From e5d993848020c24b9b7595144c7ac727075e1419 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 27 Apr 2026 09:22:07 +0930 Subject: [PATCH 01/11] update 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 774ff8d..6ee8940 100644 --- a/pages/activities/ebi_module_dev.md +++ b/pages/activities/ebi_module_dev.md @@ -1,7 +1,7 @@ --- 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 +type: Completed_activity roadmap_category: Global-connections contributors: [Jennifer Fleming, Kristina Gagalova, Johan Gustafsson, Michael Healy, Thomas Litfin, Paulyna Magaña, Katharine Michie] toc: false From b75ea49f87f173c81924f63ae7bbb5ef83d04b29 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 27 Apr 2026 09:22:57 +0930 Subject: [PATCH 02/11] update nfcore_proteinfold.md --- pages/activities/nfcore_proteinfold.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/pages/activities/nfcore_proteinfold.md b/pages/activities/nfcore_proteinfold.md index 9c7fe0b..6791cfd 100644 --- a/pages/activities/nfcore_proteinfold.md +++ b/pages/activities/nfcore_proteinfold.md @@ -1,14 +1,19 @@ --- -title: nf-core ProteinFold v2.0 Release -description: Contribute towards, and locally deploy, v2.0 of nf-core ProteinFold workflow. -type: Activity_in_progress +title: nf-core ProteinFold v2.0.0 Release +description: Contribute towards, and locally deploy, v2.0.0 of nf-core ProteinFold workflow. +type: Completed_activity roadmap: A shared platform, or platforms (Roadmap D3A) roadmap_category: Shared-platform contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] toc: false redirect_from: /website/nfcore_proteinfold +tiles: + - title: "See version 2.0.0 of the nf-core/proteinfold workflow" + url: https://nf-co.re/proteinfold/2.0.0/ --- +{% include tiles-simple.html target = "tiles" col = "1" %} + ## Details - Molecular structure prediction tools require large reference databases and varied computational infrastructure. @@ -34,7 +39,4 @@ redirect_from: /website/nfcore_proteinfold - Add miniature reference databases for fast troubleshooting. - Update documentation and metro-map. - Test for release. - -### In Progress - - Review workflow outputs for all modes. \ No newline at end of file From f2becea45890025b2dc5b3b57a3be1440fdee010 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 27 Apr 2026 09:24:22 +0930 Subject: [PATCH 03/11] update structure_prediction.md --- pages/resources/structure_prediction.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/resources/structure_prediction.md b/pages/resources/structure_prediction.md index 583bb2c..3fe4c48 100644 --- a/pages/resources/structure_prediction.md +++ b/pages/resources/structure_prediction.md @@ -1,5 +1,5 @@ --- -title: Structure Prediction +title: Structure prediction page_id: external_structure_prediction datatable: true toc: false From d8fea5777b548bb34861ba155a756e81c491fc19 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 27 Apr 2026 09:31:05 +0930 Subject: [PATCH 04/11] add website_dev.md --- pages/activities/website_dev.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 pages/activities/website_dev.md diff --git a/pages/activities/website_dev.md b/pages/activities/website_dev.md new file mode 100644 index 0000000..fad679a --- /dev/null +++ b/pages/activities/website_dev.md @@ -0,0 +1,29 @@ +--- +title: Community website +description: Development and maintenance of the Australian Structural Biology Computing (ASBC) community website. +type: Activity_in_progress +roadmap_category: Community-space +contributors: [Johan Gustafsson, Thomas Litfin, Kate Michie] +toc: false +--- + +## Details + + +### Completed + +- Initial version of the website +- Mechanisms for joining the community +- Streamlined appearance and mechanics for all pages + + +### In Progress + +- Sharing mechanism for computational workflows +- Adding contributors + + +### Future + +- Sharing mechanism for events +- Sharing mechanism for both community resources and external resources From c922ffa208dc1f897eaabdd5f320391f1d52057f Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 27 Apr 2026 09:34:50 +0930 Subject: [PATCH 05/11] update tables --- _data/tool_and_resource_list.yml | 21 ++++++++++++++++++--- _includes/resource-table-category.html | 11 ++++++++++- 2 files changed, 28 insertions(+), 4 deletions(-) diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 06fd6b0..85f1521 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -310,18 +310,22 @@ Type: - Reference database URL: https://cluster.foldseek.com/ -- Description: Reference data to support AI structural biology prediction models +- Description: Reference data to support AI structural biology prediction models. Tag: Community resource Title: NCI Structural Biology AI Reference Collection Type: - Reference database + Roadmap: + - Roadmap deliverable 2 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 +- Description: Online tutorial covering the principles of protein architecture and function. Tag: Community resource Title: Foundations of protein structure tutorial Type: - Online tutorial + Roadmap: + - Roadmap deliverable 2 & 4 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. @@ -329,5 +333,16 @@ Title: Protein design webinar series Type: - Webinar series + Roadmap: + - Roadmap deliverable 2 URL: protein_design_seminars - DOI: https://doi.org/10.5281/zenodo.17626498 \ No newline at end of file + DOI: https://doi.org/10.5281/zenodo.17626498 +- Description: A nextflow pipeline with support for numerous structure prediction tools. + Tag: Community resource + Title: nf-core ProteinFold v2.0.0 + Type: + - Workflow + Roadmap: + - Roadmap deliverable 3 + URL: nfcore_proteinfold + DOI: https://doi.org/10.5281/zenodo.7437037 \ No newline at end of file diff --git a/_includes/resource-table-category.html b/_includes/resource-table-category.html index f07dbb3..2124af2 100644 --- a/_includes/resource-table-category.html +++ b/_includes/resource-table-category.html @@ -35,7 +35,16 @@ {%- else %} {{tool.Title}} {%- endif %} - {{tool.Description}} + + {{tool.Description}} + {% if tool.Roadmap %} + {%- for type in tool.Roadmap %} + + {%- endfor %} + {%- endif %} + {% if tool.DOI%} DOI {%- else %} From 4e2aafe595aa080dd24c2320fd501f1f9b13825b Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 28 Apr 2026 11:29:09 +0930 Subject: [PATCH 06/11] update main.yml --- _data/sidebars/main.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 33c2e5f..6cf6fb4 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -15,19 +15,19 @@ subitems: url: /community_resources - title: How-to Guides url: /guides - - title: Workflows - url: /workflows - title: External resources subitems: - - title: Structure Prediction + - title: Structure prediction url: /structure_prediction - - title: Protein Design + - title: Protein design url: /protein_design - - title: Protein Search + - title: Protein search url: /protein_search - - title: Molecular Dynamics + - title: Molecular dynamics url: /molecular_dynamics - title: Infrastructure url: /infrastructure - title: Events url: /events + - title: News + url: /news \ No newline at end of file From f4f56bad432423929d4e3e03f0e592ada8aa4cea Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 28 Apr 2026 11:29:43 +0930 Subject: [PATCH 07/11] update titles --- pages/resources/molecular_dynamics.md | 2 +- pages/resources/protein_design.md | 2 +- pages/resources/protein_search.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pages/resources/molecular_dynamics.md b/pages/resources/molecular_dynamics.md index e81933c..ce77f9d 100644 --- a/pages/resources/molecular_dynamics.md +++ b/pages/resources/molecular_dynamics.md @@ -1,5 +1,5 @@ --- -title: Molecular Dynamics +title: Molecular dynamics page_id: external_resources_md datatable: true toc: false diff --git a/pages/resources/protein_design.md b/pages/resources/protein_design.md index b474f10..488972f 100644 --- a/pages/resources/protein_design.md +++ b/pages/resources/protein_design.md @@ -1,5 +1,5 @@ --- -title: Protein Design +title: Protein design page_id: external_resources_protein_design datatable: true toc: false diff --git a/pages/resources/protein_search.md b/pages/resources/protein_search.md index 4234fb8..832a2bd 100644 --- a/pages/resources/protein_search.md +++ b/pages/resources/protein_search.md @@ -1,5 +1,5 @@ --- -title: Protein Search +title: Protein search page_id: external_resources_search datatable: true toc: false From 062774473638e467f8e059cd5536f2683b0652e0 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 28 Apr 2026 11:33:55 +0930 Subject: [PATCH 08/11] add news items --- _data/news.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/_data/news.yml b/_data/news.yml index 1101faa..f3a288a 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -5,4 +5,12 @@ - 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 + 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." +- name: "ASBC @ the AI for Science Hackathon" + date: 2026-03-26 + url: https://www.biocommons.org.au/news/ai-for-science-hackathon-2026 + description: "Australian Structural Biology Computing (ASBC) community (UNSW Structural Biology Facility, WEHI, and the Monash AI Protein Design Program) contributed to the AI for Science Hackathon, bringing their expertise in optimising workflows for protein structure prediction and design." +- name: "Foundations of protein structure training module now available!" + date: 2026-04-17 + url: https://doi.org/10.6019/tol.foundations-protein-structure-t.2026.00001.1 + description: "A module added to the training material made available by EMBL-EBI. Module development was a collaboration between the ASBC community, BioCommons, and EMBL-EBI Protein Data Bank in Europe (PDBe)." \ No newline at end of file From 3e7c5d2410c00c819c24304ca0b7ea93d5b72ca5 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Tue, 28 Apr 2026 13:31:30 +0930 Subject: [PATCH 09/11] add speakers --- index.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/index.md b/index.md index a241e58..3655c06 100644 --- a/index.md +++ b/index.md @@ -43,14 +43,15 @@ Starting this year, speakers from across the structural biology community will b {% 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** - +#### All meeting dates and speakers + +| Date | Speaker | Talk title | +|------|--------------------------------------------------------------------------------------|---------------------------------------------------------------------------| +| March 11th | **Biswa Prasanna Mishra** (Institute for Biomedicine and Glycomics, Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system | +| May 20th | **Cameron Gilchrist** (Seoul National University) | Multiple protein structure alignment with FoldMason | +| 29th July | TBA | TBA | +| 16th September | **Tom Goddard** (UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX | +| 12th November | TBA | TBA | {% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %} From ecea3e69800ef3a075c14155e94235f3ebd49e15 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Tue, 28 Apr 2026 14:28:26 +1000 Subject: [PATCH 10/11] update affiliation --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 3655c06..2c46962 100644 --- a/index.md +++ b/index.md @@ -47,7 +47,7 @@ Starting this year, speakers from across the structural biology community will b | Date | Speaker | Talk title | |------|--------------------------------------------------------------------------------------|---------------------------------------------------------------------------| -| March 11th | **Biswa Prasanna Mishra** (Institute for Biomedicine and Glycomics, Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system | +| March 11th | **Biswa Prasanna Mishra** (Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system | | May 20th | **Cameron Gilchrist** (Seoul National University) | Multiple protein structure alignment with FoldMason | | 29th July | TBA | TBA | | 16th September | **Tom Goddard** (UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX | From cba304ae2de03a9700cdb0cbb2f1aa20e3ffac13 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Tue, 28 Apr 2026 14:35:54 +1000 Subject: [PATCH 11/11] update speaker table line wrap --- index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.md b/index.md index 2c46962..2377b6d 100644 --- a/index.md +++ b/index.md @@ -47,10 +47,10 @@ Starting this year, speakers from across the structural biology community will b | Date | Speaker | Talk title | |------|--------------------------------------------------------------------------------------|---------------------------------------------------------------------------| -| March 11th | **Biswa Prasanna Mishra** (Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system | -| May 20th | **Cameron Gilchrist** (Seoul National University) | Multiple protein structure alignment with FoldMason | +| March 11th | **Biswa Prasanna Mishra**
(Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system | +| May 20th | **Cameron Gilchrist**
(Seoul National University) | Multiple protein structure alignment with FoldMason | | 29th July | TBA | TBA | -| 16th September | **Tom Goddard** (UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX | +| 16th September | **Tom Goddard**
(UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX | | 12th November | TBA | TBA |