diff --git a/_data/events.yml b/_data/events.yml index 6817874..872ee1e 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -31,36 +31,36 @@ - name: Protein design seminar series startDate: 2025-07-15 endDate: 2025-07-15 - description: "Using AI protein design to design binding proteins to challenging bacterial transporters." + description: "**Topic:** Using AI protein design to design binding proteins to challenging bacterial transporters." url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online - name: Protein design seminar series startDate: 2025-08-12 endDate: 2025-08-12 - description: "Icrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors." + description: "**Topic:** Icrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors." url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online - name: Australian Structural Biology Computing community meeting startDate: 2025-08-27 endDate: 2025-08-27 - description: "Visit the rolling agenda for details on how to join the next meeting." + description: "Click to visit the rolling agenda and see details on how to join the next meeting." url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi location: Online - name: Protein design seminar series startDate: 2025-09-16 endDate: 2025-09-16 - description: "Using in silico design methods to create de novo proteins that selectively modulate apoptosis." + description: "**Topic:** Using in silico design methods to create de novo proteins that selectively modulate apoptosis." url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online - name: Protein design seminar series startDate: 2025-10-07 endDate: 2025-10-07 - description: "Introducing ProteinDJ: A modular and open-source framework for protein design workflows." + description: "**Topic:** Introducing ProteinDJ: A modular and open-source framework for protein design workflows." url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online - name: Protein design seminar series startDate: 2025-11-11 endDate: 2025-11-11 - description: TBD + description: "**Topic:** TBD" url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online \ No newline at end of file diff --git a/_includes/resource-table-category.html b/_includes/resource-table-category.html index 4baab5a..f9484b1 100644 --- a/_includes/resource-table-category.html +++ b/_includes/resource-table-category.html @@ -10,7 +10,7 @@ -
How-to Guide or resource {%- if include.tag -%} + Resource {%- if include.tag -%} {%- endif %} diff --git a/_includes/section-navigation-tiles_mod.html b/_includes/section-navigation-tiles_mod.html new file mode 100644 index 0000000..96d95bb --- /dev/null +++ b/_includes/section-navigation-tiles_mod.html @@ -0,0 +1,89 @@ +{% comment %} +Gemini 2.5 Pro used to assist with the initial creation of this code, based on existing code in events.html (2025-07-07) +Prompt 1: "Can this jekyll html include be modified to create tiles for individual pages instead of tiles for events?" +Prompt 2: "Can you also add a small category badge to the tile?" +{% endcomment %} + +{%- assign pages_to_add_as_tiles = site.pages -%} +
+
+
+ {%- for page in pages_to_add_as_tiles -%} + {%- if page.type == include.type %} + +
+
+

{{ page.title }}

+ {% if page.description %} +

{{ page.description }}

+ {% endif %} + {% if page.roadmap %} +

{{ page.roadmap }}

+ {% endif %} +
+
+ + {%- endif %} + {%- endfor -%} +
+
+
+ + \ No newline at end of file diff --git a/index.md b/index.md index 94f8ac5..e3474a2 100644 --- a/index.md +++ b/index.md @@ -16,7 +16,7 @@ This website is a virtual meeting place and hub for all users of **computing for {% include tiles-simple.html target = "tiles" col = "1" %} -## Events +## Upcoming Events {% include events.html event_type="upcoming_event" limit=4 %} diff --git a/pages/activities.md b/pages/activities.md index f866718..4467fff 100644 --- a/pages/activities.md +++ b/pages/activities.md @@ -7,15 +7,16 @@ toc: false ## In progress -{% include section-navigation-tiles-simple.html col = "2" type="activity_in_progress" except="binder_access.md" %} + +{% include section-navigation-tiles_mod.html type ="activity_in_progress" %} ## Future -{% include section-navigation-tiles-simple.html col = "2" type="activity_future"%} +{% include section-navigation-tiles_mod.html type="activity_future"%} ## Completed -{% include section-navigation-tiles-simple.html col = "2" type="activity_completed"%} +{% include section-navigation-tiles_mod.html type ="activity_completed" %} diff --git a/pages/activities/batch_structure_prediction.md b/pages/activities/batch_structure_prediction.md index 716850b..0a6a6cb 100644 --- a/pages/activities/batch_structure_prediction.md +++ b/pages/activities/batch_structure_prediction.md @@ -1,6 +1,8 @@ --- title: Batch Structure Prediction Workflows +description: Developing optimized batch workflows for structure prediction. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3A) contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Cameron Hyde, Thomas Litfin] toc: false --- diff --git a/pages/activities/bindcraft_access.md b/pages/activities/bindcraft_access.md index 0c0e4c1..fab8156 100644 --- a/pages/activities/bindcraft_access.md +++ b/pages/activities/bindcraft_access.md @@ -1,6 +1,8 @@ --- title: Community Access to BindCraft +description: Increasing community access to an end-to-end solution for protein binder design. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3Ac) contributors: [Ziad Al-Bkhetan, Thomas Litfin] toc: false --- @@ -10,7 +12,7 @@ toc: false - [BindCraft](https://github.com/martinpacesa/BindCraft) is an end-to-end solution for protein binder design. - BindCraft was widely used by participants in a recent blind evaluation (**[Adaptyv Bio](https://www.adaptyvbio.com/blog/po104)**) of protein binder design tools. -- Several independent groups generated de novo designed binders with competitive affinity to the natural ligand using the BindCraft tool. +- Several independent groups generated *de novo* designed binders with competitive affinity to the natural ligand using the BindCraft tool. - BindCraft tool is available within a NextFlow **[workflow](https://github.com/Australian-Structural-Biology-Computing/bindflow)** to support portable deployment. {% include callout.html type="warning" content="Native BindCraft tool requires PyRosetta as a filter with non-commercial license." %} diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md index 9c13762..df11872 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -1,6 +1,8 @@ --- title: Infrastructure Roadmap +description: Draft and publish an Australian infrastructure roadmap for addressing computational challenges facing structural biology. type: activity_in_progress +roadmap: Community co-authored document toc: false --- diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md index 37fc693..145c9b3 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -1,6 +1,8 @@ --- title: NCI Data Collection +description: Create a stable release of up-to-date reference data (with DOI) at the NCI. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3F) contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] toc: false --- diff --git a/pages/activities/nci_ood_proteinfold.md b/pages/activities/nci_ood_proteinfold.md index 34d9f7c..f3ac914 100644 --- a/pages/activities/nci_ood_proteinfold.md +++ b/pages/activities/nci_ood_proteinfold.md @@ -1,6 +1,8 @@ --- title: OpenOnDemand GUI ProteinFold app +description: Create and adapt a pilot ProteinFold app for OpenOnDemand. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3Ac) contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] toc: false --- diff --git a/pages/activities/nfcore_proteinfold.md b/pages/activities/nfcore_proteinfold.md index d05e71c..bbb80a4 100644 --- a/pages/activities/nfcore_proteinfold.md +++ b/pages/activities/nfcore_proteinfold.md @@ -1,6 +1,8 @@ --- title: nf-core ProteinFold v2.0 Release +description: Contribute towards, and locally deploy, v2.0 of nf-core ProteinFold workflow. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3A) contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] toc: false --- diff --git a/pages/activities/nfcore_proteinfold_pawsey.md b/pages/activities/nfcore_proteinfold_pawsey.md index 379e172..0c2bd5a 100644 --- a/pages/activities/nfcore_proteinfold_pawsey.md +++ b/pages/activities/nfcore_proteinfold_pawsey.md @@ -1,6 +1,8 @@ --- title: nf-core ProteinFold at Pawsey +description: Deploy nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre. type: activity_in_progress +roadmap: A shared platform, or platforms (Roadmap D3Ab) contributors: [Sarah Beecroft, Joshua Storm Caley] toc: false --- diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index 5754b4d..0516341 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -1,6 +1,8 @@ --- title: Protein Design Seminar Series (2025) +description: Community members will host a monthly seminar series to share knowledge on protein design strategies. type: activity_in_progress +roadmap: A computational structural biology training program (Roadmap D2) contributors: [Rhys Grinter, Gavin Knott, Cyntia Taveneau, Josh Hardy, Kate Michie, Johan Gustafsson, Melissa Burke] toc: false --- diff --git a/pages/events.md b/pages/events.md index 3a05db8..6f85082 100644 --- a/pages/events.md +++ b/pages/events.md @@ -2,6 +2,7 @@ title: Events description: Announcements for relevant courses, meetings, and information about structural biology. page_id: events +toc: false --- diff --git a/pages/news.md b/pages/news.md index f9644e5..a9f8367 100644 --- a/pages/news.md +++ b/pages/news.md @@ -1,6 +1,7 @@ --- title: News page_id: news +toc: false --- {% include news.html truncate=true %} diff --git a/pages/resources/external_communities.md b/pages/resources/external_communities.md index 0cd2004..21f6a50 100644 --- a/pages/resources/external_communities.md +++ b/pages/resources/external_communities.md @@ -2,6 +2,7 @@ title: External Communities page_id: external_resources_communities datatable: true +toc: false #type: resources --- diff --git a/pages/resources/external_databases.md b/pages/resources/external_databases.md index eba65f1..b2b4419 100644 --- a/pages/resources/external_databases.md +++ b/pages/resources/external_databases.md @@ -2,6 +2,7 @@ title: External Databases page_id: external_resources_dbs datatable: true +toc: false #type: resources --- diff --git a/pages/resources/external_guides.md b/pages/resources/external_guides.md index ef8ea00..9cbc793 100644 --- a/pages/resources/external_guides.md +++ b/pages/resources/external_guides.md @@ -2,6 +2,7 @@ title: External Guides page_id: external_resources_guides datatable: true +toc: false #type: resources --- diff --git a/pages/resources/external_servers.md b/pages/resources/external_servers.md index 52d54fe..9689547 100644 --- a/pages/resources/external_servers.md +++ b/pages/resources/external_servers.md @@ -2,6 +2,7 @@ title: External Resources & Servers page_id: external_resources_servers datatable: true +toc: false #type: resources --- diff --git a/pages/resources/external_videos.md b/pages/resources/external_videos.md index 1a053a7..72e7248 100644 --- a/pages/resources/external_videos.md +++ b/pages/resources/external_videos.md @@ -2,6 +2,7 @@ title: External Videos page_id: external_resources_videos datatable: true +toc: false #type: resources --- diff --git a/pages/resources/external_viz.md b/pages/resources/external_viz.md index d563628..a44be85 100644 --- a/pages/resources/external_viz.md +++ b/pages/resources/external_viz.md @@ -2,6 +2,7 @@ title: External Visualization page_id: external_resources_viz datatable: true +toc: false #type: resources ---