Australian-Structural-Biology-Computing · supernord · Jun 26, 2025 · May 14, 2025 · May 14, 2025 · May 14, 2025
diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -2,6 +2,7 @@ name: Jekyll site CI
 
 on:
   push:
+    branches: [ main, master, edits ]
   pull_request:
     branches: [ main, master, edits ]
   workflow_dispatch:
@@ -13,7 +14,7 @@ permissions:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -23,7 +24,7 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1.204.0
         with:
-          ruby-version: '3.1'
+          ruby-version: '3.3'
           bundler-cache: true
           cache-version: 0
 
@@ -41,7 +42,7 @@ jobs:
           bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           PAGES_REPO_NWO: ${{ github.repository }}
-          JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
+          JEKYLL_ENV: production
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
           JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
@@ -50,7 +51,7 @@ jobs:
         uses: actions/upload-pages-artifact@v3
 
   deploy:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: build
 
     if: |
@@ -63,8 +64,8 @@ jobs:
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
-    
+
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/update_guides.yml b/.github/workflows/update_guides.yml
@@ -9,7 +9,7 @@ jobs:
   update_guides:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup python
         uses: actions/setup-python@v2
@@ -35,4 +35,4 @@ jobs:
         uses: ad-m/github-push-action@v0.6.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: main
+          branch: main
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 ## What this repository is for
 
-Gathering information to get structural biologists oriented on beginninging their journey top adopt the most recent and accurate computational tools  
+Gathering information to get structural biologists oriented on beginning their journey top adopt the most recent and accurate computational tools  
 
-If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc with typical GitHub features 
+If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc, with typical GitHub features.
 
-## Where is the *website* not just the raw source code?
+## Where is the *website*, not just the raw source code?
 
 Point your browser to https://australian-structural-biology-computing.github.io/website/
diff --git a/_config.yml b/_config.yml
@@ -1,10 +1,10 @@
-title: StructBio Computing 
+title: Australian Structural Biology Computing
 # This appears in the html browser tab for the site title (seen mostly by search engines, not users)
 
 topnav_title: Australian Structural Biology Computing 
 # Optional: this appears on the top navigation bar next to the main_logo.svg icon
 
-#description: "Example of ELIXIR toolkit theme as a remote jekyll theme"
+description: "A website for the Australian Structural Biology Computing community."
 # Metadata description of the website
 
 # Following AusBioCommons minimal gh-pages with remote deploy -  https://github.com/AustralianBioCommons/how-to-guides/blob/main/_config.yml
@@ -25,6 +25,16 @@ defaults:
       permalink: /:basename
       layout: "page"
       sidebar: main
+  - scope:
+      path: "pages"
+      type: "pages"
+    values:
+      sidebar: main
+  - scope:
+      path: "workgroup_template_directory"
+      type: "pages"
+    values:
+      sidebar: workgroup_example
 
 theme_variables: 
   # git_host: GitHub

diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml
@@ -47,9 +47,71 @@ Michael Healy:
     orcid: 0000-0003-2924-9179
     affiliation: Postdoctoral Research Fellow, University of Queensland
 
-# Josh was listed as a contributor during testing - checked with him to remove -- KR
-#Joshua Storm Caley:
-#git:  jscgh 
-#email: j.caley@unsw.edu.au
-#orcid: 0000-0002-9374-0969
-#affiliation: Computational Systems Officer, Structural Biology Facility UNSW
+Joshua Storm Caley:
+    git:  jscgh 
+    email: j.caley@unsw.edu.au
+    orcid: 0000-0002-9374-0969
+    affiliation: Computational Systems Officer, Structural Biology Facility UNSW
+
+Thomas Litfin:
+    git:  tlitfin-unsw 
+    email: t.litfin@unsw.edu.au 
+    orcid: 0000-0002-4863-3865
+    affiliation: Senior Research Associate, Structural Biology Facility UNSW
+
+Ziad Al-Bkhetan:
+    git:  ziadbkh
+    orcid: 0000-0002-4032-5331
+    affiliation: Product Manager, Australian BioCommons
+
+Sarah Beecroft:
+    git: SarahBeecroft
+    affiliation: Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre
+
+Cameron Hyde:
+    git: neoformit
+    orcid: 0000-0002-5913-9766
+    affiliation: Bioinformatician, Queensland Cyber Infrastructure Foundation (QCIF)
+
+Mitchell O'Brien:
+    git: Mitchob
+    affiliation: Senior Bioinformatics Engineer, Sydney Informatics Hub
+
+Matthew Downton:
+    git: mattdton
+    orcid: 0000-0002-4693-1965
+    affiliation: Associate Director - Performance Optimisation, National Computational Infrastructure (NCI)
+
+Kisaru Liyanage:
+    git: kisarur
+    affiliation: HPC specialist (Life and Health Sciences), National Computational Infrastructure (NCI)
+
+Wenjing Xue:
+    affiliation: HPC Specialist (Life and Health Sciences), National Computational Infrastructure (NCI)
+
+Gavin Knott:
+    affiliation: Group Leader, Monash Biomedicine Discovery Institute, Monash University
+    orcid: 0000-0002-9007-6273
+
+Rhys Grinter:
+    affiliation: Lab head, University of Melbourne
+    git: RhysWG
+    orcid: 0000-0002-8195-5348
+
+Josh Hardy:
+    affiliation: Senior Research Officer, Lucet Lab, WEHI
+    git: joshhardywehi
+    email: hardy.j@wehi.edu.au
+    orcid: 0000-0002-8014-8552
+
+#Richard Birkinshaw:
+#    affiliation: Senior Research Scientist, Walter and Eliza Hall Institute of Medical Research
+#    orcid: 0000-0003-1825-0182
+
+Melissa Burke:
+    affiliation: Training Manager, Australian BioCommons
+    orcid: 0000-0002-5571-8664
+
+Cyntia Taveneau:
+    affiliation: Research Fellow, Knott Lab, Monash University
+    orcid: 0000-0002-3395-4957
diff --git a/_data/events.yml b/_data/events.yml
@@ -8,18 +8,24 @@
 #  location: Cyberspace
 - name: BioMolecular Horizons
   startDate: 2024-09-22
-  description: Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/)
+  description: "Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/)"
 - name: Computational Structural Biology Community Meeting
   startDate: 2024-10-22
-  startTime: 13:30
   endDate: 2024-10-22
-  endTime: 14:30
-  description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting.
+  description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
   location: Online
 - name: Computational Structural Biology Community Meeting
   startDate: 2025-04-09
-  startTime: 13:00
   endDate: 2025-04-09
-  endTime: 14:30
-  description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting.
-  location: Online
+  description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
+  location: Online
+- name: Computational structural biology community meeting
+  startDate: 2025-06-18
+  endDate: 2025-06-18
+  description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
+  location: Online
+- name: Australian Structural Biology Computing community meeting
+  startDate: 2025-08-27
+  endDate: 2025-08-27
+  description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
+  location: Online
diff --git a/_data/news.yml b/_data/news.yml
@@ -1,7 +1,6 @@
-- name: Script for Alphafold output validation metrics!
+- name: "Script for Alphafold output validation metrics!"
   date: 2024-11-01
-  description: Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs)
-
-- name: Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)
+  description: "Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen (<https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs>)"
+- name: "Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)"
   date: 2024-11-01
-  description: MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif)
+  description: "MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen (<https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif>)"
diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml
@@ -1,29 +1,29 @@
 subitems:
   - title: Home
     url: /index
-  - title: Example page
-    url: /example_page
-  - title: Contributing 
-    subitems: 
-    - title: Provide us your document 
-      url: /provide_documentation
-    - title: Write your own guides 
-      url: /guide_template
-  - title: Visualisations 
+  - title: Activities
+    url: /activities
+  - title: How-to Guides
+    url: /guides
+  - title: External resources
     subitems:
-    - title: Pymol  
-      url: /pymol
-  - title: Protein Structure Prediction
-    subitems: 
-    - title: AlphaFold How To Guide 
-      url: /AlphaFold2_how_to_guide
-    - title: Best practices AlphaFold models in a paper 
-      url: /best-practices-alphafold
-    - title: AlphaFold Tutorial - European Bioinformatics Institute
-      url: /EBI-alphafold-guide
-    - title: Protein structure inference options 
-      url: /protein_struct_inference
-  - title: Command Line Instructions
-    subitems:
-    - title: Basics 
-      url: /basics
+      - title: Servers
+        url: /external_servers
+      - title: Databases
+        url: /external_databases
+      - title: Guides
+        url: /external_guides
+      - title: Visualization
+        url: /external_viz
+      - title: Videos
+        url: /external_videos
+      - title: Communities
+        url: /external_communities
+  - title: Contributing
+    url: /contributing
+  - title: Contributors
+    url: /contributors
+  - title: Events
+    url: /events
+  - title: News
+    url: /news
diff --git a/_data/sidebars/workgroup_example.yml b/_data/sidebars/workgroup_example.yml
@@ -0,0 +1,5 @@
+subitems:
+  - title: Home
+    url: /index
+  - title: Working group index
+    url: /workgroup_index
diff --git a/_data/topnav.yml b/_data/topnav.yml
@@ -1,6 +1,7 @@
 ## 
 ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base.
-subitems:
-- title: Home
-  url: /index
-
+#subitems:
+#- title: Home
+#  url: /index
+#- title: Working group example
+#  url: /workgroup_index
diff --git a/_includes/resource-table-communities.html b/_includes/resource-table-communities.html
@@ -0,0 +1,56 @@
+{%- if include.tag %}
+{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag  | sort_natural: "name" %}
+{%- else %}
+{%- assign tools = site.data.tool_and_resource_list | add_related_pages  | sort_natural: "name" %}
+{%- endif %}
+{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
+{%- unless tools.size == 0 or tools == nil %}
+<a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
+<div class="table-responsive mt-4 mb-5">
+    <table class="tooltable table display">
+        <thead>
+            <tr class="text-nowrap">
+                <th>How-to Guide or resource {%- if include.tag -%}
+                    <a data-bs-toggle="tooltip" data-bs-original-title="This is a curated list which means that not all tools or resources that exist for this topic are listed here. This is mainly because we do not intend to be a registry.">
+                        <i class="fa-solid fa-info-circle"></i>
+                    </a>{%- endif %}
+                </th>
+                <th>Description</th>
+            </tr>
+        </thead>
+        <tbody>
+            {%- for tool in tools %}
+            {% assign found = false %}
+            {% for desc in tool.Type %}
+                {% if desc == "Online communities" %}
+                {% assign found = true %}
+                {% endif %}
+            {% endfor %}
+            {% if found %}
+            <tr>
+                {% if tool.URL %}
+                <td><a href="{{tool.URL}}">{{tool.Title}}</a></td>
+                {%- else %}
+                <td>{{tool.Title}}</td>
+                {%- endif %}
+                <td>{{tool.Description}}
+                    {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %}
+                    {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %}
+                    <div class="d-block mt-1">
+                        {%- if linked_tool %}
+                        <span class="d-inline-block" tabindex="0" data-bs-toggle="tooltip" title="This resource is an instance of {{linked_tool.name}}"><span class="badge text-primary border border-primary">{{linked_tool.name}}</span></span>
+                        {%- endif %}
+                        {%- if tool.how_to_access %}
+                        <span class="d-inline-block" tabindex="0" data-bs-toggle="tooltip" title="{{tool.how_to_access}}"><span class="badge text-primary border border-primary"> <i class="fa-solid fa-key"></i></span></span>
+                        {%- endif %}
+                    </div>
+                    {%- endif %}
+                </td>
+            </tr>
+            {%- endif %}
+            {%- endfor %}
+        </tbody>
+    </table>
+</div>
+{%- endunless %}
+<div id="skip-tool-table"></div>