From dc44bb67146ebb3c782ca197079b7ac82ec164db Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:01:25 +1030 Subject: [PATCH 01/24] update nci_data_collections.md --- pages/activities/nci_data_collections.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md index d27e134..d9423e2 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -7,12 +7,15 @@ roadmap_category: Shared-platform contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] toc: false redirect_from: /website/nci_data_collections +tiles: + - title: "Access the data collection at NCI" + url: https://dx.doi.org/10.25914/q48c-9a86 --- ## Availability -The data collection is currently available here: ****. -The collection has also been added to the **[community resources list](community_resources)**. +{% include tiles-simple.html target = "tiles" col = "1" %} + ## Details @@ -23,7 +26,8 @@ The collection has also been added to the **[community resources list](community This activity aims to create a stable release of up-to-date reference data (with DOI) to support reproducible structure prediction workflows. -### Completed + +## Completed - Catalog latest version of reference data. - Harmonize data across different structure prediction models (AlphaFold2, AlphaFold3, Boltz, ColabFold, HelixFold3, RosettaFold-AA). From 1d5a534be392bc892bbf41b81a8905247fc8f10d Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:01:30 +1030 Subject: [PATCH 02/24] update nci_data_collections.md --- pages/activities/nci_data_collections.md | 1 - 1 file changed, 1 deletion(-) diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md index d9423e2..fb9b765 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -12,7 +12,6 @@ tiles: url: https://dx.doi.org/10.25914/q48c-9a86 --- -## Availability {% include tiles-simple.html target = "tiles" col = "1" %} From 165e672f6fa386144bb048ece888a249bebb9b8a Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:02:01 +1030 Subject: [PATCH 03/24] update main.yml --- _data/sidebars/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 9ce69d6..33c2e5f 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -11,11 +11,11 @@ subitems: url: /contributors - title: Community library subitems: - - title: Community resources + - title: General resources url: /community_resources - title: How-to Guides url: /guides - - title: Community workflows + - title: Workflows url: /workflows - title: External resources subitems: From f1e49bf8a76b1f7a87a6e3171fec1f5656294f4a Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:05:59 +1030 Subject: [PATCH 04/24] update join_conversation.md --- pages/join_conversation.md | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/pages/join_conversation.md b/pages/join_conversation.md index bfbaf79..9395344 100644 --- a/pages/join_conversation.md +++ b/pages/join_conversation.md @@ -1,28 +1,26 @@ --- -title: Join the conversation +title: Ways to join the conversation description: page_id: join toc: false redirect_from: /website/join_conversation tiles: - - title: "Attend the regular community meetings" + - title: "View the rolling agenda for the community meetings" url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi - - title: "Attend events" + - title: "View the events page" url: /events - - title: "Join the mailing list" - url: /join_conversation#mailing-list --- +If you would like to, there are multiple ways to join the conversation. -### Ways to join -If you would like to, there are multiple ways to join the conversation. +### Attend the regular community meetings and other events -{% include tiles-simple.html col = "3" target = "tiles" %} +{% include tiles-simple.html col = "2" target = "tiles" %} -### Mailing list +### Join the mailing list If you join the mailing list (subscribe below), you will receive community updates and notifications, including information From f6d9d44eb99f27953dea26b2841ca619cf040302 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:08:10 +1030 Subject: [PATCH 05/24] update infrastructure_roadmap.md --- pages/activities/infrastructure_roadmap.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md index d8f7efe..9f30a98 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -7,11 +7,20 @@ roadmap: Community co-authored document roadmap_category: No-category toc: false redirect_from: /website/infrastructure_roadmap +tiles: + - title: "Read the Australian Structural Biology Deep-Learning Infrastructure Roadmap" + url: https://doi.org/10.5281/zenodo.15786982 --- + +{% include tiles-simple.html target = "tiles" col = "1" %} + + ## Citation -> Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. [https://doi.org/10.5281/zenodo.15786982](https://doi.org/10.5281/zenodo.15786982) +``` +Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. [https://doi.org/10.5281/zenodo.15786982](https://doi.org/10.5281/zenodo.15786982) +``` ## Executive Summary from roadmap From 266b62b39b48fd84048fa8d3209c00abd377763c Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 10 Mar 2026 17:09:13 +1030 Subject: [PATCH 06/24] update infrastructure_roadmap.md --- index.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index ee18fa3..e6d01dd 100644 --- a/index.md +++ b/index.md @@ -8,6 +8,8 @@ redirect_from: /website/ tiles: - title: "Join the mailing list, meetings etc." url: /join_conversation + - title: "Read the community infrastructure roadmap" + url: https://doi.org/10.5281/zenodo.15786982 - title: "See activities that are in progress" url: /activities - title: "Share your work with the community" @@ -17,9 +19,10 @@ tiles: This website is a virtual meeting place and hub for all users of **computing for structural biology research in Australia**. This is a collective community effort. It can be what we make it! + ## Getting involved -{% include tiles-simple.html target = "tiles" col = "3" %} +{% include tiles-simple.html target = "tiles" col = "2" %} ## Protein design seminar series - watch the recordings @@ -40,7 +43,7 @@ This website is a virtual meeting place and hub for all users of **computing for ## Acknowledgements -This website represents a joint effort by many people at multiple Australian institutions. +This community represents a joint effort by people at multiple Australian institutions. A list of contributors is [available here](contributors). {% include affiliation-tiles-selection.html %} From c302e0d406f0ce93c66aca5afddfd146043da94d Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 12 Mar 2026 11:45:07 +1030 Subject: [PATCH 07/24] update CONTRIBUTORS.yml --- _data/CONTRIBUTORS.yml | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 69932c5..1dcf30c 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -27,13 +27,13 @@ Keiran Rowell: git: keiran-rowell-unsw email: k.rowell@unsw.edu.au orcid: 0000-0001-6955-1167 - affiliation: Computational Scientist, Structural Biology Facility UNSW + affiliation: Computational Scientist, Structural Biology Facility, UNSW -Kate Michie: +Katharine Michie: git: katemichie email: k.michie@unsw.edu.au orcid: 0000-0002-2133-2237 - affiliation: Chief Scientist, Structural Biology Facility UNSW + affiliation: Chief Scientist, Structural Biology Facility, UNSW James Lingford: git: jlingford @@ -57,7 +57,7 @@ Thomas Litfin: git: tlitfin-unsw email: t.litfin@unsw.edu.au orcid: 0000-0002-4863-3865 - affiliation: Senior Research Associate, Structural Biology Facility UNSW + affiliation: Senior Research Associate, Structural Biology Facility, UNSW Ziad Al-Bkhetan: git: ziadbkh @@ -159,4 +159,18 @@ Farah Zaib Khan: Sehrish Kanwal: affiliation: Senior Research Fellow (Bioinformatics), The University of Melbourne git: skanwal - orcid: https://orcid.org/0000-0002-5044-4692 \ No newline at end of file + orcid: https://orcid.org/0000-0002-5044-4692 + +Paulyna Magaña: + affiliation: Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) + git: paulynamagana + orcid: https://orcid.org/0009-0004-1524-2966 + +Kristina Gagalova: + affiliation: Curtin University and Centre for Crop and Disease Management (CCDM), Perth, Australia + git: KristinaGagalova + orcid: https://orcid.org/0000-0002-5975-0805 + +Jennifer Fleming: + affiliation: Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) + orcid: https://orcid.org/0000-0003-4016-8740 \ No newline at end of file From 337aa089e8c0c51fb577554f2e6d1f508babf931 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 12 Mar 2026 13:51:55 +1030 Subject: [PATCH 08/24] add ebi_module_dev.md --- pages/activities/ebi_module_dev.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 pages/activities/ebi_module_dev.md diff --git a/pages/activities/ebi_module_dev.md b/pages/activities/ebi_module_dev.md new file mode 100644 index 0000000..bf18fff --- /dev/null +++ b/pages/activities/ebi_module_dev.md @@ -0,0 +1,28 @@ +--- +title: EMBL-EBI Foundations of Protein Structure module development +description: Developing the content for an online EMBL-EBI tutorial covering the principles of protein architecture and function. +type: Activity_in_progress +roadmap_category: Global-connections +contributors: [Jennifer Fleming, Kristina Gagalova, Johan Gustafsson, Michael Healy, Thomas Litfin, Paulyna Magaña, Katharine Michie] +toc: false +tiles: + - title: "View the Foundations of Protein Structure module" + url: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ +--- + + +{% include tiles-simple.html target = "tiles" col = "1" %} + + +## Details + +A collaboration developing the content for a `Foundations of Protein Structure` module that will be +added to the training material made available by EMBL-EBI. The development of the module is a +collaboration between members of the Australian Structural Biology Computing community, and the +team from [Protein Data Bank in Europe (PDBE)](https://www.ebi.ac.uk/pdbe/). + + +## Future + +- Development of additional modules +- Contributions from additional community members From 2d8155b24e694869ae3fb05d4a5a8e8bf1a3507f Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 12 Mar 2026 13:52:51 +1030 Subject: [PATCH 09/24] update tool_and_resource_list.yml --- _data/tool_and_resource_list.yml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 1964e0e..413021e 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -312,7 +312,13 @@ URL: https://cluster.foldseek.com/ - Description: Reference data to support AI structural biology prediction models Tag: Community resource - Title: NCI Structural Biology AI Reference Collection + Title: NCI Structural Biology AI Reference Collection Type: - Reference database - URL: https://dx.doi.org/10.25914/q48c-9a86 \ No newline at end of file + URL: https://dx.doi.org/10.25914/q48c-9a86 +- Description: Online tutorial covering the principles of protein architecture and function + Tag: Community resource + Title: Foundations of protein structure tutorial + Type: + - Online tutorial + URL: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ \ No newline at end of file From 55ccbb3a806279a721a0e40722351b6647b2bf2d Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 10 Apr 2026 13:32:02 +0930 Subject: [PATCH 10/24] update index.md --- index.md | 39 +++++++++++++++++++++++++++++---------- 1 file changed, 29 insertions(+), 10 deletions(-) diff --git a/index.md b/index.md index e6d01dd..cd7bed4 100644 --- a/index.md +++ b/index.md @@ -14,6 +14,9 @@ tiles: url: /activities - title: "Share your work with the community" url: /contributing +community_meeting: + - title: "Click to visit the rolling agenda and find out more." + url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi --- @@ -25,20 +28,36 @@ This website is a virtual meeting place and hub for all users of **computing for {% include tiles-simple.html target = "tiles" col = "2" %} -## Protein design seminar series - watch the recordings +## News -| Speaker | Topic & link to YouTube | -|--------------------|------------------------------------------------------------------------------|----------| -| Rhys Grinter | [Using AI protein design to design binding proteins to challenging bacterial transporters](https://youtu.be/3Ad2gUjeSL8) | -| Cyntia Taveneau | [AIcrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors](https://www.youtube.com/watch?v=GSoOfyJUYSA) | -| Richard Birkinshaw | [Using in silico design methods to create *de novo* proteins that selectively modulate apoptosis](https://youtu.be/9-3sHy1ybpE) | -| Josh Hardy | [Introducing ProteinDJ: A modular and open-source framework for protein design workflows](https://www.youtube.com/watch?v=xwvF62HxaF0) | -| Joel Mackay | [Baby steps in the AI-guided design of proteins to modulate gene transcription](https://www.youtube.com/watch?v=tKqH8WlkIX4) | +{% include news.html limit = 2 %} -## Upcoming Events +## Community talk series for 2026 + +Starting this year, speakers from across the structural biology community will be invited to present their work at the regular community meetings. The current plan is for there to be five of these meetings every year. + + +#### Next meeting is on May 20th + +{% include tiles-simple.html target = "community_meeting" col = "1" %} + + +#### All meeting dates + +- **11th March 2026** +- **20th May 2026** +- **29th July 2026** +- **16th September 2026** +- **4th November 2026** + +**Note:** these dates may change depending on other community events and the availability of speakers. + + +## Other upcoming events + +{% include events.html event_type = "upcoming_event" limit = 4 %} -{% include events.html event_type="upcoming_event" limit=4 %} ## Acknowledgements From 14fc7a5cc823fc3e6c9a7a81915fddafc2d2d859 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 10 Apr 2026 13:40:43 +0930 Subject: [PATCH 11/24] update news --- _data/news.yml | 10 +- _includes/news.html | 237 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 241 insertions(+), 6 deletions(-) create mode 100644 _includes/news.html diff --git a/_data/news.yml b/_data/news.yml index ed0dc0a..5e4e42a 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -1,6 +1,4 @@ -- name: "Script for Alphafold output validation metrics!" - date: 2024-11-01 - description: "Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen ()" -- name: "Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)" - date: 2024-11-01 - description: "MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen ()" +- name: "View the webinar series for protein design" + date: 2025-11-11 + url: https://youtube.com/playlist?list=PL3KeWF8P6MjzKtxXLp83w78K_AGUskL0a&si=eMvuLoQzcg9sIws5 + description: "A limited series webinar from 2025 that shared strategies to get the best outcomes from protein design projects. Speakers included: Richard Birkinshaw, Rhys Grinter, Josh Hardy, Joel Mackay, and Cyntia Taveneau." \ No newline at end of file diff --git a/_includes/news.html b/_includes/news.html new file mode 100644 index 0000000..d2959bd --- /dev/null +++ b/_includes/news.html @@ -0,0 +1,237 @@ +
+
+
+ {%- assign current_date = "now" | date: "%s" -%} +
+ {%- assign news = site.data.news | sort: "date" | reverse %} + {%- assign count = 0 -%} +
+ {%- for item in news -%} +
+
+
+
{{ item.date | date: "%d" | escape }}
+
{{ item.date | date: "%b" | escape }}
+
{{ item.date | date: "%Y" | escape }}
+
+
+

{{ item.name | escape }}

+

{{ item.description | markdownify }}

+
+
→
+
+
+ {%- assign count = count | plus: 1 -%} + {%- if include.limit and count == include.limit -%} + {%- break -%} + {%- endif -%} + {%- endfor -%} +
+
+
+
+ + + + +
\ No newline at end of file From 5c0066652d788a0476d6573d27c0b3dde1bb0146 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 10 Apr 2026 13:45:09 +0930 Subject: [PATCH 12/24] update tool_and_resource_list.yml --- _data/tool_and_resource_list.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 413021e..f7c04a4 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -316,9 +316,17 @@ Type: - Reference database URL: https://dx.doi.org/10.25914/q48c-9a86 + DOI: https://dx.doi.org/10.25914/q48c-9a86 - Description: Online tutorial covering the principles of protein architecture and function Tag: Community resource Title: Foundations of protein structure tutorial Type: - Online tutorial - URL: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ \ No newline at end of file + URL: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ + DOI: https://doi.org/10.6019/tol.foundations-protein-structure-t.2026.00001.1 +- Description: A limited series of webinars from 2025 that shared strategies to get the best outcomes from protein design projects. + Tag: Community resource + Title: Protein design webinar series + Type: + - Webinar series + URL: protein_design_seminars \ No newline at end of file From 55d08321c527b64bef5c06ec5ed54fe36594ec5c Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 10 Apr 2026 13:45:40 +0930 Subject: [PATCH 13/24] update events.yml --- _data/events.yml | 31 +------------------------------ 1 file changed, 1 insertion(+), 30 deletions(-) diff --git a/_data/events.yml b/_data/events.yml index acdda39..8d5ffe1 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -8,6 +8,7 @@ # location: Cyberspace - name: BioMolecular Horizons startDate: 2024-09-22 + endDate: 2024-09-22 description: "Launch of the website at BioMolecular Horizons 2024" url: https://www.bmh2024.com/ - name: Australian Structural Biology Computing community meeting @@ -81,34 +82,4 @@ endDate: 2025-11-27 description: "Leveraging peak Australian compute to enable workflows for predictive structural biology at scale" url: https://blackochrelabs.au/abacbs2025_workshops/ - location: Online -- name: Australian Structural Biology Computing community meeting - startDate: 2026-03-11 - endDate: 2026-03-11 - 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: Australian Structural Biology Computing community meeting - startDate: 2026-05-20 - endDate: 2026-05-20 - 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: Australian Structural Biology Computing community meeting - startDate: 2026-07-29 - endDate: 2026-07-29 - 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: Australian Structural Biology Computing community meeting - startDate: 2026-09-16 - endDate: 2026-09-16 - 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: Australian Structural Biology Computing community meeting - startDate: 2026-11-04 - endDate: 2026-11-04 - 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 \ No newline at end of file From 97e3bbce9bfbf0363c608a663ee83d7618c8a1f1 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 10 Apr 2026 13:48:31 +0930 Subject: [PATCH 14/24] update events.html --- _includes/events.html | 25 +------------------------ 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/_includes/events.html b/_includes/events.html index d557ff0..0d96c47 100644 --- a/_includes/events.html +++ b/_includes/events.html @@ -93,30 +93,7 @@

{{ event.name | escape }}

.events-category:last-child { margin-bottom: 0; } - - .category-title { - font-size: 1.3rem; - font-weight: 600; - color: #012152; - margin-bottom: 20px; - text-transform: uppercase; - letter-spacing: 0.1em; - position: relative; - padding-left: 20px; - } - - .category-title::before { - content: ''; - position: absolute; - left: 0; - top: 50%; - transform: translateY(-50%); - width: 4px; - height: 18px; - background: #012152; - border-radius: 2px; - } - + .events-list { display: grid; grid-template-columns: 1fr 1fr; From 8b210a53e976c4d8c8ed732bf4cb8ce98697ffd1 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 13 Apr 2026 08:59:27 +0930 Subject: [PATCH 15/24] update protein_design_seminars.md --- pages/activities/protein_design_seminars.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index 71f7353..6ab40c2 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -7,16 +7,21 @@ roadmap_category: Training contributors: [Rhys Grinter, Gavin Knott, Cyntia Taveneau, Josh Hardy, Joel Mackay, Kate Michie, Johan Gustafsson, Melissa Burke] toc: false redirect_from: /website/protein_design_seminars +tiles: + - title: "View the 2025 Protein Design Seminar Series" + url: https://youtube.com/playlist?list=PL3KeWF8P6MjzKtxXLp83w78K_AGUskL0a&si=eMvuLoQzcg9sIws5 --- +{% include tiles-simple.html target = "tiles" col = "1" %} + + ## Details - Computational protein design can produce synthetic proteins that disrupt the function of a target protein. - Australian community members are actively using protein design technology to solve biological problems. - Community members will host a monthly seminar series to share knowledge on protein design strategies to get the best outcomes from protein design projects. - Registration is **[available here](https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator)**. | Date | Time | Speaker(s) | Topic | Recording | Presentation | |---------------|------------|--------------------|-------|-----------|----------| From 834018bcdbfef45bc1f82eb8d55defd36c9a3d9d Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 13 Apr 2026 09:01:14 +0930 Subject: [PATCH 16/24] update tool_and_resource_list.yml --- _data/tool_and_resource_list.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index f7c04a4..06fd6b0 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -329,4 +329,5 @@ Title: Protein design webinar series Type: - Webinar series - URL: protein_design_seminars \ No newline at end of file + URL: protein_design_seminars + DOI: https://doi.org/10.5281/zenodo.17626498 \ No newline at end of file From 9ca738c411bee763be918426437b16a27da0a102 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 13 Apr 2026 09:03:15 +0930 Subject: [PATCH 17/24] update resource-table-category.html --- _includes/resource-table-category.html | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/_includes/resource-table-category.html b/_includes/resource-table-category.html index 68e22a1..f07dbb3 100644 --- a/_includes/resource-table-category.html +++ b/_includes/resource-table-category.html @@ -16,6 +16,7 @@ {%- endif %} Description + DOI Type @@ -35,6 +36,11 @@ {{tool.Title}} {%- endif %} {{tool.Description}} + {% if tool.DOI%} + DOI + {%- else %} + + {%- endif %} {% if tool.Type %} {%- for type in tool.Type %} From 5720bbea1fe84cc7009b89a40d5102f3d915f9b1 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Wed, 15 Apr 2026 12:34:16 +1000 Subject: [PATCH 18/24] fix code block wrapping --- _sass/_custom_classes.scss | 10 ++++++++++ pages/activities/infrastructure_roadmap.md | 5 ++--- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index a6c4c8a..bbf1798 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -69,5 +69,15 @@ margin-bottom: $spacer * 3; #content { margin-bottom: 0 !important; + + // Allow long Markdown code lines to wrap instead of overflowing. + pre { + white-space: pre-wrap; + word-break: break-word; + } + + pre code { + white-space: inherit; + } } } diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md index 9f30a98..72593ee 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -19,10 +19,9 @@ tiles: ## Citation ``` -Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. [https://doi.org/10.5281/zenodo.15786982](https://doi.org/10.5281/zenodo.15786982) +Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. https://doi.org/10.5281/zenodo.15786982 ``` - ## Executive Summary from roadmap Enabled by advances in deep learning methods for protein structure prediction and de novo protein @@ -86,4 +85,4 @@ included in D3. Globe image: Clker-Free-Vector-Images, CC0, via Wikimedia Common ### Contributors - Australian Structural Biology Computing Community -- Australian BioCommons and infrastructure partners \ No newline at end of file +- Australian BioCommons and infrastructure partners From 4d1d39e119a7da0831746252b2c595e936379207 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 15 Apr 2026 12:10:10 +0930 Subject: [PATCH 19/24] update news.yml --- _data/news.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/_data/news.yml b/_data/news.yml index 5e4e42a..1101faa 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -1,4 +1,8 @@ - name: "View the webinar series for protein design" date: 2025-11-11 url: https://youtube.com/playlist?list=PL3KeWF8P6MjzKtxXLp83w78K_AGUskL0a&si=eMvuLoQzcg9sIws5 - description: "A limited series webinar from 2025 that shared strategies to get the best outcomes from protein design projects. Speakers included: Richard Birkinshaw, Rhys Grinter, Josh Hardy, Joel Mackay, and Cyntia Taveneau." \ No newline at end of file + description: "A limited series webinar from 2025 that shared strategies to get the best outcomes from protein design projects. Speakers included: Richard Birkinshaw, Rhys Grinter, Josh Hardy, Joel Mackay, and Cyntia Taveneau." +- name: "NCI Data Collection now available!" + date: 2026-02-23 + url: https://dx.doi.org/10.25914/q48c-9a86 + description: "This collection replicates key reference databases used for protein structure prediction and analysis. These resources enable NCI users to leverage deep learning models for molecular structure prediction. The datasets support AlphaFold3, AlphaFold2, Boltz, RoseTTaFold-All-Atom, ESMFold and HelixFold3 structure prediction tools." \ No newline at end of file From 4b33106c94c0e4e8a8b50f80a7973a4aeaff1133 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 15 Apr 2026 12:10:32 +0930 Subject: [PATCH 20/24] update events.yml --- _data/events.yml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/_data/events.yml b/_data/events.yml index 8d5ffe1..8cad6a1 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -82,4 +82,34 @@ endDate: 2025-11-27 description: "Leveraging peak Australian compute to enable workflows for predictive structural biology at scale" url: https://blackochrelabs.au/abacbs2025_workshops/ + location: Online +- name: Australian Structural Biology Computing community meeting + startDate: 2026-03-11 + endDate: 2026-03-11 + 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: Australian Structural Biology Computing community meeting + startDate: 2026-05-20 + endDate: 2026-05-20 + 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: Australian Structural Biology Computing community meeting + startDate: 2026-07-29 + endDate: 2026-07-29 + 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: Australian Structural Biology Computing community meeting + startDate: 2026-09-16 + endDate: 2026-09-16 + 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: Australian Structural Biology Computing community meeting + startDate: 2026-11-04 + endDate: 2026-11-04 + 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 \ No newline at end of file From 936a5f1972bfc914c8ef35b5366433577aa1be87 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 15 Apr 2026 12:10:46 +0930 Subject: [PATCH 21/24] fix ebi_module_dev.md --- pages/activities/ebi_module_dev.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/activities/ebi_module_dev.md b/pages/activities/ebi_module_dev.md index bf18fff..774ff8d 100644 --- a/pages/activities/ebi_module_dev.md +++ b/pages/activities/ebi_module_dev.md @@ -19,7 +19,7 @@ tiles: A collaboration developing the content for a `Foundations of Protein Structure` module that will be added to the training material made available by EMBL-EBI. The development of the module is a collaboration between members of the Australian Structural Biology Computing community, and the -team from [Protein Data Bank in Europe (PDBE)](https://www.ebi.ac.uk/pdbe/). +team from [Protein Data Bank in Europe (PDBe)](https://www.ebi.ac.uk/pdbe/). ## Future From badd38de162859c17203a225e8dcfb7b3e22c528 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Wed, 15 Apr 2026 12:16:47 +0930 Subject: [PATCH 22/24] update index.md --- index.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/index.md b/index.md index cd7bed4..69c794d 100644 --- a/index.md +++ b/index.md @@ -54,10 +54,7 @@ Starting this year, speakers from across the structural biology community will b **Note:** these dates may change depending on other community events and the availability of speakers. -## Other upcoming events - -{% include events.html event_type = "upcoming_event" limit = 4 %} - +{% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %} ## Acknowledgements From 3dbf9b284a1f182d0b4b59f6761a5d44c4c525c1 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Wed, 15 Apr 2026 13:21:34 +1000 Subject: [PATCH 23/24] Apply suggestion from @supernord Co-authored-by: Johan Gustafsson <50811354+supernord@users.noreply.github.com> --- index.md | 1 - 1 file changed, 1 deletion(-) diff --git a/index.md b/index.md index 69c794d..a241e58 100644 --- a/index.md +++ b/index.md @@ -51,7 +51,6 @@ Starting this year, speakers from across the structural biology community will b - **16th September 2026** - **4th November 2026** -**Note:** these dates may change depending on other community events and the availability of speakers. {% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %} From 86092f8baeb0d938bc11c5daa4e19f58e1234d06 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Wed, 15 Apr 2026 14:18:20 +1000 Subject: [PATCH 24/24] fix news tiles --- _includes/news.html | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/_includes/news.html b/_includes/news.html index d2959bd..75524e7 100644 --- a/_includes/news.html +++ b/_includes/news.html @@ -1,4 +1,4 @@ -
+
{%- assign current_date = "now" | date: "%s" -%} @@ -18,7 +18,7 @@

{{ item.name | escape }}

{{ item.description | markdownify }}

-
→
+
→
{%- assign count = count | plus: 1 -%} @@ -38,7 +38,7 @@

{{ item.name | escape }}

box-sizing: border-box; } - .news{ + .news { display: block; }; @@ -181,7 +181,7 @@

{{ item.name | escape }}

color: #012152; } - .news-item:hover .event-arrow { + .news-item:hover .news-arrow { opacity: 1; } @@ -234,4 +234,4 @@

{{ item.name | escape }}

window.open(`${news_url}`, '_blank'); } -
\ No newline at end of file +