New tutorial: "Phylogenetics: back to basics"

CONTRIBUTORS.yaml

@@ -195,6 +195,11 @@ astrovsky01:
     orcid: 0000-0002-7901-7109
     joined: 2019-06
 
+adamtaranto:
+    name: Adam Taranto
+    email: adam.p.taranto@gmail.com
+    joined: 2023-01
+
 aurelienmoumbock:
     name: Aurélien F. A. Moumbock
     email: amaf.aurelien@yahoo.com
@@ -362,7 +367,9 @@ burkemlou:
     name: Melissa Burke
     email: melissa@biocommons.org.au
     joined: 2023-12
-
+    affiliations: 
+        - AustralianBioCommons
+
 B0r1sD:
     name: Boris Depoortere
     joined: 2024-04
@@ -1364,6 +1371,13 @@ mccalluc:
     name: Chuck McCallum
     joined: 2018-06
 
+mcharleston:
+    name: Michael Charleston
+    email: michael.charleston@utas.edu.au
+    joined: 2023-01
+    affiliations: 
+        - UTas
+
 mcmaniou:
     name: Maria Christina Maniou
     joined: 2021-09
@@ -1635,6 +1649,12 @@ RareSeas:
     name: Adelaide Rhodes
     joined: 2021-05
 
+PatCapon39:
+    name: Patrick Capon
+    joined: 2024-02
+    affiliations: 
+        - AustralianBioCommons
+
 patrick-austin:
     name: Patrick Austin
     email: patrick.austin@stfc.ac.uk

ORGANISATIONS.yaml

@@ -73,6 +73,17 @@ ifb:
     avatar: "/training-material/shared/images/ifb.png"
     github: false
 
+AustralianBioCommons:
+    name: Australian BioCommons
+    url: https://www.biocommons.org.au/
+    avatar: "/training-material/shared/images/Australian-Biocommons-Favicon-RGB.png"
+
+UTas:
+    name: University of Tasmania
+    url: https://www.utas.edu.au/
+    avatar: "/training-material/shared/images/UTas_logo.png"
+    github: false
+
 pndb:
     name: Pôle National de Données de Biodiversité
     url: https://www.pndb.fr/
@@ -88,4 +99,4 @@ vib:
 qiime2:
     name: QIIME2
     url: https://qiime2.org/
-    avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4
+    avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4

_config.yml

@@ -108,7 +108,11 @@ icon-tag:
   feedback: far fa-comments
   galaxy-advanced-search: fas fa-angle-double-down
   galaxy-show-active: fa fa-map-marker
-  galaxy-barchart: fas fa-chart-bar
+  galaxy-barchart: fas fa-chart-column
+  galaxy-visualise: fas fa-chart-column
+  galaxy-visualize: fas fa-chart-column
+  galaxy-vis-config: fas fa-angle-double-left
+  galaxy-viz-config: fas fa-angle-double-left
   galaxy-bug: fas fa-bug
   galaxy-chart-select-data: fas fa-database
   galaxy-clear: fas fa-times-circle

_includes/contributors-line.html

@@ -1,7 +1,7 @@
 <div markdown="0">
 {% if include.page.contributors %}
 	<div class="contributors-line">
-		{{ locale['authors'] | default: "Authors" }}: {% include _includes/contributor-list.html contributors=include.page.contributors badge=true newcontributors=include.newcontributors %}
+		{% unless include.authorsonly %}{{ locale['authors'] | default: "Authors" }}: {% endunless %}{% include _includes/contributor-list.html contributors=include.page.contributors badge=true newcontributors=include.newcontributors %}
 	</div>
 {% elsif include.page.contributions %}
 	<div class="contributors-line">

_includes/slides-youtube-selector.html

@@ -0,0 +1,54 @@
+<blockquote class="agenda">
+	<div class="box-title hands-on-title" id="slides-{{ include.slides }}">{{ include.title }}</div>
+	<p class="text-muted">This content is available in multiple, equivalent formats. Choose your preferred format below.</p>
+<ul class="nav nav-pills mb-3" id="pills-tab" role="tablist">
+  <li class="nav-item" role="presentation">
+    <button class="nav-link active" id="pills-home-tab" data-toggle="pill" data-target="#pills-home" type="button" role="tab" aria-controls="pills-home" aria-selected="true">Teacher Recording</button>
+  </li>
+  <li class="nav-item" role="presentation">
+    <button class="nav-link" id="pills-profile-tab" data-toggle="pill" data-target="#pills-profile" type="button" role="tab" aria-controls="pills-profile" aria-selected="false">Slides</button>
+  </li>
+  <li class="nav-item" role="presentation">
+    <button class="nav-link" id="pills-contact-tab" data-toggle="pill" data-target="#pills-contact" type="button" role="tab" aria-controls="pills-contact" aria-selected="false">Plain Text</button>
+  </li>
+</ul>
+<div class="tab-content" id="pills-tabContent">
+  <div class="tab-pane show active" id="pills-home" role="tabpanel" aria-labelledby="pills-home-tab">
+    <div class="embed-responsive embed-responsive-16by9">
+    <iframe class="embed-responsive-item"
+      credentialless
+      allowfullscreen
+      referrerpolicy="no-referrer"
+      sandbox="allow-scripts allow-same-origin"
+      allow="accelerometer 'none'; ambient-light-sensor 'none'; autoplay 'none'; battery 'none'; bluetooth 'none'; browsing-topics 'none'; camera 'none'; ch-ua 'none'; display-capture 'none'; domain-agent 'none'; document-domain 'none'; encrypted-media 'none'; execution-while-not-rendered 'none'; execution-while-out-of-viewport 'none'; gamepad 'none'; geolocation 'none'; gyroscope 'none'; hid 'none'; identity-credentials-get 'none'; idle-detection 'none'; keyboard-map 'none'; local-fonts 'none'; magnetometer 'none'; microphone 'none'; midi 'none'; navigation-override 'none'; otp-credentials 'none'; payment 'none'; picture-in-picture 'none'; publickey-credentials-create 'none'; publickey-credentials-get 'none'; screen-wake-lock 'none'; serial 'none'; speaker-selection 'none'; sync-xhr 'none'; usb 'none'; web-share 'none'; window-management 'none'; xr-spatial-tracking 'none'"
+      src="https://www.youtube-nocookie.com/embed/{{ include.id }}"
+      title="{{ include.title }}"
+      csp="sandbox allow-scripts allow-same-origin;"
+      frameborder="0"
+      loading="lazy"></iframe>
+    </div>
+  </div>
+  <div class="tab-pane" id="pills-profile" role="tabpanel" aria-labelledby="pills-profile-tab">
+    <a href="{{ site.baseurl }}/{{ include.slides }}/slides.html">Open in new tab</a><br/>
+    <div class="embed-responsive embed-responsive-16by9">
+    <iframe class="embed-responsive-item"
+      src="{{ site.baseurl }}/{{ include.slides }}/slides.html"
+      title="{{ include.title }}"
+      frameborder="0"
+      loading="lazy"></iframe>
+    </div>
+  </div>
+  <div class="tab-pane" id="pills-contact" role="tabpanel" aria-labelledby="pills-contact-tab">
+    <a href="{{ site.baseurl }}/{{ include.slides }}/slides-plain.html">Open in new tab</a><br/>
+    <div class="embed-responsive embed-responsive-16by9">
+    <iframe class="embed-responsive-item"
+      width="100%"
+      height="500"
+      src="{{ site.baseurl }}/{{ include.slides }}/slides-plain.html"
+      title="{{ include.title }}"
+      frameborder="0"
+      loading="lazy"></iframe>
+    </div>
+  </div>
+</div>
+</blockquote>

_includes/youtube.html

@@ -0,0 +1,14 @@
+<iframe
+    credentialless
+    allowfullscreen
+    referrerpolicy="no-referrer"
+    sandbox="allow-scripts allow-same-origin"
+    allow="accelerometer 'none'; ambient-light-sensor 'none'; autoplay 'none'; battery 'none'; bluetooth 'none'; browsing-topics 'none'; camera 'none'; ch-ua 'none'; display-capture 'none'; domain-agent 'none'; document-domain 'none'; encrypted-media 'none'; execution-while-not-rendered 'none'; execution-while-out-of-viewport 'none'; gamepad 'none'; geolocation 'none'; gyroscope 'none'; hid 'none'; identity-credentials-get 'none'; idle-detection 'none'; keyboard-map 'none'; local-fonts 'none'; magnetometer 'none'; microphone 'none'; midi 'none'; navigation-override 'none'; otp-credentials 'none'; payment 'none'; picture-in-picture 'none'; publickey-credentials-create 'none'; publickey-credentials-get 'none'; screen-wake-lock 'none'; serial 'none'; speaker-selection 'none'; sync-xhr 'none'; usb 'none'; web-share 'none'; window-management 'none'; xr-spatial-tracking 'none'"
+    csp="sandbox allow-scripts allow-same-origin;"
+    width="560"
+    height="315"
+    src="https://www.youtube-nocookie.com/embed/{{ include.id }}"
+    title="{{ include.title }}"
+    frameborder="0"
+    loading="lazy"
+></iframe>

_layouts/base_slides.html

@@ -95,9 +95,13 @@
 <img src="{{ site.baseurl }}/{% if page.logo %}{{ page.logo }}{% else %}{{ page.logo }}{% endif %}" alt="page logo" class="cover-logo" />
   {% endif %}
 {% endif %}
+<br/>
+<br/>
 
 # {{ page.title | default: topic.title }}
 
+<br/>
+<br/>
 
 {% include _includes/contributors-line.html page=page authorsonly=true %}
 
@@ -211,8 +215,16 @@
         }
     </script>
         {{ 'main' | load_bundle }}
-        {% if page.mathjax %}
-        <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        {% if page.js_requirements.mathjax %}
+	<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS-MML_HTMLorMML&delayStartupUntil=configured" type="text/javascript"></script>
+	<script>
+	MathJax.Hub.Config({
+          tex2jax: {
+            skipTags: ['script', 'noscript', 'style', 'textarea', 'pre']
+          }
+      });
+      MathJax.Hub.Configured();
+	</script>
         {% endif %}
     </body>
 </html>

_layouts/base_slides_ai4life.html

@@ -205,7 +205,7 @@
         }
     </script>
         {{ 'main' | load_bundle }}
-        {% if page.mathjax %}
+        {% if page.js_requirements.mathjax %}
         <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
         {% endif %}
     </body>

_plugins/jekyll-mathjax.rb

@@ -1,6 +1,15 @@
+
 Jekyll::Hooks.register :pages, :post_init do |page|
   page.data['js_requirements'] = {
-    'mathjax' => page.content =~ /\$\$/,
+    'mathjax' => page.content =~ /\$\$/ || page.content =~ /\\\(/,
     'mermaid' => page.content =~ /```mermaid/ || page.content =~ /pre class="mermaid"/ || page.data['layout'] == 'workflow-list',
   }
+
+  # some fixes for mathjax: escape underscores
+  # both in inline mode \\( .. \\) and block mode $$ ..$$
+  if page.content
+    page.content = page.content.gsub(/\$\$(.*?)\$\$/) { |m| m.gsub('_', '\\\\_') }
+    page.content = page.content.gsub(/\\\\\((.*?)\\\\\)/) { |m| m.gsub('_', '\\\\_') }
+
+  end
 end

assets/css/slides.scss

@@ -377,6 +377,11 @@ body.remark-container {
 		text-align: left !important;
 	}
 
+    .pull-bottom {
+        position: fixed;
+        bottom: 3em;
+    }
+
 	.requirements li {
 		list-style-type: none;
 		text-align: left;
@@ -447,6 +452,13 @@ body.remark-container {
 		margin-right: 0.5em;
 	}
 
+	.center {
+		// Tables aren't centered by text-align: center
+		* {
+			margin: auto;
+		}
+	}
+
 
 	.btn {
 		display: inline-block;
@@ -532,6 +544,6 @@ body.remark-container {
 		text-align: center;
 		font-size: 150%;
 		padding: 0.3em;
-		
+
 	}
 }

bin/schema-slides.yaml

@@ -204,6 +204,7 @@ mapping:
           - /assets/images/BioNT_Logo.png
           - topics/ai4life/images/AI4Life-logo_giraffe-nodes.png
           - assets/images/genomics_intro.png
+          - shared/images/biocommons-utas.png
         required: true
         description: |
             A logo identifier (e.g. GTN) should be used by default, but may be swapped out for special logos from the assets folder.

topics/contributing/tutorials/create-new-tutorial-content/tutorial.md

@@ -349,6 +349,8 @@ Surround your math expression with two `$` signs on each side (like in LaTeX mat
 
    $$ 5 + 5 $$
 
+- Note: if inline mode is not working correctly, you can force it by using the following delimiters instead of dollar signs: `\\( 5 +5 \\)`
+
 Dollar signs are therefore *reserved characters* for instructing the templating system to open/close LaTeX math blocks. If you want to use a `$` within your expression, you will need to *escape* it: `$$ a + 3\$ = 5\$ $$` will be rendered as: $$ a + 3\$ = 5\$ $$
 
 

topics/evolution/metadata.yaml

@@ -8,7 +8,14 @@ requirements:
 - type: internal
   topic_name: introduction
 docker_image: ''
+
+subtopics:
+  - id: phylogenetics
+    title: "Phylogenetics"
+    description: "Learn about evolution through Phylogenetics, the study of evolutionary relationships among groups of organisms."
+
 editorial_board:
 - cstritt
 - pvanheus
+
 edam_ontology: ["topic_3299"]

topics/evolution/tutorials/abc_intro_phylo-intro/images

@@ -0,0 +1 @@
+../abc_intro_phylo/images

topics/evolution/tutorials/abc_intro_phylo-intro/slides.html

@@ -0,0 +1,56 @@
+---
+layout: tutorial_slides
+logo: shared/images/biocommons-utas.png
+title: "Phylogenetics - Back to Basics - Introduction"
+zenodo_link: ""
+subtopic: phylogenetics
+priority: 1
+contributors:
+  - mcharleston  
+---
+
+
+
+![Hand drawn phylogenetic tree from Charles Darwin’s notebook with clades A, B, C, D branching from a common ancestor. Prefaced with handwriting that reads ‘I think’ and annotated with other illegible notes.](images/Darwin_tree.png )
+
+Charles Darwin, 1837 Notebeook entry
+---
+![Model of the external structure of the SARS-CoV-2 virion](images/SARS-CoV-2-www.ncbi.nlm.nih.png)
+.right[https://en.wikipedia.org/wiki/Coronavirus; CC BY-SA 4.0]
+---
+
+![Two-part figure showing a phylogenetic tree of SARS-CoV-2 strains on the left and genomic epidemiology of SARS-CoV-2 with subsampling focused globally over the 6 months leading up to November 2023 on the right](images/CovidNextStrain20231102.png)
+.right[https://nextstrain.org/ncov/gisaid/global/6m]
+---
+# Covid-19, latest tree from NextStrain
+
+![Phylogenetic tree for SARS-CoV-2 strains coloured by strain grouping](images/CovidTree20231102NextStrain.png)
+---
+# Terminology
+
+![Schematic of a phylogenetic tree where features such as nodes/taxa, edges/branches are annotated and colour coded. The root of the tree is at the top of the image and the tree branches into two clades as you move towards the bottom of the image. The clades are formed of hypothetical common ancestors and five extant taxa which are labelled as the ‘in group’. Two additional taxa are appended to the right hand side of the tree and are labelled as the outgroup.](images/TreeAnatomy.png)
+---
+# Phylogenetic tree of hexapods
+
+![Circular phylogenetic tree of hexapods (insects). Clades are colour coded and labelled with common names e.g. ‘Fleas’. Silhouettes of representative species are shown around the outside of the tree.](images/Hexapoda_phylogenetic_tree.png)
+.left[https://doi.org/10.1371/journal.pone.0109085; CCBY 4.0 DEED license]
+---
+# Sequence alignment
+
+![Screenshot of sequence visualisation output from Galaxy. Fifteen Anolis DNA sequences are arranged in rows. The nucleotides are colour coded and arranged in columns: A(blue), T (green), C (pink), G (orange). The top half of the image shows approximately 50 bases of each sequence. The lower half of the image shows a zoomed out heatmap-like image of a larger portion of the sequences.](images/UnalignedAnolis.png)
+---
+# Building trees from distances
+
+![Flow chart illustrating how sequence alignment data or dis/similarity measures are used to calculate and calculate phylogenetic distances. Colours and shapes are used to differentiate different sections of the flowchart, guiding the viewer through each step from left to right. The flowchart begins with Sequence Alignment or Dis/Similarity Measures. These are used to form a distance matrix (D) which is used to select two nodes (x and y) forming a new node z. The distance matrix is updated with the new node z until no further nodes can be formed.](images/TreeConstruction.drawio.png)
+---
+# Searching for trees
+
+![Screenshot of a phylogenetic tree of Anolis species. The root of the tree is on the left and the species are listed vertically on the right. The tree consists of multiple branching events and clades and includes bootstrap values.](images/PhyloVisTree.png)
+---
+# Phylogenetic Networks
+
+![Screenshot of a phylogenetic network of Anolis species. The root of the network is at the centre of the image and clades radiate outwards forming a circular network.](images/ST4-HKY85.png)
+---
+# Thank you!
+
+Let's begin

topics/evolution/tutorials/abc_intro_phylo-mle-trees/images

@@ -0,0 +1 @@
+../abc_intro_phylo/images