website updates

Gemfile

@@ -5,6 +5,8 @@ gem "webrick", "~> 1.8.1"
 gem "jekyll", "~> 4.3.2"
 gem "jemoji", "~> 0.13.0"
 gem "kramdown-parser-gfm", "~> 1.1"
+gem "csv"
+gem "openssl", "~> 3.3.1"
 
 group :jekyll_plugins do
   gem "jekyll-redirect-from", "~> 0.16.0"

_config.yml

@@ -2,7 +2,7 @@
 title: ABLeS
 topnav_title: ABLeS
 description: ABLeS
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@5.0.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
 permalink: pretty
 gtag: G-T8GWK081T9
 
@@ -21,6 +21,7 @@ defaults:
       path: ""
       type: "pages"
     values:
+      permalink: /:basename
       layout: "page"
       sidebar: main
 

_data/footer.yml

@@ -1,6 +1,5 @@
 # see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
-copyright: 'This site uses cookies to help the website run effectively. To find out more, read our [cookies](https://www.biocommons.org.au/cookies) statement.'
-extra_line: ABLeS is subject to the Australian BioCommons [Code of Conduct](https://doi.org/10.5281/zenodo.4276854) and [Privacy Policy](https://www.biocommons.org.au/privacy).
+copyright: 'This site uses cookies to help the website run effectively. To find out more, read our [cookies](https://www.biocommons.org.au/cookies) statement. ABLeS is subject to the Australian BioCommons [Code of Conduct](https://doi.org/10.5281/zenodo.4276854) and [Privacy Policy](https://www.biocommons.org.au/privacy).'
 columns:
   - type: image
     image_width: 320px

_data/sidebars/main.yml

@@ -2,16 +2,22 @@
 subitems:
   - title: Home
     url: /index
+  - title: About
+    url: /about
   - title: News & events
     url: /news-events
-  - title: Eligibility
-    url: /eligibility
   - title: Getting started
-    url: /projects_allocations
-  - title: Resources & Training
-    url: /resources
-  - title: Available software and data
-    url: /if89
+    subitems:
+      - title: Eligibility
+        url: /eligibility
+      - title: Projects
+        url: /projects_allocations
+      - title: Resources & Training
+        url: /resources
+      - title: Available software and data
+        url: /if89
+  - title: Sharing project outputs
+    url: sharing
   - title: ABLeS participants
     url: /participants
   - title: Acknowledging ABLeS

_data/tiles.yml

@@ -0,0 +1,48 @@
+- title: "Request a new project"
+  type: new
+  url: https://docs.google.com/forms/d/e/1FAIpQLScTzDsJeLxB9if4PnuOiDsDCtSESKTc5d39rDSTUGu5fjCw3Q/viewform?usp=header
+- title: "Request additional resources"
+  type: existing
+  url: https://docs.google.com/forms/d/e/1FAIpQLSe_zrqiE7QSh1FFlmzMxFV6F_u5G-4dnAJ1H7vpN6kkkATyww/viewform?usp=header
+- title: "Request software installation"
+  type: existing
+  url: https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link
+- title: "Request general help"
+  type: existing
+  url: https://docs.google.com/forms/d/e/1FAIpQLSere1PvgPEuJkpvQUk1-11C88IAeQNQKEUFc-Qgbn5GgKK2jw/viewform?usp=sf_link
+- title: "Report project outcome"
+  type: existing
+  url: https://docs.google.com/forms/d/e/1FAIpQLSdO1w-RY8OexUBwJx8BHNMwSRNPA3_-5r6pefdQW8ancbKZqw/viewform?usp=sf_link
+- title: "See available tools"
+  type: new
+  url: /resources#3-collectively-maintained-software-and-reference-data-project-if89
+- title: "Help, this is the first time I'm requesting an ABLeS project"
+  type: new
+  url: /eligibility
+- title: "General software"
+  type: sharing
+  url: /sharing#general-software
+- title: "Computational workflows"
+  type: sharing
+  url: /sharing#workflows
+- title: "Reference data"
+  type: sharing
+  url: /sharing#reference-data
+- title: "SOPs and protocols"
+  type: sharing
+  url: /sharing#sops-and-protocols
+- title: "Pawsey user training"
+  url: https://pawsey.atlassian.net/wiki/spaces/US/pages/51917528/User+Training
+  type: pawsey
+- title: "Setonix user guide"
+  url: https://pawsey.atlassian.net/wiki/spaces/US/pages/51925434/Setonix+User+Guide
+  type: pawsey
+- title: "Calendar of upcoming training opportunities"
+  url: https://opus.nci.org.au/display/Help/NCI+Training+and+Educational+Events
+  type: nci
+- title: "User guides"
+  url: https://opus.nci.org.au/
+  type: nci
+- title: "Register to become a NCI user"
+  url:
+  type: nci

_data/topnav.yml

@@ -0,0 +1,5 @@
+#subitems:
+#- title: About
+#  url: /about
+#- title: News & Events
+#  url: /news-events

_includes/affiliation-tiles-selection_mod.html

@@ -0,0 +1,15 @@
+{%- assign alllogos = site.data.affiliations %}
+<div class="affiliation-tiles row row-cols-2 row-cols-sm-3 row-cols-md-3 g-4 my-3">
+  {%- assign filtered_logos = alllogos | where: "type", include.type %}
+  {%- for affiliation in filtered_logos %}
+  {%- if affiliation.image_url and affiliation.expose == true %}
+  <div class="col">
+    <div class="card h-100 border-0">
+      <div class="my-auto d-flex justify-content-center">
+        {% if affiliation.url %}<a class="w-100" href="{{ affiliation.url }}">{% endif %}<img class="rounded p-3" src="{{ affiliation.image_url | relative_url }}" alt="{{ affiliation.name }}">{%- if affiliation.url %}</a>{% endif %}
+      </div>
+    </div>
+  </div>
+  {%- endif %}
+  {%- endfor %}
+</div>

_includes/tiles.html

@@ -0,0 +1,72 @@
+{% comment %}
+include source was modified from that available at https://github.com/Australian-Structural-Biology-Computing/australian-structural-biology-computing.github.io/blob/2ad8159cddd12b3ec4dfbf33fbbf310af9d686ba/_includes/section-navigation-tiles_mod.html
+{% endcomment %}
+
+{%- assign links_to_add_as_tiles = site.data.tiles -%}
+<div class="tiles">
+  <div class="tiles-container">
+    <div class="tiles-list">
+      {%- for item in links_to_add_as_tiles -%}
+      {%- if item.type == include.type -%}
+      <a href="{{ item.url | relative_url }}" class="tile-link">
+          <div class="tile-item">
+            <div class="tile-content">
+              <h3 class="tile-title" style="margin-top: 0.4rem">{{ item.title }}</h3>
+            </div>
+          </div>
+      </a>
+      {%- endif -%}
+      {%- endfor -%}
+    </div>
+  </div>
+</div>
+
+<style>
+
+  .tiles-list {
+    display: grid;
+    grid-template-columns: repeat(auto-fill, minmax(200px, 1fr));
+    gap: 10px;
+  }
+
+  .tile-link {
+    text-decoration: none;
+    color: inherit;
+    display: flex;
+  }
+
+  .tile-item {
+    border-radius: 12px;
+    padding: 10px;
+    transition: all 0.3s ease;
+    background: #f0f3fa;
+    width: 100%;
+    display: flex;
+    flex-direction: column;
+    justify-content: space-between;
+    border: 1px solid #ffffff;
+    color: #012152;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    text-align: center;
+  }
+
+  .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;
+  }
+
+  .tile-title {
+    color: inherit;
+    font-size: 0.9rem;
+    font-weight: 200;
+    margin-bottom: 8px;
+    text-align: center;
+    vertical-align: middle;
+  }
+
+</style>

_sass/_bootstrap_variables.scss

@@ -14,7 +14,7 @@ $nav-link-hover-color: $primary;
 $link-color: $blue;
 $navbar-dark-color: $white;
 $navbar-dark-hover-color: $white;
-$navbar-light-hover-color: $light;
+$navbar-light-hover-color: $primary;
 $link-color: #205a86;
 $nav-link-color: $white;
 $nav-link-hover-color: $light;

_sass/_custom_classes.scss

@@ -13,6 +13,15 @@ img {
     @extend .img-fluid;
 }
 
+h1 {
+    font-size: 2.4rem;
+    font-weight: bolder;
+}
+
+h2 {
+    font-size: 1.7rem;
+    font-weight: bolder;
+}
 
 .accordion-button:not(.collapsed) {
  color:#FFFFFF;
@@ -28,7 +37,7 @@ img {
 header .navbar {
     .navbar-brand {
         font-size: 2.25rem;
-        //color: $white !important;
+        color: $black !important;
             img {
                 max-height: 80px;
             }
@@ -59,4 +68,43 @@ header .navbar {
             background-color: #5ac3b1;       
         }
     }
-}
+}
+
+.navbar-nav .nav-item > a {
+    &.active {
+        color: $white;
+        background-color: $primary;
+        border-radius: $border-radius;
+    }
+}
+
+
+.index-main-container {
+  display: flex;
+  flex-wrap: wrap;
+}
+
+.index-panel {
+  padding: 20px;
+  flex: 1;
+  min-width: 300px;
+}
+
+.index-left-panel {
+  flex: 1;
+}
+
+.index-right-panel {
+  flex: 1.5;
+}
+
+.video-wrapper {
+  width: 100%;
+  aspect-ratio: 16 / 9;
+}
+
+.video-wrapper iframe {
+  width: 100%;
+  height: 100%;
+  border-radius: 8px;
+}

about.md

@@ -0,0 +1,31 @@
+---
+title: About
+toc: false
+---
+
+The ABLeS (Australian BioCommons Leadership Share) program was established in April 2021 to more readily support data-driven bioinformatics. This effort is supported by [Australian BioCommons](https://www.biocommons.org.au/) in partnership with [Bioplatforms Australia](https://bioplatforms.com/), the [National Computational Infrastructure (NCI, Canberra)](https://nci.org.au/), and the [Pawsey Supercomputing Research Centre (Pawsey, Perth)](https://pawsey.org.au/). 
+
+ABLeS offers access to:
+
+- computational and data infrastructure;
+- specialized expertise;
+- support on adopting best practices and effectively sharing outputs;
+- a community-driven repository of bioinformatics software, including tools and workflows.
+
+If you want to read more about ABLeS, more details are available in the ABLeS publication:
+
+*Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (2023). Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share (3.0). Zenodo. [https://doi.org/10.5281/zenodo.10139651](https://doi.org/10.5281/zenodo.10139651)*
+<br/>
+
+
+
+## Acknowledgements
+
+ABLeS is co-funded by <a href="https://bioplatforms.com/biocommons/">Bioplatforms Australia</a>, <a href="https://nci.org.au/">the National Computational Infrastructure (NCI)</a> and <a href="https://pawsey.org.au/">Pawsey Supercomputing Research Centre</a>. This program forms part of the national Australian BioCommons infrastructure.
+
+<br/>
+
+
+{% include affiliation-tiles-selection_mod.html type="infrastructure" %}
+
+

acknowledgements.md

@@ -37,4 +37,4 @@ Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (
 
 Authorship is NOT expected for routine / simple services provided (e.g. tool installation) and an acknowledgement is sufficient in these cases. We approach authorship issues with a generous spirit and aim to fairly attribute contributions.
 
-In some cases, it may be appropriate for ABLeS support staff, or specialists at NCI or Pawsey to be co-authors on publications. Examples of this include when these specialists provide significant input into the publication, including a significant contribution to method / protocol / pipeline development, study design, data and results analysis, or interpretation.
+In some cases, it may be appropriate for ABLeS support staff, or specialists at NCI or Pawsey, to be co-authors on publications. Examples of this include when these specialists provide significant input into the publication, including a significant contribution to method / protocol / pipeline development, study design, data and results analysis, or interpretation.

contact-us.md

@@ -2,11 +2,33 @@
 title: Help and Contact Details
 ---
 
-| **Type of problem / challenge / issue**                                                      | **Contact details**                                                                   |
-|----------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------|
-| Compute system issues at the NCI                                                             | Email:  <br/> <ziad@biocommons.org.au> <br/> <help@nci.org.au>          |
-| Compute system issues at Pawsey                                                             | Email: <br/> <ziad@biocommons.org.au> <br/> <help@pawsey.org.au>        |
-| Questions about the ABLeS program                                                                | Email: <br/> <ziad@biocommons.org.au> <br/>  <steven@biocommons.org.au> |
-| Requesting tool installations                                                                | Please use the [ABLeS GoogleForm](https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link)                |
-| Reporting challenges with a specific bioinformatics workflow, or requesting assistance with this workflow | Please use the [ABLeS GoogleForm](https://docs.google.com/forms/d/e/1FAIpQLSere1PvgPEuJkpvQUk1-11C88IAeQNQKEUFc-Qgbn5GgKK2jw/viewform?usp=sf_link)                |
-| Any other issue                                                                             | Email: <br/> <ziad@biocommons.org.au> <br/> <steven@biocommons.org.au>  |
+
+#### Issues with compute systems
+
+For **NCI**, email Ziad and the NCI helpdesk.
+
+```
+ziad@biocommons.org.au
+help@nci.org.au
+```
+
+For **Pawsey**, email Ziad and the Pawsey helpdesk.
+
+```
+ziad@biocommons.org.au
+help@pawsey.org.au
+```
+
+
+#### Requesting tool installations
+
+Complete the [**GoogleForm here**](https://docs.google.com/forms/d/e/1FAIpQLScpiyqERdxw6gMxjlq_CkiI3qvJ60YaeWHKTJChMjcnv8aBBA/viewform?usp=sf_link).
+
+
+#### Questions about the ABLeS program, and any other issue
+
+Email the ABLeS team.
+
+```
+ables@biocommons.org.au
+```