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2 changes: 2 additions & 0 deletions Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -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"
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3 changes: 2 additions & 1 deletion _config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -21,6 +21,7 @@ defaults:
path: ""
type: "pages"
values:
permalink: /:basename
layout: "page"
sidebar: main

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3 changes: 1 addition & 2 deletions _data/footer.yml
Original file line number Diff line number Diff line change
@@ -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
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20 changes: 13 additions & 7 deletions _data/sidebars/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,22 @@
subitems:
- title: Home
url: /index
- title: About
url: /about
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I can't deploy/find this page, and I think we don't need it ;)

- 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
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48 changes: 48 additions & 0 deletions _data/tiles.yml
Original file line number Diff line number Diff line change
@@ -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
5 changes: 5 additions & 0 deletions _data/topnav.yml
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@@ -0,0 +1,5 @@
#subitems:
#- title: About
# url: /about
#- title: News & Events
# url: /news-events
15 changes: 15 additions & 0 deletions _includes/affiliation-tiles-selection_mod.html
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@@ -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>
6 changes: 3 additions & 3 deletions _includes/events.html
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ <h2 class="events-title">Events</h2>
{%- assign current_date = "now" | date: "%s" -%}
<!-- Upcoming Events -->
<div class="events-category">
<h3 class="category-title">Upcoming</h3>
<!--<h3 class="category-title">Upcoming</h3>-->
{%- assign events = site.data.events | sort: 'date' -%}
{%- assign count = 0 -%}
<div class="events-list">
Expand Down Expand Up @@ -39,7 +39,7 @@ <h3 class="event-title">{{ event.name | escape }}</h3>
</div>
</div>

<!-- Past Events -->
<!-- Past Events
<div class="events-category past-events">
<h3 class="category-title">Past</h3>
<div class="events-list">
Expand Down Expand Up @@ -69,7 +69,7 @@ <h3 class="event-title">{{ event.name | escape }}</h3>
{% endif %}
{%- endfor %}
</div>
</div>
</div>-->
</div>
</div>

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72 changes: 72 additions & 0 deletions _includes/tiles.html
Original file line number Diff line number Diff line change
@@ -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>
2 changes: 1 addition & 1 deletion _sass/_bootstrap_variables.scss
Original file line number Diff line number Diff line change
Expand Up @@ -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;
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52 changes: 50 additions & 2 deletions _sass/_custom_classes.scss
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -28,7 +37,7 @@ img {
header .navbar {
.navbar-brand {
font-size: 2.25rem;
//color: $white !important;
color: $black !important;
img {
max-height: 80px;
}
Expand Down Expand Up @@ -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;
}
31 changes: 31 additions & 0 deletions about.md
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@@ -0,0 +1,31 @@
---
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This is mainly a repetition of what you have in the 'Home' section. I don't think it's needed. I would probably keep the Home section as it was previously.

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" %}


22 changes: 19 additions & 3 deletions acknowledgements.md
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
---
title: Acknowledgements and Authorship
title: ABLeS Acknowledgment guidelines
toc: false
---

Researchers who use ABLeS resources are expected to acknowledge ABLeS in any resulting publications, presentations, or research outputs.

## Citing and acknowledging ABLeS

The ABLeS program should be both cited and acknowledged in any publication, presentation or grant application that was supported by data or services provided by ABLeS.
Expand Down Expand Up @@ -35,6 +37,20 @@ Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (

## ABLeS co-authorship policy

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.
For routine or standard services (e.g. tool installation or access to compute infrastructure), a formal acknowledgement of ABLeS is sufficient.

In some cases, co-authorship may be appropriate.

This typically applies where ABLeS support staff or specialists at NCI or Pawsey have made a substantial intellectual contribution to the work, such as:
- Development or optimisation of methods, protocols, or pipelines
- Study design input
- Data or results analysis
- Interpretation of findings

We approach authorship discussions collaboratively and in the spirit of fair and transparent attribution.

## Share your outputs

We encourage all projects to inform the ABLeS team of publications, software releases, datasets, and other outputs arising from ABLeS-supported work. Sharing outcomes helps demonstrate national impact and strengthens continued support for the community.

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.
Visit our [**Sharing project outputs** page](ables/sharing.md) to learn how to notify us and be featured.
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