Add introductory course materials

.gitignore

@@ -0,0 +1,6 @@
+_site
+*.dvi
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+Gemfile.lock

Gemfile

@@ -0,0 +1,12 @@
+source "https://rubygems.org"
+
+gem "github-pages", group: :jekyll_plugins
+
+group :jekyll_plugins do
+  gem "jekyll-include-cache"
+  gem "jekyll-paginate"
+  gem "jekyll-sitemap"
+  gem "jekyll-gist"
+  gem "jekyll-feed"
+  gem "jemoji"
+end

NOTICE

@@ -0,0 +1,25 @@
+This website includes software developed by the reveal.js project (https://revealjs.com/).
+All original source code and derivatives are released under the following license:
+
+MIT License
+
+Copyright (c) 2024 NeuroGEARS Ltd
+Copyright (C) 2017 Hakim El Hattab, http://hakim.se, and reveal.js contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1 +1,3 @@
 # st-andrews-2024
+
+Support materials for the Visual Reactive Programming course.

_config.yml

@@ -0,0 +1,44 @@
+title: Visual Reactive Programming
+description: A course on Visual Reactive Programming using Bonsai, developed by NeuroGEARS, Ltd.
+funding: This course was prepared and developed for
+funding_logo: st-andrews
+funding_url: https://www.st-andrews.ac.uk/
+google_analytics:
+theme: minima
+baseurl: "/st-andrews-2024"
+docsurl: "https://bonsai-rx.org/docs"
+
+twitter_username: bonsai_rx
+github_username:  neurogears
+
+kramdown:
+  parse_block_html: true
+
+plugins:
+  - jekyll-seo-tag
+
+include:
+  - _pages
+  - _slides
+
+exclude:
+  - Gemfile
+  - Gemfile.lock
+  - "**README.md"
+
+header_pages:
+  - _pages/neurokit.md
+  - _pages/slides.md
+  - _pages/worksheets.md
+
+collections:
+  # Ideally we would use collections for slides but this
+  # breaks reveal.js markdown processing because of issue:
+  # https://github.com/jekyll/jekyll/issues/6209
+  # slides:
+  #   output: true
+  #   permalink: /:collection/:path/
+
+  worksheets:
+    output: true
+    permalink: /:collection/:path/

_diagrams/go-nogo-task.tex

@@ -0,0 +1,37 @@
+\documentclass{standalone}
+\usepackage{tikz}
+\usetikzlibrary[automata,positioning,arrows]
+\tikzset{node distance=2.5cm,
+         every state/.style={
+             semithick,
+             fill=gray!10
+         },
+         initial text={},
+         double distance=2pt,
+         every edge/.style={
+             draw,
+             ->,>=stealth',
+             auto,
+             semithick
+         }}
+\let\epsilon\varepsilon
+
+\begin{document}
+
+\begin{tikzpicture}
+  \node[state] (iti) {ITI};
+  \node[state, above right=1cm and 1cm of iti] (go) {Go};
+  \node[state, below right=1cm and 1cm of iti] (nogo) {No-Go};
+  \node[above right=0.25cm and 1cm of go] (hit) {Hit};
+  \node[below right=0.25cm and 1cm of go] (miss) {Miss};
+  \node[above right=0.25cm and 1cm of nogo, align=center] (false-alarm) {False\\Alarm};
+  \node[below right=0.25cm and 1cm of nogo, align=center] (correct-reject) {Correct\\Reject};
+  \draw (iti) edge node[below right] {\tt 50\%} (go);
+  \draw (iti) edge node {\tt 50\%} (nogo);
+  \draw (go) edge (hit);
+  \draw (go) edge (miss);
+  \draw (nogo) edge (false-alarm);
+  \draw (nogo) edge (correct-reject);
+\end{tikzpicture}
+
+\end{document}

_diagrams/placepreference.tex

@@ -0,0 +1,30 @@
+\documentclass{standalone}
+\usepackage{tikz}
+\usetikzlibrary[automata,positioning,arrows]
+\tikzset{node distance=2.5cm,
+         every state/.style={
+             semithick,
+             fill=gray!10
+         },
+         initial text={},
+         double distance=2pt,
+         every edge/.style={
+             draw,
+             ->,>=stealth',
+             auto,
+             semithick
+         }}
+\let\epsilon\varepsilon
+
+\begin{document}
+
+\begin{tikzpicture}
+  \node[state] (iti) {ITI};
+  \node[state, right of=iti] (stim) {Ready};
+  \node[state, right of=stim] (resp) {Reward};
+  \draw (iti) edge node {\tt elapsed} (stim);
+  \draw (stim) edge node[sloped] {\tt enter} (resp);
+  \draw (resp) edge[bend right=45] node[above] {\tt leave} (iti);
+\end{tikzpicture}
+
+\end{document}

_diagrams/reactiontime-task.tex

@@ -0,0 +1,33 @@
+\documentclass{standalone}
+\usepackage{tikz}
+\usetikzlibrary[automata,positioning,arrows]
+\tikzset{node distance=2.5cm,
+         every state/.style={
+             semithick,
+             fill=gray!10
+         },
+         initial text={},
+         double distance=2pt,
+         every edge/.style={
+             draw,
+             ->,>=stealth',
+             auto,
+             semithick
+         }}
+\let\epsilon\varepsilon
+
+\begin{document}
+
+\begin{tikzpicture}
+  \node[state] (iti) {ITI};
+  \node[state, right of=iti] (stim) {ON};
+  \node[state, right of=stim] (succ) {Reward};
+  \node[state, below right of=stim] (fail) {Fail};
+  \draw (iti) edge node {\tt elapsed} (stim);
+  \draw (stim) edge node[sloped] {\tt success} (succ);
+  \draw (stim) edge node[sloped] {\tt miss} (fail);
+  \draw (succ) edge[bend right=45] (iti);
+  \draw (fail) edge[bend left] (iti);
+\end{tikzpicture}
+
+\end{document}

_diagrams/reactiontime.tex

@@ -0,0 +1,30 @@
+\documentclass{standalone}
+\usepackage{tikz}
+\usetikzlibrary[automata,positioning,arrows]
+\tikzset{node distance=2.5cm,
+         every state/.style={
+             semithick,
+             fill=gray!10
+         },
+         initial text={},
+         double distance=2pt,
+         every edge/.style={
+             draw,
+             ->,>=stealth',
+             auto,
+             semithick
+         }}
+\let\epsilon\varepsilon
+
+\begin{document}
+
+\begin{tikzpicture}
+  \node[state] (iti) {ITI};
+  \node[state, right of=iti] (stim) {ON};
+  \node[state, right of=stim] (resp) {OFF};
+  \draw (iti) edge node {\tt elapsed} (stim);
+  \draw (stim) edge node[sloped] {\tt response} (resp);
+  \draw (resp) edge[bend right=45] (iti);
+\end{tikzpicture}
+
+\end{document}

_includes/favicon.html

@@ -0,0 +1,7 @@
+<!-- start custom head snippets -->
+
+<!-- insert favicons. use http://realfavicongenerator.net/ -->
+<link href="{{ site.baseurl }}/favicon.ico" rel="icon" type="image/x-icon">
+<link href="{{ site.baseurl }}/favicon.ico" rel="shortcut icon" type="image/x-icon">
+
+<!-- end custom head snippets -->

_includes/footer.html

@@ -0,0 +1,60 @@
+<footer class="site-footer">
+
+      <div class="wrapper">
+
+        <h2 class="footer-heading">{{ site.title | escape }}</h2>
+
+        <div class="footer-col-wrapper">
+          <div class="footer-col footer-col-1">
+            <ul class="contact-list">
+              <li>{{ site.description | escape }}</li>
+              <li><a href="/" target="_blank"><img src="{{ site.baseurl }}/assets/images/neurogears.svg"></a></li>
+            </ul>
+          </div>
+
+          <div class="footer-col footer-col-2">
+            <ul class="social-media-list">
+              {% if site.github_username %}
+              <li>
+                {% include icon-github.html username=site.github_username %}
+              </li>
+              {% endif %}
+
+              {% if site.twitter_username %}
+              <li>
+                {% include icon-twitter.html username=site.twitter_username %}
+              </li>
+              {% endif %}
+            </ul>
+            <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">
+              <img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" />
+            </a><br />This work is licensed under <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA-4.0</a>.
+          </div>
+
+          <div class="footer-col footer-col-3">
+                <ul class="contact-list">
+                  <li>
+                    {% if site.author %}
+                      developed by {{ site.author | escape }}
+                    {% endif %}
+                    </li>
+                    {% if site.email %}
+                    <li><a href="mailto:{{ site.email }}">{{ site.email }}</a></li>
+                    {% endif %}
+                    {% if site.funding %}
+                    <li>{{ site.funding }}</li>
+                    {% endif %}
+                    {% if site.funding_logo %}
+                    <li>
+                      {% if site.funding_url %}<a href="{{ site.funding_url }}" target="_blank">{% endif %}
+                        <img src="{{ site.baseurl }}/assets/images/{{ site.funding_logo | slugify: 'pretty' }}.png"/>
+                      {% if site.funding_url %}</a>{% endif %}
+                    </li>
+                    {% endif %}
+                </ul>
+          </div>
+        </div>
+
+      </div>
+
+    </footer>

_includes/head.html

@@ -0,0 +1,12 @@
+<head>
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    {% seo %}
+    <link rel="stylesheet" href="{{ "/assets/main.css" | relative_url }}">
+    <link rel="alternate" type="application/rss+xml" title="{{ site.title | escape }}" href="{{ "/feed.xml" | relative_url }}">
+    {% if jekyll.environment == 'production' and site.google_analytics %}
+        {% include google-analytics.html %}
+    {% endif %}
+    {% include favicon.html %}
+</head>

_layouts/archive.html

@@ -0,0 +1,13 @@
+---
+layout: default
+---
+
+<div class="home">
+
+  <h1 class="page-heading">{{ page.title | escape }}</h1>
+
+  <div class="post-content">
+    {{ content }}
+  </div>
+
+</div>