Australian-Structural-Biology-Computing · supernord · Jun 16, 2026 · Jun 15, 2026 · Jun 15, 2026 · Jun 15, 2026
diff --git a/_data/news.yml b/_data/news.yml
@@ -13,4 +13,8 @@
 - 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)."
+  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)."
+- name: "17M protein structures added to the AlphaFold Database"
+  date: 2026-06-05
+  url: https://www.biocommons.org.au/news/colabfold-setonix
+  description: "An Australian researcher has recently contributed 17 million protein predictions to the AlphaFold Protein Structure Database, which will have a transformative impact on the international fight to combat antimicrobial resistance."
diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml
@@ -19,6 +19,8 @@ subitems:
         url: /community_resources
       - title: How-to Guides
         url: /guides
+      - title: Software
+        url: /software
   - title: External resources
     subitems:
       - title: Structure prediction

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
@@ -338,11 +338,57 @@
   URL: protein_design_seminars
   DOI: https://doi.org/10.5281/zenodo.17626498
 - Description: A nextflow pipeline with support for numerous structure prediction tools.
-  Tag: Community resource
+  Tag: Software
   Title: nf-core ProteinFold v2.0.0
   Type:
   - Workflow
-  Roadmap:
-  - Roadmap deliverable 3
   URL: nfcore_proteinfold
-  DOI: https://doi.org/10.5281/zenodo.7437037
+  DOI: https://doi.org/10.5281/zenodo.7437037
+- Description: Predicts the structure of target proteins using MSAs generated by hhblits/jackhmmer.
+  Tag: Software
+  Title: AlphaFold2
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/611418237/Using+AlphaFold2+on+AMD+GPUs
+  DOI: https://doi.org/10.1038/s41586-021-03819-2
+- Description: Predicts the structure of target molecules (proteins, nucleic acids, small molecules) using MSAs generated by MMSeqs2.
+  Tag: Software
+  Title: Boltz-2
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/1767571575/Using+Boltz+v.2.2.1+on+AMD+GPUs
+  DOI: https://doi.org/10.1101/2025.06.14.659707
+- Description: Predicts the structure of target proteins using MSAs generated by MMSeqs2.
+  Tag: Software
+  Title: ColabFold
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/611123341/Using+ColabFold+on+AMD+GPUs
+  DOI: https://doi.org/10.1038/s41592-022-01488-1
+- Description: Predicts the structure of a target sequence using the ESM pre-trained language model.
+  Tag: Software
+  Title: ESMFold
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/1028816938/Using+ESMFold+on+AMD+GPUs
+  DOI: https://doi.org/10.1126/science.ade2574
+- Description: Predicts a sequence composition compatible with an input target structure.
+  Tag: Software
+  Title: ProteinMPNN
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/613089393/Using+ProteinMPNN+on+AMD+GPUs
+  DOI: https://doi.org/10.1126/science.add2187
+- Description: Diffusion-based model to generate new protein structures.
+  Tag: Software
+  Title: RFdiffusion
+  Type:
+  - Software
+  - For AMD GPUs
+  URL: https://pawsey.atlassian.net/wiki/spaces/US/pages/808091691/Using+RFDiffusion+on+AMD+GPUs
+  DOI: https://doi.org/10.1038/s41586-023-06415-8
diff --git a/index.md b/index.md
@@ -38,20 +38,20 @@ This website is a virtual meeting place and hub for all users of **computing for
 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 
+#### Next meeting is on July 29th 
 
 {% include tiles-simple.html target = "community_meeting" col = "1" %}
 
 
 #### All meeting dates and speakers
 
-| Date | Speaker                                                                              | Talk title                                                                |
-|------|--------------------------------------------------------------------------------------|---------------------------------------------------------------------------|
-| March 11th | **Biswa Prasanna Mishra**<br>(Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system |
-| May 20th | **Cameron Gilchrist**<br>(Korea Basic Science Institute Ochang-center)                                    | Multiple protein structure alignment with FoldMason |
-| 29th July | TBA           |  TBA          |
-| 16th September | **Tom Goddard**<br>(UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX |
-| 12th November | TBA | TBA  |
+| Date | Speaker                                                                | Talk title                                                             |
+|------|------------------------------------------------------------------------|------------------------------------------------------------------------|
+| March 11th | **Biswa Prasanna Mishra**<br>(Griffith University)                     | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system |
+| May 20th | **Cameron Gilchrist**<br>(Korea Basic Science Institute Ochang-center) | Multiple protein structure alignment with FoldMason |
+| July 29th | **Roland Dunbrack**<br>(Fox Chase Cancer Center)                       |  Structural bioinformatics and AlphaFold modeling of the human kinome and its interactions          |
+| September 16th | **Tom Goddard**<br>(UCSF)                                              | Predicting atomic structures using OpenFold 3 in ChimeraX |
+| November 12th | TBA                                                                    | TBA  |
 
 
 {% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %}

diff --git a/pages/activities/amd_software.md b/pages/activities/amd_software.md
@@ -0,0 +1,41 @@
+---
+title: Porting high priority software to AMD GPUs
+description: Porting software prioritised by the community to AMD to allow software execution at Pawsey Supercomputing Research Centre and other centres operating AMD GPUs.
+type: Activity_in_progress
+roadmap: A shared platform, or platforms (Roadmap D3Ab)
+roadmap_category: Shared-platform
+contributors: [Sarah Beecroft, Joshua Storm Caley]
+toc: false
+tiles:
+  - title: "Visit the software resources page to see the tools ported to AMD GPUs"
+    url: /software
+---
+
+
+{% include tiles-simple.html target = "tiles" col = "1" %}
+
+
+## Details
+
+- Deep Learning models work natively with NVIDIA hardware.
+- Setonix at Pawsey contains a large number of AMD GPUs.
+- Models can be made to work with AMD hardware available at Pawsey.
+- This ongoing activity is specifically for the identification, prioritisation, and porting of structural biology software from NVIDIA to AMD GPUs.
+
+
+### Completed
+
+- [AMD compatible containers for nf-core proteinfold](nfcore_proteinfold_pawsey).
+
+
+### In Progress
+
+
+### Future
+
+- Continue to port software to AMD that has been prioritised by the community.
+
+
+### Acknowledgements
+
+This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.
diff --git a/pages/activities/nfcore_proteinfold_pawsey.md b/pages/activities/nfcore_proteinfold_pawsey.md
@@ -1,20 +1,30 @@
 ---
-title: nf-core ProteinFold at Pawsey
-description: Deploy nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre.
+title: Porting software to AMD to enable nf-core ProteinFold at Pawsey
+description: Port software to AMD to allow the deployment of the nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre.
 type: Activity_in_progress
 roadmap: A shared platform, or platforms (Roadmap D3Ab)
 roadmap_category: Shared-platform
 contributors: [Sarah Beecroft, Joshua Storm Caley]
 toc: false
 redirect_from: /website/nfcore_proteinfold_pawsey
+tiles:
+  - title: "Visit the software resources page to see the tools ported to AMD GPUs"
+    url: /software
+  - 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 = "2" %}
+
+
 ## Details
 
 - Deep Learning models work natively with NVIDIA hardware.
 - Setonix at Pawsey contains a large number of AMD GPUs.
 - Models can be made to work with AMD hardware available at Pawsey.
 
+
 ### Completed
 
 - Build AMD compatible container for AlphaFold2.
@@ -25,8 +35,17 @@ redirect_from: /website/nfcore_proteinfold_pawsey
 - Adapt containers for compatibility with nf-core proteinfold.
 - Test nfcore proteinfold workflow at Pawsey.
 
+
 ### In Progress
 
 - ProteinFold config optimized for Pawsey.
 
+
 ### Future
+
+- Port software to AMD that has been prioritised by the community.
+
+
+### Acknowledgements
+
+This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.
diff --git a/pages/contributing/contributing.md b/pages/contributing/contributing.md
@@ -3,9 +3,38 @@ title: Contributing
 page_id: contributing
 toc: false
 #type: resources
-toc: false
 redirect_from: /website/contributing
 ---
 
-{% include callout.html type="important" content="Contributing guidelines will be available soon." %}
 
+A key aim of the community is to enable sharing of knowledge, methods (i.e. software and workflows), and expertise: to accelerate progress across the community, foster collaborations, and reduce replication of effort.
+
+Here, we outline an initial set of contribution mechanisms that are intended to allow for community sharing, and 
+attribution of credit to those who have created the work being shared.
+
+{% include callout.html type="important" content="Additional contribution guidelines will be added as they are prioritised by the community." %}
+
+
+## Sharing computational workflows
+
+{% include callout.html type="important" content="Workflows from a [ASBC community collection on the WorkflowHub registry](https://workflowhub.eu/collections/40) will be automatically imported and displayed on a dedicated software page soon. Additional instructions will be available soon. For now, if you would like your workflows listed on the website when the integration with WorkflowHub is ready, please follow the instructions below." %}
+
+
+#### 1. [Register as a WorkflowHub user and either set up, or join, a Team](https://about.workflowhub.eu/docs/organising-and-setup/)
+
+
+#### 2. [Register your workflow(s) on WorkflowHub](https://about.workflowhub.eu/docs/registering_workflows/registering-a-workflow/)
+
+
+#### 3. Annotate these workflows by adding the minimum metadata highlighted here
+
+| Field                      | Description / extra information |
+|----------------------------|--------------------------------------------------------------------|
+| Workflow title             | Make sure the title is descriptive and highlights what the workflow does.|
+| Creator(s)               | If you have included a `CITATION.cff` file in your GitHub repository, WorkflowHub can parse this and automatically populate the creator field. |
+| Description              | Note that descriptions included in GitHub repository README files will be automatically parsed by WorkflowHub. |
+| Maturity                 | Indicate if the workflow is `mature` or a `work-in-progress`. |
+| License                    | Note that if a license file is included in your GitHub repository it will be automatically parsed by WorkflowHub. |
+| EDAM Topics and Operations | Add concepts from [EDAM](https://github.com/edamontology/edamontology) as standardised short descriptions of workflow domain, purpose, and function. You can search for EDAM terms within the WorkflowHub workflow registration wizard. You can also use [EDAM browser](https://edamontology.github.io/edam-browser/) to explore and search the EDAM ontology for appropriate concepts. |
+
+The metadata included above is based on a BioCommons [example available here](https://australianbiocommons.github.io/how-to-workflowhub-space/new_workflow#add-minimum-metadata).
diff --git a/pages/resources/software.md b/pages/resources/software.md
@@ -0,0 +1,10 @@
+---
+title: Software
+page_id: software
+toc: false
+---
+
+The software listed here is made available on Australian national infrastructure in support of activities across the ASBC community.
+
+{% include resource-table-category.html category="Software" %}
+
diff --git a/pages/software.md b/pages/software.md