ELIXIR-IE · aedin · Sep 25, 2025 · Sep 25, 2025 · Sep 25, 2025 · Sep 25, 2025
diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,45 @@ _site
 .sass-cache
 .jekyll-cache
 .jekyll-metadata
-vendor
+ivendo
+
+# macOS system files
+.DS_Store
+
+# Jekyll build output
+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+
+# Logs and temp files
+*.log
+*.tmp
+
+# Bundler dependencies
+/vendor/
+.bundle/
+
+# Ruby gems
+Gemfile.lock
+
+# Node dependencies (if used)
+/node_modules/
+
+# VS Code settings
+.vscode/
+
+# Other IDE files
+.idea/
+*.swp
+
+# Ignore PDFs if generated (keep if source)
+/pdfs/*.pdf
+
+# Ignore compiled CSS/JS if generated by build tool
+/css/*.css.map
+/js/*.js.map
+
+
+
+
diff --git a/Events/AHM/ahm.html b/Events/AHM/ahm.html
@@ -1,77 +1,41 @@
-<!DOCTYPE html>
-<html lang="en">
-
-<head>
-  <meta charset="utf-8">
-  <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
-  <title>ELIXIR All Hands Meeting 2023</title>
-  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css">
-  <link rel="stylesheet" type="text/css" href="css/styles.css">
-  <style>
-    header {
-      width: 100%;
-      background-color: #f2f2f2;
-      padding: 20px;
-      text-align: center;
-    }
-
-
-    .text {
-      font-size: 16px;
-    }
-
-    main {
-      display: grid;
-      padding: 2rem;
-      grid-template-columns: 1fr 1fr; /* Sets two equal-width columns */
-      gap: 1rem;
-      align-items: center;
-
-      margin: 0 auto;
-      font: 500 100%/1.5 system-ui;
-    }
-
-    img {
-      max-width: auto;
-      height: auto;
-    }
-  </style>
-</head>
-
-<body>
- <header>
-  <h1>Ireland hosts ELIXIR All Hands Meeting 2023</h1>
- </header>
-  <main>
-<figure>
-  <img src="images/denis_combined.jpg" class="img" alt="Denis">
-  <figcaption>Irish Head of Node, Prof. Denis Shields, welcomes meeting attendees during the opening presentation.</figcaption>
-</figure>
-
-  <p class="text">From 5th-8th June 2023, ELIXIR Ireland had the pleasure of welcoming ELIXIR members from all over Europe to the 9th ELIXIR All Hands Meeting (AHM) hosted at Dublin's Convention Centre. The event brought together approximately 400 in-person guests, with a further 114 remote guests joining online. The annual event offered members from each of the 23 nodes 
-    the opportunity to discuss the successes of the previous year and plan for the future.</p>
-
-<figure>
-
-    <img src="images/des_combined_fin_small.jpg" class="img" alt="Des" >
-  <figcaption> Prof. Des Higgins presenting the keynote talk "35 years since Clustal1".</figcaption>
-  </figure>
- <p class="text">The keynote talk was given by Des Higgins, Professor Emeritus of Bioinformatics at University College Dublin, who reflected on the last 35 years of working on the revolutionary bioinformatics tool CLUSTAL for multiple sequence alignment. Prof. Higgins highlighted the challenges faced by early bioinformaticians and emphasized the benefits of using FAIR (Findable, Accessible, Interoperable, and Reusable) and Open Research principles in research. Unsurprisingly, Prof. Higgins received a roaring applause from the audience and his presentation was a highlight of the week.</p>
-<figure>
-  <img src="images/jp.jpg" class="img" alt="GDI" >
-  <figcaption> Prof. Gianpiero Cavalleri presenting an overview of ELIXIR, Ireland and Human Genomics. </figcaption>
-</figure>
-   <p>ELIXIR Ireland node members were well-represented throughout the event. Prof. Gianpiero Cavalleri (RCSI) gave an update on "ELIXIR, Ireland, and Human Genomics" during the Human Genomics and Translational Data 2024-28 mini-symposium. Prof. Cavalleri highlighted the genomics challenges Ireland has been experiencing and the changes that are currently taking place. These changes were recently announced in the <a href="https://www.hse.ie/eng/services/news/media/pressrel/hse-launches-first-national-genetics-and-genomics-strategy-for-ireland.html" >HSE National Genetics and Genomics Strategy for Ireland </a> as well as through Ireland’s participation in GDI co-led by Prof. Cavalleri with ELIXIR Ireland Head of Node, Prof. Denis Shields. This gives hope to a brighter future for genomics healthcare in Ireland through continued coordination between Genomic Data Infrastructure (GDI) Ireland and the emerging national strategy. Prof. Aedin Culhane (UL) and Dr. Maria Doyle (UL) alongside Prof. Leo Lahti (ELIXIR-FI) led a successful workshop titled "Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure" on 9th June. The workshop fostered an engaging discussion on connecting ELIXIR and Bioconductor to encourage collaboration in terms of training, data development, and infrastructure.</p>
-<figure>
-   <img src="images/52969038599_80008e922d_o.jpg">
-<figcaption>Group photo of all ELIXIR members attending the meeting in Dublin.</figcaption>
-</figure>
-  <p>The meeting provided plenty of opportunities to socialize and network, with the main social event of the week taking place at the <a href="https://epicchq.com"> EPIC </a> museum. Attendees had the chance to learn about the Irish diaspora and its global impact on science, politics, literature, and more. Entertainment was provided in the form of a traditional music session with Irish dancers showcasing Irish culture and it didn’t take much encouragement for all to join in, with ELIXIR Ireland members proudly stepping forward to lead everyone in their own rendition of the ”Siege of Ennis” céilí dance.</p>
-<p>Photo Credits: ELIXIR-EUR</p>
-  <p>For more information about this event see the <a href="https://f1000research.com/documents/12-1126"> ELIXIR All Hands Meeting Report </a>. We look forward to next year's ELIXIR All Hands Meeting in Uppsala, Sweden!</p>
-</main>
-  <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/js/bootstrap.bundle.min.js"></script>
-
-</body>
-
-</html>
+<!-- All Hands Meeting 2023 Carousel -->
+<div id="ahmCarousel" class="carousel slide" data-bs-ride="carousel">
+  <div class="carousel-inner">
+    <div class="carousel-item active">
+      <img src="/images/all_hands/1.jpg" class="d-block w-100" alt="Opening presentation">
+      <div class="carousel-caption d-none d-md-block">
+        <h5>Opening Presentation</h5>
+        <p>Head of Node, Prof. Denis Shields, welcomes meeting attendees during the opening presentation.</p>
+      </div>
+    </div>
+    <div class="carousel-item">
+      <img src="/images/all_hands/2.jpg" class="d-block w-100" alt="Keynote">
+      <div class="carousel-caption d-none d-md-block">
+        <h5>Keynote: 35 years since Clustal1</h5>
+        <p>Prof. Des Higgins presenting the keynote talk.</p>
+      </div>
+    </div>
+    <div class="carousel-item">
+      <img src="/images/all_hands/3.jpg" class="d-block w-100" alt="Human Genomics">
+      <div class="carousel-caption d-none d-md-block">
+        <h5>ELIXIR & Human Genomics</h5>
+        <p>Prof. Gianpiero Cavalleri presenting an overview of ELIXIR, Ireland and Human Genomics.</p>
+      </div>
+    </div>
+    <div class="carousel-item">
+      <img src="/images/all_hands/4.jpg" class="d-block w-100" alt="Group Photo">
+      <div class="carousel-caption d-none d-md-block">
+        <h5>Group Photo</h5>
+        <p>Group photo of all ELIXIR members attending the meeting in Dublin.</p>
+      </div>
+    </div>
+  </div>
+  <button class="carousel-control-prev" type="button" data-bs-target="#ahmCarousel" data-bs-slide="prev">
+    <span class="carousel-control-prev-icon" aria-hidden="true"></span>
+    <span class="visually-hidden">Previous</span>
+  </button>
+  <button class="carousel-control-next" type="button" data-bs-target="#ahmCarousel" data-bs-slide="next">
+    <span class="carousel-control-next-icon" aria-hidden="true"></span>
+    <span class="visually-hidden">Next</span>
+  </button>
+</div>
diff --git a/_config.yml b/_config.yml
@@ -1,4 +1,4 @@
-# Welcome to Jekyll!
+n# Welcome to Jekyll!
 #
 # This config file is meant for settings that affect your whole blog, values
 # which you are expected to set up once and rarely edit after that. If you find
@@ -19,20 +19,17 @@
 # in the templates via {{ site.myvariable }}.
 
 title: ELIXIR Ireland Node webpage
-email: denis.shields2@gmail.com
-description: >- # this means to ignore newlines until "baseurl:"
-  Write an awesome description for your new site here. You can edit this
-  line in _config.yml. It will appear in your document head meta (for
-  Google search results) and in your feed.xml site description.
+email: elixir@ul.ie
+description: ELIXIR-Ireland node.
 baseurl: elixir-ireland.github.io # the subpath of your site, e.g. /blog
 url:
-  https://elixir-ireland.github.io
+  https://aedin.github.io
   # the base hostname & protocol for your site, e.g. http://example.com
 twitter_username: elixir-ireland
 github_username: elixir-ireland
 
 # Build settings
-theme: minima
+theme: 
 plugins:
   - jekyll-feed
 # Exclude from processing.

diff --git a/_includes/footer.html b/_includes/footer.html
@@ -0,0 +1,14 @@
+<footer class="main-footer">
+  <section>
+    <div class="container">
+      <div class="thin-footer">
+        <address class="footer-right">
+          ELIXIR Ireland<br />
+          Head of Node: Aedin Culhane<br />
+          Limerick Digital Cancer Research Centre<br />
+          University of Limerick, Castletroy, Limerick Ireland
+        </address>
+      </div>
+    </div>
+  </section>
+</footer>
diff --git a/_includes/header.html b/_includes/header.html
@@ -0,0 +1,24 @@
+<header class="main-header" id="header">
+  <div class="container">
+    <a class="hidden" href="index.html#main-content">Skip to content</a>
+    <div id="logo">
+      <a href="index.html">
+        <img src="images/logos/elixir_ireland_logo.png" alt="ELIXIR logo" title="Home" />
+      </a>
+    </div>
+    <label class="show-nav" for="nav-checkbox" title="Show main menu"></label>
+    <input type="checkbox" id="nav-checkbox" class="nav-checkbox" />
+    <nav id="main-nav">
+      <ul class="floated-inline">
+        <li class="active"><a href="index.html">Home</a></li>
+        <li><a href="training.html">Training</a></li>
+        <li><a href="databases.html">Databases</a></li>
+        <li><a href="software.html">Software</a></li>
+        <li><a href="platforms.html">Platforms</a></li>
+        <li><a href="events.html">Events</a></li>
+                <li><a href="news.html">News</a></li>
+        <li><a href="elix_ire_funded.html">Funded Projects</a></li>
+      </ul>
+    </nav>
+  </div>
+</header>
diff --git a/_includes/nav.html b/_includes/nav.html
@@ -0,0 +1,2 @@
+<!-- Banner/header bar -->
+<!-- Navigation now included directly in header.html -->
diff --git a/_layouts/default.html b/_layouts/default.html
@@ -0,0 +1,32 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <title>{% if page.title %}{{ page.title }} | {% endif %}{{ site.title }}</title>
+    <meta name="description" content="{{ site.description | default: 'ELIXIR-Ireland Website' }}" />
+    <link rel="shortcut icon" href="https://elixir-europe.org/sites/all/themes/elixir/images/favicons/favicon.ico" type="image/vnd.microsoft.icon" />
+    <link href="https://fonts.googleapis.com/css?family=Lato:400,400i,700" rel="stylesheet" />
+    <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
+    <link rel="stylesheet" type="text/css" href="{{ '/css/styles.css' | relative_url }}" />
+    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/js/bootstrap.bundle.min.js" integrity="sha384-MrcW6ZMFYlzcLA8Nl+NtUVF0sA7MsXsP1UyJoMp4YLEuNSfAP+JcXn/tWtIaxVXM" crossorigin="anonymous"></script>
+    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1" />
+    {% if site.seo %}
+      {% seo %}
+    {% endif %}
+
+  </head>
+  <body>
+    {% include header.html %}
+    <div id="wrapper">
+      {% include nav.html %}
+      <div class="body-content one-column">
+        <div class="container">
+          <main class="main-column" id="main-content">
+            {{ content }}
+          </main>
+        </div>
+      </div>
+      {% include footer.html %}
+    </div>
+  </body>
+</html>
diff --git a/_layouts/default_archive.html b/_layouts/default_archive.html
@@ -0,0 +1,13 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <!-- ... your head content ... -->
+  </head>
+  <body>
+    <div id="wrapper">
+      <!-- ... your header, navigation, and page content ... -->
+
+      {% include footer.html %}
+    </div>
+  </body>
+</html>
diff --git a/about.markdown → about.md b/about.markdown → about.md
diff --git a/headings.html → archive/headings.html b/headings.html → archive/headings.html
diff --git a/icon-fonts.html → archive/icon-fonts.html b/icon-fonts.html → archive/icon-fonts.html
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		@@ -0,0 +1,2 @@
		<!-- Banner/header bar -->
		<!-- Navigation now included directly in header.html -->