Sydney-Informatics-Hub · georgiesamaha · Jul 30, 2026 · Jul 28, 2026 · Jul 28, 2026 · Jul 28, 2026
diff --git a/Gemfile b/Gemfile
@@ -1,6 +1,8 @@
 source "https://rubygems.org"
 
 gem "openssl", "~> 3.3.1"
+gem "csv"
+gem "webrick"
 
 group :jekyll_plugins do
     gem "github-pages"

diff --git a/README.md b/README.md
@@ -2,11 +2,50 @@
 
 Please see the [How-to Guide for the template](https://australianbiocommons.github.io/how-to-guide-template/) for more information on how to get started.  
 
+This template is based on the [ELIXIR Toolkit Theme example](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme-example).
+
+## Contribute to BioShell User Guides
+
+This site is built with [Jekyll](https://jekyllrb.com/) using the [ELIXIR Toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme). To fix a typo, update a page, or add a new guide:
+
+1. Fork or clone the [**BioShell-User-Guide repository**](https://github.com/Sydney-Informatics-Hub/BioShell-User-Guide)
+2. Edit or add pages under `pages/`, following the layout in `pages/example_page.md`
+3. [Render the site locally](#rendering-locally) to preview your changes
+4. Open a pull request with your changes
+
+See the [ELIXIR Toolkit theme markdown cheat sheet](https://elixir-belgium.github.io/elixir-toolkit-theme/markdown_cheat_sheet) for formatting help (message boxes, images, etc).
+
+#### Rendering locally {#rendering-locally}
+
+You'll need Ruby and [Bundler](https://bundler.io/) installed. This site uses the `github-pages` gem, which needs Ruby 2.7–3.2.
+
+**macOS (Homebrew):**
+
+```bash
+brew install ruby@3.2
+```
+
+`ruby@3.2` is keg-only, so it won't override your system Ruby automatically. Rather than relying on `PATH` (which tools like conda can silently reorder between terminals), call it explicitly:
+
+```bash
+/opt/homebrew/opt/ruby@3.2/bin/gem install bundler
+/opt/homebrew/opt/ruby@3.2/bin/bundle install
+```
+
+{% include callout.html type="tip" content="Sanity check before installing: run <code>/opt/homebrew/opt/ruby@3.2/bin/ruby -v</code> and confirm it prints 3.2.x. If a plain <code>ruby -v</code> already prints 3.2.x, you can drop the full paths and just use <code>gem</code>/<code>bundle</code> directly." %}
+
+**Start the local server, with live-reload so the browser updates automatically on save:**
+
+```bash
+/opt/homebrew/opt/ruby@3.2/bin/bundle exec jekyll serve --livereload
+```
+
+Then open the printed URL (e.g. `http://127.0.0.1:4000/BioShell-User-Guide/`) in your browser. Every time you save a page, Jekyll rebuilds it and the open browser tab refreshes on its own — no need to restart the server or reload manually.
+
+{% include callout.html type="note" content="If bundle install fails with a dependency resolution error (e.g. a bundler version mismatch in Gemfile.lock), delete Gemfile.lock and run bundle install again." %}
 
 ## Acknowledgements for the guides
 
 This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/), the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
 
-This repository makes use of the ELIXIR toolkit theme: [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
-
-This template is based on the [ELIXIR Toolkit Theme example](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme-example).
+This repository makes use of the ELIXIR toolkit theme: [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml
@@ -43,3 +43,15 @@ Johan Gustafsson:
     orcid: 0000-0002-2977-5032
     role: author
     affiliation: Australian BioCommons
+
+Eden Zhang:
+    git: edenz93
+    orcid: 0000-0003-0294-3734
+    role: author
+    affiliation: Sydney Informatics Hub
+
+Giorgia Mori:
+    git: GiorgiaMori
+    orcid: 0000-0003-3469-5632
+    role: author
+    affiliation: Australian BioCommons
diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml
@@ -3,30 +3,39 @@ subitems:
     url: /index
   - title: Getting started
     url: /why-bioshell
-  - title: Using BioShell
+  - title: Access BioShell
+    url: /access
+  - title: BioShell for research
     url: /using-bioshell
     subitems:
-      - title: Accessing BioShell
-        url: /access
-      - title: Choosing an environment size
+      - title: Choose the right environment
         url: /flavours
-      - title: Connecting to BioShell
+      - title: Connect to BioShell
         url: /connecting
-      - title: Tools and reference data
+      - title: Find tools and datasets
         url: /tools
-      - title: How to use Shelley
-        url: /shelley-howto
-      - title: Interactive environments
+      - title: Use interactive environments
         url: /interactive
-      - title: Using Nextflow with CVMFS
-        url: /nextflow
-  - title: Setting up a training VM
+  - title: BioShell for training
     url: /training-development
-  - title: BioShell community and outcomes
-    url: /community
-  - title: Get involved
-    url: /contributing
-  - title: Contributors
-    url: /contributors
+  - title: Tutorials
+    url: /tutorials
+    subitems:
+      - title: Generate ssh keys
+        url: ssh-keys-howto
+      - title: Use Shelley
+        url: /shelley-howto
+      - title: Use Nextflow in BioShell
+        url: nextflow-howto
+      - title: Move data in and out of BioShell
+        url: globus-howto
+  - title: Community and outcomes
+    subitems:
+      - title: Community
+        url: /community
+      - title: Get involved
+        url: /contributing
+      - title: Contributors
+        url: /contributors
   - title: Acceptable use policy and service terms
     url: /aup
diff --git a/_includes/section-navigation-tiles_mod.html b/_includes/section-navigation-tiles_mod.html
@@ -20,65 +20,3 @@ <h3 class="page-tile-title" style="margin-top: 0.0rem">{{ page.title }}</h3>
   </div>
 </div>
 
-<style>
-
-  .page-tiles-list {
-    display: grid;
-    grid-template-columns: repeat(var(--tile-cols, 4), 1fr);
-    gap: 20px;
-  }
-
-  @media (max-width: 992px) {
-    .page-tiles-list {
-      grid-template-columns: repeat(2, 1fr);
-    }
-  }
-
-  @media (max-width: 600px) {
-    .page-tiles-list {
-      grid-template-columns: repeat(1, 1fr);
-    }
-  }
-
-  .page-tile-link {
-    text-decoration: none;
-    color: inherit;
-    display: flex;
-  }
-
-  .page-tile-item {
-    border-radius: 12px;
-    padding: 25px;
-    transition: all 0.3s ease;
-    background: #f0f3fa;
-    width: 100%;
-    display: flex;
-    flex-direction: column;
-    justify-content: space-between;
-    border: 1px solid #ffffff;
-    color: #012152;
-  }
-
-  .page-tile-item:hover {
-    background: #012152;
-    color: #ffffff;
-    transform: translateY(-4px);
-    box-shadow: 0 8px 25px rgba(0,0,0,0.1);
-    border: 1px solid #000000;
-  }
-
-  .page-tile-title {
-    color: inherit;
-    font-size: 1.3rem;
-    font-weight: 600;
-    margin-bottom: 8px;
-  }
-
-  .page-tile-description {
-    color: inherit;
-    font-size: 0.9rem;
-    line-height: 1.5;
-    flex-grow: 1;
-  }
-
-</style>
diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html
@@ -3,58 +3,23 @@
 {% else %}
 {%- assign tiles = page[include.target] %}
 {%- endif %}
-<div class="simple-tiles">
-    <div class="simple-tiles-container">
-        <div class="simple-tiles-list row row-cols-1 row-cols-md-2 row-cols-lg-{{ include.col | default: 2 }} gy-2 gx-4">
-            {%- for item in tiles %}
-            {%- if item.title %}
-                <a href="{{ item.url | relative_url }}" class="simple-tile-link">
-                    <div class="simple-tile-item">
-                        <div class="simple-tile-content">
-                            <p class="simple-tile-title" style="font-size: 1.3rem; text-align: center">{{ item.title }}</p>
-                        </div>
-                    </div>
-                </a>
+<div class="page-tiles">
+  <div class="page-tiles-container">
+    <div class="page-tiles-list" style="--tile-cols: {{ include.col | default: 2 }};">
+      {%- for item in tiles %}
+      {%- if item.title %}
+      <a href="{{ item.url | relative_url }}" class="page-tile-link">
+        <div class="page-tile-item">
+          <div class="page-tile-content">
+            <h3 class="page-tile-title" style="margin-top: 0.0rem">{{ item.title }}</h3>
+            {%- if item.description %}
+            <p class="page-tile-description">{{ item.description }}</p>
             {%- endif %}
-            {%- endfor %}
+          </div>
         </div>
+      </a>
+      {%- endif %}
+      {%- endfor %}
     </div>
-</div>
-
-
-<style>
-
-  .simple-tile-link {
-          text-decoration: none;
-          color: #012152;
-          display: flex;
-  }
-
-  .simple-tile-item {
-           border-radius: 12px;
-           padding: 25px;
-           transition: all 0.3s ease;
-           background: #f0f3fa;
-           width: 100%;
-           display: flex;
-           flex-direction: column;
-           justify-content: space-between;
-           color: #012152;
-  }
-
-  .simple-tile-item:hover {
-           transform: translateY(-4px);
-           box-shadow: 0 8px 25px rgba(0,0,0,0.1);
-           border-color: #012152;
-           background: #012152;
-           color: #fff;
-  }
-
-  .simple-tile-title {
-           color: inherit;
-           font-weight: 400;
-           margin-top: 0px;
-           margin-bottom: 0px;
-  }
-
-</style>
+  </div>
+</div>
diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss
@@ -36,6 +36,69 @@ h2 {
 /*-----Copied and adapted from https://github.com/elixir-europe/infectious-diseases-toolkit/blob/main/_sass/_custom_classes.scss-----*/
 /*-----Section navigation tiles-----*/
 
+/*-----Page tiles (section-navigation-tiles_mod.html)-----*/
+
+.page-tiles-list {
+  display: grid;
+  grid-template-columns: repeat(var(--tile-cols, 4), 1fr);
+  gap: 20px;
+}
+
+@media (max-width: 992px) {
+  .page-tiles-list {
+    grid-template-columns: repeat(2, 1fr);
+  }
+}
+
+@media (max-width: 600px) {
+  .page-tiles-list {
+    grid-template-columns: repeat(1, 1fr);
+  }
+}
+
+.page-tile-link {
+  text-decoration: none;
+  color: inherit;
+  display: flex;
+}
+
+.page-tile-item {
+  border-radius: 12px;
+  padding: 25px;
+  transition: all 0.3s ease;
+  background: #f0f3fa;
+  width: 100%;
+  display: flex;
+  flex-direction: column;
+  justify-content: space-between;
+  border: 1px solid #ffffff;
+  color: #012152;
+
+  &:hover {
+    background: #012152;
+    color: #ffffff;
+    transform: translateY(-4px);
+    box-shadow: 0 8px 25px rgba(0, 0, 0, 0.1);
+    border: 1px solid #000000;
+  }
+}
+
+.page-tile-title {
+  color: inherit;
+  font-size: 1.3rem;
+  font-weight: 600;
+  margin-bottom: 8px;
+}
+
+.page-tile-description {
+  color: inherit;
+  font-size: 0.9rem;
+  line-height: 1.5;
+  flex-grow: 1;
+}
+
+/*-----Section navigation tiles-----*/
+
 .navigation-tiles {
     .card:hover {
         box-shadow: $box-shadow;

diff --git a/assets/img/shelley-orchestrator.png b/assets/img/shelley-orchestrator.png
diff --git a/assets/img/shelley_motd.png b/assets/img/shelley_motd.png
diff --git a/contributing.md b/contributing.md
@@ -13,6 +13,7 @@ Contact the [**BioCommons Training Team**](https://www.biocommons.org.au/event-s
 
 If you have published research or training materials using BioShell, [**let us know**](mailto:comms@biocommons.org.au) so we can feature it here.
 
-### Contribute
+### Contribute to BioShell
 
 Visit the [**BioShell GitHub repository**](https://github.com/AustralianBioCommons/BioShell) to report issues or contribute to development.
+