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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.11.0","generation_timestamp":"2024-10-08T07:31:15","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.11.0","generation_timestamp":"2024-10-08T09:10:52","documenter_version":"1.7.0"}}
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Expand Up @@ -525,9 +525,9 @@ version = "1.15.1"

[[deps.DifferentiationInterface]]
deps = ["ADTypes", "Compat", "LinearAlgebra", "PackageExtensionCompat"]
git-tree-sha1 = "624e283ddac6d608742e857b0487238f11940f57"
git-tree-sha1 = "75d1716eb46e1b77304f7d79ec9ac6a4e6185d02"
uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
version = "0.6.6"
version = "0.6.7"

[deps.DifferentiationInterface.extensions]
DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Release Notes · Neuroblox</title><meta name="title" content="Release Notes · Neuroblox"/><meta property="og:title" content="Release Notes · Neuroblox"/><meta property="twitter:title" content="Release Notes · Neuroblox"/><meta name="description" content="Documentation for Neuroblox."/><meta property="og:description" content="Documentation for Neuroblox."/><meta property="twitter:description" content="Documentation for Neuroblox."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link 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href="#v0.3">v0.3</a><a id="v0.3-1"></a><a class="docs-heading-anchor-permalink" href="#v0.3" title="Permalink"></a></h2><p>Initial Release!</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../api/">« API</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option 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15 changes: 7 additions & 8 deletions dev/tutorials/basal_ganglia_tutorial.jl → dev/tutorials/basal_ganglia.jl
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Expand Up @@ -9,7 +9,6 @@

using Neuroblox
using StochasticDiffEq ## For building and solving differential equations problems
using MetaGraphs ## use its MetaGraph type to build the circuit
using CairoMakie ## For plotting
using Random ## For setting a random seed

Expand All @@ -28,12 +27,12 @@ unknowns(sys)

# Create and solve the SDE problem
## Define simulation parameters
tspan = (0.0, 5500.0) ## simulation time span [ms]
tspan = (0.0, 2000.0) ## simulation time span [ms]
dt = 0.05 ## time step for solving and saving [ms]

## Create a stochastic differential equation problem and use the RKMil method to solve it
prob = SDEProblem(sys, [], tspan, [])
sol = solve(prob, RKMil(); dt=dt, saveat=dt)
sol = solve(prob, RKMil(); dt=dt, saveat=dt, abstol = 1e-2, reltol = 1e-2)

# Plot voltage of a single neuron
plot(sol, idxs=1, axis = (xlabel = "time (ms)", ylabel = "membrane potential (mV)"))
Expand Down Expand Up @@ -71,7 +70,7 @@ fig

# We can also run multiple simulations in parallel and compute the average power spectrum
ens_prob = EnsembleProblem(prob)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=5)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=3, abstol = 1e-2, reltol = 1e-2);

powerspectrumplot(msn, ens_sol; state = "G",
method=welch_pgram, window=hanning,
Expand Down Expand Up @@ -104,7 +103,7 @@ add_edge!(g, 2, 1, Dict(:weight => weight_FSI_MSN, :density => density_FSI_MSN))
@named sys = system_from_graph(g)
prob = SDEProblem(sys, [], tspan, [])
ens_prob = EnsembleProblem(prob)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=5)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=3, abstol = 1e-2, reltol = 1e-2);

# Detect spikes and compute firing rates
spikes_msn = detect_spikes(msn, ens_sol[1]; threshold=-35)
Expand Down Expand Up @@ -170,7 +169,7 @@ add_edge!(g, 4, 2, Dict(:weight => weight_STN_FSI, :density => density_STN_FSI))
@named sys = system_from_graph(g)
prob = SDEProblem(sys, [], tspan, [])
ens_prob = EnsembleProblem(prob)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=5)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=3, abstol = 1e-2, reltol = 1e-2);

# Compute and plot power spectra for all components
fig = Figure(size = (1500, 600))
Expand Down Expand Up @@ -249,7 +248,7 @@ add_edge!(g, 4, 2, Dict(:weight => weight_STN_FSI, :density => density_STN_FSI))

prob = SDEProblem(sys, [], tspan, [])
ens_prob = EnsembleProblem(prob)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=5)
ens_sol = solve(ens_prob, RKMil(); dt=dt, saveat=dt, trajectories=3, abstol = 1e-2, reltol = 1e-2);

# Compute and compare power spectra for all neural populations in Parkinsonian condition against their counterparts in baseline conditions.
powerspectrumplot(fig[2,1], msn, ens_sol; state = "G",
Expand Down Expand Up @@ -291,4 +290,4 @@ fig


# ## References
# [Adam, Elie M., et al. "Deep brain stimulation in the subthalamic nucleus for Parkinson's disease can restore dynamics of striatal networks." Proceedings of the National Academy of Sciences 119.19 (2022): e2120808119.](https://doi.org/10.1073/pnas.2120808119)
# [Adam, Elie M., et al. "Deep brain stimulation in the subthalamic nucleus for Parkinson's disease can restore dynamics of striatal networks." Proceedings of the National Academy of Sciences 119.19 (2022): e2120808119.](https://doi.org/10.1073/pnas.2120808119)
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