build based on 8e89df0

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-04T22:49:37","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-05T02:13:19","documenter_version":"1.4.1"}}

dev/assets/Manifest.toml

@@ -1736,9 +1736,9 @@ version = "0.20.5"
 
 [[deps.MLJBalancing]]
 deps = ["MLJBase", "MLJModelInterface", "MLUtils", "OrderedCollections", "Random", "StatsBase"]
-git-tree-sha1 = "f02e28f9f3c54a138db12a97a5d823e5e572c2d6"
+git-tree-sha1 = "f707a01a92d664479522313907c07afa5d81df19"
 uuid = "45f359ea-796d-4f51-95a5-deb1a414c586"
-version = "0.1.4"
+version = "0.1.5"
 
 [[deps.MLJBase]]
 deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LearnAPI", "LinearAlgebra", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "RecipesBase", "Reexport", "ScientificTypes", "Serialization", "StatisticalMeasuresBase", "StatisticalTraits", "Statistics", "StatsBase", "Tables"]

dev/getting_started/index.html

@@ -22,7 +22,7 @@
 \end{align}
  \]</p><p>To solve the system, we first create an ODEProblem and then solve it over the tspan of (0,100) using a stiff solver.  The solution is saved every 0.1ms. The unit of time in Neuroblox is 1ms.</p><pre><code class="language-julia hljs">prob = ODEProblem(sys, [], (0.0, 100), [])
 sol = solve(prob, Rodas4(), saveat=0.1)
-plot(sol)</code></pre><img src="92aa700f.svg" alt="Example block output"/><h2 id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models"><a class="docs-heading-anchor" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models">Example 2 : Building a Brain Circuit from literature using Neural Mass Models</a><a id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models-1"></a><a class="docs-heading-anchor-permalink" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models" title="Permalink"></a></h2><p>In this example, we will construct a Parkinsons model from eight Jansen-Rit Neural Mass Models as described in Liu et al. (2020). DOI: 10.1016/j.neunet.2019.12.021. The Jansen-Rit Neural Mass model is defined by the following differential equations:</p><p class="math-container">\[\frac{dx}{dt} = y-\frac{2}{\tau}x
+plot(sol)</code></pre><img src="13d97753.svg" alt="Example block output"/><h2 id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models"><a class="docs-heading-anchor" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models">Example 2 : Building a Brain Circuit from literature using Neural Mass Models</a><a id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models-1"></a><a class="docs-heading-anchor-permalink" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models" title="Permalink"></a></h2><p>In this example, we will construct a Parkinsons model from eight Jansen-Rit Neural Mass Models as described in Liu et al. (2020). DOI: 10.1016/j.neunet.2019.12.021. The Jansen-Rit Neural Mass model is defined by the following differential equations:</p><p class="math-container">\[\frac{dx}{dt} = y-\frac{2}{\tau}x
 \frac{dy}{dt} = -\frac{x}{\tau^2} + \frac{H}{\tau} [\frac{2\lambda}{1+\text{exp}(-r*\sum{jcn})} - \lambda]\]</p><pre><code class="language-julia hljs">using Neuroblox
 using DifferentialEquations
 using Graphs
@@ -121,4 +121,4 @@
  1.0
  1.0</code></pre><p>We select an algorithm and solve the system</p><pre><code class="language-julia hljs">alg = Tsit5()
 sol_dde_no_delays = solve(prob, alg, saveat=1)
-plot(sol_dde_no_delays)</code></pre><img src="1ec1351b.svg" alt="Example block output"/><p>In a later tutorial, we will show how to introduce edge delays.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Neuroblox</a><a class="docs-footer-nextpage" href="../tutorials/resting_state_wb/">Tutorial on resting state simulation using neural mass models »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 4 June 2024 22:49">Tuesday 4 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot(sol_dde_no_delays)</code></pre><img src="364e0986.svg" alt="Example block output"/><p>In a later tutorial, we will show how to introduce edge delays.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Neuroblox</a><a class="docs-footer-nextpage" href="../tutorials/resting_state_wb/">Tutorial on resting state simulation using neural mass models »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Wednesday 5 June 2024 02:13">Wednesday 5 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -4,4 +4,4 @@
 using PkgAuthentication
 PkgAuthentication.install("juliahub.com")
 Pkg.Registry.add()
-Pkg.add(&quot;Neuroblox&quot;)</code></pre><h2 id="Licensing"><a class="docs-heading-anchor" href="#Licensing">Licensing</a><a id="Licensing-1"></a><a class="docs-heading-anchor-permalink" href="#Licensing" title="Permalink"></a></h2><p>Neuroblox is free for non-commerical and academic use. For full details of the license, please see  <a href="https://github.com/Neuroblox/NeurobloxEULA">the Neuroblox EULA</a>. For commercial use, get in contact with sales@neuroblox.org.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="getting_started/">Getting Started »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Tuesday 4 June 2024 22:49">Tuesday 4 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Pkg.add(&quot;Neuroblox&quot;)</code></pre><h2 id="Licensing"><a class="docs-heading-anchor" href="#Licensing">Licensing</a><a id="Licensing-1"></a><a class="docs-heading-anchor-permalink" href="#Licensing" title="Permalink"></a></h2><p>Neuroblox is free for non-commerical and academic use. For full details of the license, please see  <a href="https://github.com/Neuroblox/NeurobloxEULA">the Neuroblox EULA</a>. For commercial use, get in contact with sales@neuroblox.org.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="getting_started/">Getting Started »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Wednesday 5 June 2024 02:13">Wednesday 5 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>