb connections
anandpathak31 Jul 12, 2024
90b5977
Full model implementation
anandpathak31 Jul 19, 2024
721cd16
add packages in example env
anandpathak31 Jul 19, 2024
975746d
full working example
anandpathak31 Jul 22, 2024
70df53e
edit example
anandpathak31 Jul 22, 2024
7025ee4
change parameter in wta
anandpathak31 Aug 26, 2024
ba1a047
example
anandpathak31 Aug 28, 2024
55e98ea
Merge remote-tracking branch 'origin/master' into Adam_ketamine
anandpathak31 Sep 18, 2024
ee3a3ee
merge master
anandpathak31 Sep 18, 2024
486e120
rename abstract composite blox
anandpathak31 Sep 18, 2024
6962a9f
rename abstract composite blox in CMC
anandpathak31 Sep 18, 2024
cdfc0b9
rename composite blox
anandpathak31 Sep 19, 2024
93f18fc
rename composite blox
anandpathak31 Sep 19, 2024
62fc902
rename composite blox
anandpathak31 Sep 19, 2024
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2 changes: 2 additions & 0 deletions Project.toml
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Expand Up @@ -40,6 +40,8 @@ OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
Peaks = "18e31ff7-3703-566c-8e60-38913d67486b"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
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Pluto and Plots shouldn't be in the Neuroblox project.

The way I'd recommend doing this would be to add a Project.toml in the examples folder that has things like Plots and Pluto in it.

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@MasonProtter thanks for checking out. Once the code is straightened, I always remove those packages before merging. Its not an oversight I assure.

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Sure, but I think it'd actually be helpful to have those tools in a separate project so that users can use them in the examples.

The way this would be done is you'd do something like

cd Neuroblox
julia --project=examples

and then from within julia you'd do

julia> using Pkg; pkg"dev ." # add Neuroblox itself to the current environment

julia> pkg"add Plots Pluto DifferentialEquations Graphs MetaGraphs"

and then whenever you work on code that goes in the examples, you just need to activate the Neuroblox/examples folder instead of the Neuroblox folder itself.

Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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34 changes: 34 additions & 0 deletions examples/Adam_NMDA_MWE.jl
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@@ -0,0 +1,34 @@
using Neuroblox
using DifferentialEquations
using Graphs
using MetaGraphs
using Plots

@named n1=HHNeuronExci_pyr_Adam_Blox(σ=3;N_nmda=1,namespace=:g)
@named n2=HHNeuronExci_pyr_Adam_Blox(σ=3;N_nmda=1,namespace=:g)

assembly = [n1,n2]
g = MetaDiGraph()
add_blox!.(Ref(g), assembly)
add_edge!(g,1,2,Dict(:weight=>0,:nmda=>true,:nmda_weight=>1))

@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)
7 changes: 5 additions & 2 deletions src/Neuroblox.jl
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Expand Up @@ -59,9 +59,10 @@ abstract type Merger end
# subtypes of Blox define categories of Blox that are displayed in separate sections of the GUI
abstract type AbstractNeuronBlox <: AbstractBlox end
abstract type NeuralMassBlox <: AbstractBlox end
abstract type CompositeBlox <: AbstractBlox end
abstract type AbstractCompositeBlox <: 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
Expand Down Expand Up @@ -99,6 +100,7 @@ include("blox/cortical_blox.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")
Expand Down Expand Up @@ -188,7 +190,8 @@ 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,
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
HHNeuronInhib_GPe_Adam_Blox, Striatum_MSN_Adam, Striatum_FSI_Adam, GPe_Adam, STN_Adam, 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
export Matrisome, Striosome, Striatum, GPi, GPe, Thalamus, STN, TAN, SNc
export HebbianPlasticity, HebbianModulationPlasticity
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8 changes: 4 additions & 4 deletions src/blox/DBS_Model_Blox_Adam_Brown.jl
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Expand Up @@ -2,7 +2,7 @@
Subcortical Blox used for DBS model in Adam et al,2021
"""

struct Striatum_MSN_Adam <: CompositeBlox
struct Striatum_MSN_Adam <: AbstractCompositeBlox
namespace
parts
odesystem
Expand Down Expand Up @@ -69,7 +69,7 @@ struct Striatum_MSN_Adam <: CompositeBlox

end

struct Striatum_FSI_Adam <: CompositeBlox
struct Striatum_FSI_Adam <: AbstractCompositeBlox
namespace
parts
odesystem
Expand Down Expand Up @@ -165,7 +165,7 @@ struct Striatum_FSI_Adam <: CompositeBlox

end

struct GPe_Adam <: CompositeBlox
struct GPe_Adam <: AbstractCompositeBlox
namespace
parts
odesystem
Expand Down Expand Up @@ -232,7 +232,7 @@ struct GPe_Adam <: CompositeBlox

end

struct STN_Adam <: CompositeBlox
struct STN_Adam <: AbstractCompositeBlox
namespace
parts
odesystem
Expand Down
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