diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index d3adb06..bc51110 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -2,6 +2,7 @@ name: Jekyll site CI on: push: + branches: [ main, master, edits ] pull_request: branches: [ main, master, edits ] workflow_dispatch: @@ -13,7 +14,7 @@ permissions: jobs: build: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 steps: - name: Checkout uses: actions/checkout@v4 @@ -23,7 +24,7 @@ jobs: - name: Setup Ruby uses: ruby/setup-ruby@v1.204.0 with: - ruby-version: '3.1' + ruby-version: '3.3' bundler-cache: true cache-version: 0 @@ -41,7 +42,7 @@ jobs: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" env: PAGES_REPO_NWO: ${{ github.repository }} - JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }} + JEKYLL_ENV: production JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} JEKYLL_BUILD_BRANCH: ${{ github.ref_name }} JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} @@ -50,7 +51,7 @@ jobs: uses: actions/upload-pages-artifact@v3 deploy: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04 needs: build if: | @@ -63,8 +64,8 @@ jobs: environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }} - + steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v4 + uses: actions/deploy-pages@v4 \ No newline at end of file diff --git a/.github/workflows/update_guides.yml b/.github/workflows/update_guides.yml index f622165..dab6c38 100644 --- a/.github/workflows/update_guides.yml +++ b/.github/workflows/update_guides.yml @@ -9,7 +9,7 @@ jobs: update_guides: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: setup python uses: actions/setup-python@v2 @@ -35,4 +35,4 @@ jobs: uses: ad-m/github-push-action@v0.6.0 with: github_token: ${{ secrets.GITHUB_TOKEN }} - branch: main \ No newline at end of file + branch: main diff --git a/README.md b/README.md index 9add3f3..c724c31 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ ## What this repository is for -Gathering information to get structural biologists oriented on beginninging their journey top adopt the most recent and accurate computational tools +Gathering information to get structural biologists oriented on beginning their journey top adopt the most recent and accurate computational tools -If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc with typical GitHub features +If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc, with typical GitHub features. -## Where is the *website* not just the raw source code? +## Where is the *website*, not just the raw source code? Point your browser to https://australian-structural-biology-computing.github.io/website/ diff --git a/_config.yml b/_config.yml index 4b08d6b..ed250bc 100644 --- a/_config.yml +++ b/_config.yml @@ -1,10 +1,10 @@ -title: StructBio Computing +title: Australian Structural Biology Computing # This appears in the html browser tab for the site title (seen mostly by search engines, not users) topnav_title: Australian Structural Biology Computing # Optional: this appears on the top navigation bar next to the main_logo.svg icon -#description: "Example of ELIXIR toolkit theme as a remote jekyll theme" +description: "A website for the Australian Structural Biology Computing community." # Metadata description of the website # Following AusBioCommons minimal gh-pages with remote deploy - https://github.com/AustralianBioCommons/how-to-guides/blob/main/_config.yml @@ -25,6 +25,16 @@ defaults: permalink: /:basename layout: "page" sidebar: main + - scope: + path: "pages" + type: "pages" + values: + sidebar: main + - scope: + path: "workgroup_template_directory" + type: "pages" + values: + sidebar: workgroup_example theme_variables: # git_host: GitHub diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 61f9550..3681820 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -47,9 +47,71 @@ Michael Healy: orcid: 0000-0003-2924-9179 affiliation: Postdoctoral Research Fellow, University of Queensland -# Josh was listed as a contributor during testing - checked with him to remove -- KR -#Joshua Storm Caley: -#git: jscgh -#email: j.caley@unsw.edu.au -#orcid: 0000-0002-9374-0969 -#affiliation: Computational Systems Officer, Structural Biology Facility UNSW +Joshua Storm Caley: + git: jscgh + email: j.caley@unsw.edu.au + orcid: 0000-0002-9374-0969 + affiliation: Computational Systems Officer, Structural Biology Facility UNSW + +Thomas Litfin: + git: tlitfin-unsw + email: t.litfin@unsw.edu.au + orcid: 0000-0002-4863-3865 + affiliation: Senior Research Associate, Structural Biology Facility UNSW + +Ziad Al-Bkhetan: + git: ziadbkh + orcid: 0000-0002-4032-5331 + affiliation: Product Manager, Australian BioCommons + +Sarah Beecroft: + git: SarahBeecroft + affiliation: Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre + +Cameron Hyde: + git: neoformit + orcid: 0000-0002-5913-9766 + affiliation: Bioinformatician, Queensland Cyber Infrastructure Foundation (QCIF) + +Mitchell O'Brien: + git: Mitchob + affiliation: Senior Bioinformatics Engineer, Sydney Informatics Hub + +Matthew Downton: + git: mattdton + orcid: 0000-0002-4693-1965 + affiliation: Associate Director - Performance Optimisation, National Computational Infrastructure (NCI) + +Kisaru Liyanage: + git: kisarur + affiliation: HPC specialist (Life and Health Sciences), National Computational Infrastructure (NCI) + +Wenjing Xue: + affiliation: HPC Specialist (Life and Health Sciences), National Computational Infrastructure (NCI) + +Gavin Knott: + affiliation: Group Leader, Monash Biomedicine Discovery Institute, Monash University + orcid: 0000-0002-9007-6273 + +Rhys Grinter: + affiliation: Lab head, University of Melbourne + git: RhysWG + orcid: 0000-0002-8195-5348 + +Josh Hardy: + affiliation: Senior Research Officer, Lucet Lab, WEHI + git: joshhardywehi + email: hardy.j@wehi.edu.au + orcid: 0000-0002-8014-8552 + +#Richard Birkinshaw: +# affiliation: Senior Research Scientist, Walter and Eliza Hall Institute of Medical Research +# orcid: 0000-0003-1825-0182 + +Melissa Burke: + affiliation: Training Manager, Australian BioCommons + orcid: 0000-0002-5571-8664 + +Cyntia Taveneau: + affiliation: Research Fellow, Knott Lab, Monash University + orcid: 0000-0002-3395-4957 \ No newline at end of file diff --git a/_data/events.yml b/_data/events.yml index e915243..2a81d98 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -8,18 +8,24 @@ # location: Cyberspace - name: BioMolecular Horizons startDate: 2024-09-22 - description: Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/) + description: "Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/)" - name: Computational Structural Biology Community Meeting startDate: 2024-10-22 - startTime: 13:30 endDate: 2024-10-22 - endTime: 14:30 - description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting. + description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting." location: Online - name: Computational Structural Biology Community Meeting startDate: 2025-04-09 - startTime: 13:00 endDate: 2025-04-09 - endTime: 14:30 - description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting. - location: Online \ No newline at end of file + description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting." + location: Online +- name: Computational structural biology community meeting + startDate: 2025-06-18 + endDate: 2025-06-18 + description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting." + location: Online +- name: Australian Structural Biology Computing community meeting + startDate: 2025-08-27 + endDate: 2025-08-27 + description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting." + location: Online diff --git a/_data/news.yml b/_data/news.yml index 406004c..ed0dc0a 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -1,7 +1,6 @@ -- name: Script for Alphafold output validation metrics! +- 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 (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs) - -- name: Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch) + 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 (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif) + description: "MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen ()" diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 21f7588..4ec2e90 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -1,29 +1,29 @@ subitems: - title: Home url: /index - - title: Example page - url: /example_page - - title: Contributing - subitems: - - title: Provide us your document - url: /provide_documentation - - title: Write your own guides - url: /guide_template - - title: Visualisations + - title: Activities + url: /activities + - title: How-to Guides + url: /guides + - title: External resources subitems: - - title: Pymol - url: /pymol - - title: Protein Structure Prediction - subitems: - - title: AlphaFold How To Guide - url: /AlphaFold2_how_to_guide - - title: Best practices AlphaFold models in a paper - url: /best-practices-alphafold - - title: AlphaFold Tutorial - European Bioinformatics Institute - url: /EBI-alphafold-guide - - title: Protein structure inference options - url: /protein_struct_inference - - title: Command Line Instructions - subitems: - - title: Basics - url: /basics + - title: Servers + url: /external_servers + - title: Databases + url: /external_databases + - title: Guides + url: /external_guides + - title: Visualization + url: /external_viz + - title: Videos + url: /external_videos + - title: Communities + url: /external_communities + - title: Contributing + url: /contributing + - title: Contributors + url: /contributors + - title: Events + url: /events + - title: News + url: /news diff --git a/_data/sidebars/workgroup_example.yml b/_data/sidebars/workgroup_example.yml new file mode 100644 index 0000000..2ca7d54 --- /dev/null +++ b/_data/sidebars/workgroup_example.yml @@ -0,0 +1,5 @@ +subitems: + - title: Home + url: /index + - title: Working group index + url: /workgroup_index diff --git a/_data/topnav.yml b/_data/topnav.yml index 5a5266d..5e72aac 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -1,6 +1,7 @@ ## ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. -subitems: -- title: Home - url: /index - +#subitems: +#- title: Home +# url: /index +#- title: Working group example +# url: /workgroup_index diff --git a/_includes/resource-table-communities.html b/_includes/resource-table-communities.html new file mode 100644 index 0000000..ed606bd --- /dev/null +++ b/_includes/resource-table-communities.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "Online communities" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-dbs.html b/_includes/resource-table-dbs.html new file mode 100644 index 0000000..9a2b7f8 --- /dev/null +++ b/_includes/resource-table-dbs.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "Reference databases" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-guides.html b/_includes/resource-table-guides.html new file mode 100644 index 0000000..0a5ded8 --- /dev/null +++ b/_includes/resource-table-guides.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "Computational structural bio guides and tutorials" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-servers.html b/_includes/resource-table-servers.html new file mode 100644 index 0000000..762ee2a --- /dev/null +++ b/_includes/resource-table-servers.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "Webservers and computing resources" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-videos.html b/_includes/resource-table-videos.html new file mode 100644 index 0000000..6bbee88 --- /dev/null +++ b/_includes/resource-table-videos.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "YouTube talks and tutorials" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-viz.html b/_includes/resource-table-viz.html new file mode 100644 index 0000000..b4e7a78 --- /dev/null +++ b/_includes/resource-table-viz.html @@ -0,0 +1,56 @@ +{%- if include.tag %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + {%- for tool in tools %} + {% assign found = false %} + {% for desc in tool.Type %} + {% if desc == "Protein viz guides and tutorials" %} + {% assign found = true %} + {% endif %} + {% endfor %} + {% if found %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + {%- endif %} + {%- endfor %} + +
How-to Guide or resource {%- if include.tag -%} + + + {%- endif %} + Description
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} + {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} +
+ {%- if linked_tool %} + {{linked_tool.name}} + {%- endif %} + {%- if tool.how_to_access %} + + {%- endif %} +
+ {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/sidebar-events.html b/_includes/sidebar-events.html new file mode 100644 index 0000000..213783e --- /dev/null +++ b/_includes/sidebar-events.html @@ -0,0 +1,31 @@ +
+

Events

+
    + {%- assign events = site.data.events | reverse %} + {%- assign count = 0 %} + {%- for event in events %} +
  • +
    + +

    + {% if event.endDate or event.endTime %} - {% endif %}

    + {%- if event.location %} +
    {{ event.location | markdownify}}
    + {%- endif %} +
    + {{ event.description | markdownify }} +
    +
    +
    • + {%- assign count = count | plus: 1 %} + {%- endfor %} +
+
+

See the full list of events, including past events, on the events page.

+
+ +
\ No newline at end of file diff --git a/_includes/sidebar-news.html b/_includes/sidebar-news.html new file mode 100644 index 0000000..0d6ebc8 --- /dev/null +++ b/_includes/sidebar-news.html @@ -0,0 +1,27 @@ +{%- if site.data.news.size > 0 -%} +
+

News

+
    + {%- assign news = site.data.news | sort: "date" %} + {%- assign count = 0 %} + {%- for post in news reversed%} +
  • +
    + +
    {{ post.date | date: site.date_format }} +
    + {{ post.description | markdownify }} +
    +
    +
    • + {%- assign count = count | plus: 1 %} + {%- if include.limit and count == include.limit %} + {%- break %} + {%- endif %} + {%- endfor %} +
+
+

For more news please visit our news page

+
+
+{%- endif -%} \ No newline at end of file diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html new file mode 100644 index 0000000..885acdf --- /dev/null +++ b/_includes/tiles-simple.html @@ -0,0 +1,14 @@ +
+ {%- if include.yaml %} + {%- assign tiles = site.data.tiles[include.target] %} + {% else %} + {%- assign tiles = page[include.target] %} + {%- endif %} + {%- for item in tiles %} + {%- if item.title %} +
+ {{item.title}} +
+ {%- endif %} + {%- endfor %} +
diff --git a/_sass/_bootstrap_variables.scss b/_sass/_bootstrap_variables.scss index a4c14fa..56055fc 100644 --- a/_sass/_bootstrap_variables.scss +++ b/_sass/_bootstrap_variables.scss @@ -1,11 +1,11 @@ /*-----Theme colors-----*/ -$primary: #0d6efd; +$primary: #012152; $secondary: #6c757d; $light: #f8f9fa; $dark: #212529; /*-----Custom values for Bootstrap variables-----*/ $link-decoration: none; -$navbar-light-hover-color: $primary; +$navbar-light-hover-color: $light; // Find out which bootstrap variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/bootstrap/_variables.scss diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index 0e651d3..c0afd33 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -3,6 +3,10 @@ //Example for highlighting the active page in the navigation: /*-----Top navigation-----*/ +.nav-link { + color: $white; +} + .navbar-nav .nav-item > a { &.active { color: $white; @@ -10,3 +14,50 @@ border-radius: $border-radius; } } + +// see https://github.com/workflowhub-eu/about/blob/596b18d7ab1055ee1e53bc98a3bd120a06518e06/_sass/_custom_classes.scss +/*-----News and events-----*/ + +.events > ul > li, +.news > ul > li { + margin: 10px 0px; +} + +// News section front-page + +.news-sidebar { + background-color: $light; + + .news-item { + padding: 7px 11px; + position: relative; + a { + color: $primary; + } + a:not(.stretched-link), button:not(.stretched-link) { + z-index: 2; + position: relative; + } + .clean-md { + p { + margin-bottom: 0; + } + } + } + + .news-hover:hover { + text-decoration: none; + background-color: $primary; + color: $white; + a.stretched-link { + color: $light; + } + } + + h2 { + font-size: 1.6em; + font-weight: 700; + color: $primary; + padding: 7px 11px; + } +} \ No newline at end of file diff --git a/_sass/_custom_variables.scss b/_sass/_custom_variables.scss index 8aec083..541e50e 100644 --- a/_sass/_custom_variables.scss +++ b/_sass/_custom_variables.scss @@ -1,2 +1,11 @@ // Find out which theme variables you can use to fine tune the styling of your website here: https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/blob/main/_sass/_variables.scss // Copy paste theme here and change where necessary . + +$topnav-bg: $primary; +$topnav-title-color: $white; + +/*-----Section navigation tiles-----*/ +$nav-card-bg: $primary; +$nav-card-color: $white; +$nav-card-bg-hover: $light; +$nav-card-color-hover: $primary; \ No newline at end of file diff --git a/contributing/contributing.md b/contributing/contributing.md new file mode 100644 index 0000000..52d6f65 --- /dev/null +++ b/contributing/contributing.md @@ -0,0 +1,8 @@ +--- +title: Contributing +page_id: contributing +type: resources +--- + +{% include callout.html type="important" content="Contributing guidelines will be available soon." %} + diff --git a/example_page.md b/example_page.md new file mode 100644 index 0000000..b3d10d4 --- /dev/null +++ b/example_page.md @@ -0,0 +1,8 @@ +--- +title: Example page +--- + +# + +This page serves as an example. + diff --git a/images/activities/ood-proteinfold.png b/images/activities/ood-proteinfold.png new file mode 100644 index 0000000..93f065d Binary files /dev/null and b/images/activities/ood-proteinfold.png differ diff --git a/index.md b/index.md index f6916a9..4957d24 100644 --- a/index.md +++ b/index.md @@ -1,108 +1,29 @@ --- -title: Welcome to the Community for Structural Biology Computing in Australia -toc: true -sidebar: false -datatable: true +title: Welcome +toc: false +# Special sidebar rules for news on the index page are included in layouts/default.html, as in https://github.com/workflowhub-eu/about/blob/596b18d7ab1055ee1e53bc98a3bd120a06518e06/_layouts/default.html +#hide_sidebar: true +#sidebar: true + +tiles: + - title: "Join the conversation" + url: /join_conversation --- -## About -Welcome! This website is the virtual meeting place for all users of computing for structural biology research in Australia. This page currently serves as a knowledge resource for use of Deep Learning methods in Structural Biology, but could expand to link together Cryo-EM processing and crystallographic methods in time. This page contains How-to Guides for the use of Deep Learning methods in Structural Biology as well as news items and announcements for relevant courses, meetings and information about structural biology. It can be what we make it! +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! +{% include tiles-simple.html target = "tiles" col = "1" %} -## Join the conversation -If you would like to, there are multiple ways to join the conversation. The most straightforward is to attend the next quarterly [community meeting](#upcoming-events). If you join the mailing list (see below), you will receive community updates and automatic community meeting invitations. - - -
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- Exploring how to increase access to RFdiffusion
A collaborative activity bringing together members of the computational structural biology community, infrastructure providers, and the Australian BioCommons, in order to determine how to increase access to RFdiffusion for life science researchers. -
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- Computational Structural Biology Infrastructure Roadmap
The Roadmap is in the final stages of drafting and will be announced here and directly to the community by the end of October. -
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- - -## Upcoming events - -{% include events.html event_type="upcoming_event" truncate=true %} - - -## News - -{% include news.html %} - - -## Guides - -{% include section-navigation-tiles.html type="guide"%} - - -## External resources - -{% include resource-table-all.html %} +## Events +{% include events.html event_type="upcoming_event" limit=3 %} -## Contributors -The projects included here represent a joint effort by the following people at multiple Australian institutions. +## Acknowledgements -{% include contributor-tiles-all.html %} +This website represents a joint effort by many people at multiple Australian institutions. +A list of contributors is [available here](contributors). {% include affiliation-tiles-selection.html %} - - - diff --git a/pages/activities.md b/pages/activities.md new file mode 100644 index 0000000..e9dc0d4 --- /dev/null +++ b/pages/activities.md @@ -0,0 +1,21 @@ +--- +title: Community Activities +page_id: activities +type: resources +toc: false +--- + + +## In progress +{% include section-navigation-tiles-simple.html col = "2" type="activity_inprogress" except="binder_access.md" %} + + +## Future + +{% include section-navigation-tiles-simple.html col = "2" type="activity_future"%} + + +## Completed + +{% include section-navigation-tiles-simple.html col = "2" type="activity_completed"%} + diff --git a/pages/activities/batch_structure_prediction.md b/pages/activities/batch_structure_prediction.md new file mode 100644 index 0000000..1293d2c --- /dev/null +++ b/pages/activities/batch_structure_prediction.md @@ -0,0 +1,32 @@ +--- +title: Batch Structure Prediction Workflows +type: activity_inprogress +contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Cameron Hyde, Thomas Litfin] +--- + +### Details: + +- Structure prediction software often natively supports single predictions. +- Specific workflows can re-use MSA input to massively improve efficiency over naive implementation. + - Interaction screening where 1 protein is predicted in combination with many others. + - Conformation sampling where 1 system is predicted with downsampled MSA with many random seeds. + - Epitope mapping where 1 antibody-antigen system is predicted with many seeds to identify candidate binding epitope. + - Stoichiometry screen where 1 system is predicted with many candidate stoichiometries. + +This activity involves developing optimized batch workflows for structure prediction. + +### Completed: + +- [x] Add support for re-using MSAs to Galaxy Australia AlphaFold2 service. + +### In Progress: + +- [ ] Add local implementation of batch colabfoldsearch to the nfcore [proteinfold](https://nf-co.re/proteinfold/1.1.1) pipeline. +- [ ] Add mmseqs-GPU support to the nfcore [proteinfold](https://nf-co.re/proteinfold/1.1.1) pipeline. +- [ ] Add boltz interaction screening workflow to screen multiple potential partners against a protein (re-using MSA for anchor protein). +- [ ] Add option for extreme replicate sampling for AlphaFold2. + +### Future: + +- [ ] Develop Galaxy workflow to take advantage of re-using MSAs. +- [ ] Add stoichiometry screening workflow to the nfcore [proteinfold](https://nf-co.re/proteinfold/1.1.1) pipeline. \ No newline at end of file diff --git a/pages/activities/bindcraft_access.md b/pages/activities/bindcraft_access.md new file mode 100644 index 0000000..e122a3f --- /dev/null +++ b/pages/activities/bindcraft_access.md @@ -0,0 +1,31 @@ +--- +title: Community Access to BindCraft +type: activity_inprogress +contributors: [Ziad Al-Bkhetan, Thomas Litfin] +--- + +### Details + +- [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. +- BindCraft tool is available within a NextFlow [workflow](https://github.com/Australian-Structural-Biology-Computing/bindflow) to support portable deployment. + +:warning: Native BindCraft tool requires PyRosetta as a filter with non-commercial license + +### Completed: + +- [x] Wrap the BindCraft tool in a Nextflow workflow ([bindflow](https://github.com/Australian-Structural-Biology-Computing/bindflow)). +- [x] Add support for parallel execution across multiple GPUs. +- [x] Negotiate PyRosetta license for non-commercial use at NCI. +- [x] Output partial results when HPC scheduler jobs time out. + +### In Progress: + +- [ ] Install workflow at NCI. +- [ ] Release BindCraft fork without PyRosetta dependancy. +- [ ] Release BindCraft fork with open-source replacements for PyRosetta filters. + +### Future: + +- [ ] OpenOnDemand app for running BindCraft from a graphical web interface. \ No newline at end of file diff --git a/pages/activities/binder_access.md b/pages/activities/binder_access.md new file mode 100644 index 0000000..38e9c11 --- /dev/null +++ b/pages/activities/binder_access.md @@ -0,0 +1,6 @@ +--- +title: Exploring how to increase access to RFdiffusion +type: activity_inprogress +--- + +A collaborative activity bringing together members of the computational structural biology community, infrastructure providers, and the Australian BioCommons, in order to determine how to increase access to binder code (e.g. RFdiffusion) for life science researchers. diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md new file mode 100644 index 0000000..c62eb0b --- /dev/null +++ b/pages/activities/infrastructure_roadmap.md @@ -0,0 +1,26 @@ +--- +title: Infrastructure Roadmap +type: activity_inprogress +--- + +### Details: + +The infrastructure roadmap document describes the existing national landscape, identifies and prioritizes critical research bottlenecks, and proposes a national strategy to unlock the immense potential of computational structural biology for Australian researchers. + +### Completed: + +- [x] Initial draft of infrastructure roadmap. +- [x] Initial community feedback incorporated, content updated, implementation section added. +- [x] Review and updates based on feedback from co-authors and academic panel. +- [x] Review and updates based on feedback from community and BioCommons infrastructure partners. +- [x] Review and updates based on feedback from international experts. + +### In Progress: +- [ ] Addressing final review comments. + +### Future: +- [ ] Publication to Zenodo. + +### Contributors: +- Australian Structural Biology Computing Community +- Australian BioCommons and infrastructure partners \ No newline at end of file diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md new file mode 100644 index 0000000..df566db --- /dev/null +++ b/pages/activities/nci_data_collections.md @@ -0,0 +1,22 @@ +--- +title: NCI Data Collection +type: activity_inprogress +contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] +--- + +### Details + +- Structure prediction requires constructing multiple sequence alignments of homologous sequences from large reference databases. +- Different tools use different versions of the same reference databases with different naming conventions. This leads to excessive duplication and data bloat. +- Reference data are frequently updated (at differing schedules) but local copies are likely updated infrequently. +- Up-to-date reference data can dramatically improve prediction quality. + +This activity aims to create a stable release of up-to-date reference data (with DOI) to support reproducible structure prediction workflows. + +### Completed: + +- [x] Catalog latest version of reference data. +- [x] Harmonize data across different structure prediction models (AlphaFold2, AlphaFold3, Boltz, ColabFold, HelixFold3, RosettaFold-AA). + +### In Progress: +- [ ] NCI Data Collection EOI. \ No newline at end of file diff --git a/pages/activities/nci_ood_proteinfold.md b/pages/activities/nci_ood_proteinfold.md new file mode 100644 index 0000000..86b4511 --- /dev/null +++ b/pages/activities/nci_ood_proteinfold.md @@ -0,0 +1,26 @@ +--- +title: OpenOnDemand GUI ProteinFold app +type: activity_inprogress +contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] +--- + +### Details: + +- Numerous structure prediction methods are available via the command line. +- Web services with graphical interfaces are freely available with limited capacity. +- OpenOnDemand provides a simple graphical interface to HPC systems. +- Several institutional HPCs have an OpenOnDemand deployment (eg KOD @ UNSW, ARE @ NCI). + +### Completed: +- [x] Pilot app developed and hosted on Katana at UNSW. + +### In Progress +- [ ] Adapt pilot ProteinFold app for ARE at NCI. + +### Future: +- [ ] Add support for more optional settings in web form interface. + +
+KOD-proteinfold +
Screenshot from the Katana OnDemand ProteinFold app deployed at UNSW.
+
\ No newline at end of file diff --git a/pages/activities/nfcore_proteinfold.md b/pages/activities/nfcore_proteinfold.md new file mode 100644 index 0000000..e6aa8bc --- /dev/null +++ b/pages/activities/nfcore_proteinfold.md @@ -0,0 +1,30 @@ +--- +title: nf-core ProteinFold v2.0 Release +type: activity_inprogress +contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] +--- + +### Details: + +- Molecular structure prediction tools require large reference databases and varied computational infrastructure. +- Nextflow provides the tools to standardize workflows for portable and optimized deployment. +- nfcore [ProteinFold](https://nf-co.re/proteinfold/1.1.1) is a nextflow pipeline with support for numerous structure prediction tools under a unified API. +- The upcoming v2.0 release contributes significant new functionality to the pipeline. +- [Collaboration](https://www.biocommons.org.au/news/nf-core-hackathon-2025) with Barcelona Centre for Genomic Regulation ([CRG](https://www.crg.eu/)). + +### Completed + +- [x] Config optimized for efficient utilization for Gadi at NCI. +- [x] Add RosettaFold-All-Atom. +- [x] Add HelixFold3. +- [x] Add Boltz-1. +- [x] Add AlphaFold3 (BYO weights). +- [x] Add support for local MSA search for Boltz-1. +- [x] Add standardized reporting with visualisation. +- [x] Add support for quality metrics in output reporting. +- [x] Add process labels to improve efficient use of infrastructure. + +### In Progress + +- [ ] Add minituare reference databases for fast troubleshooting. +- [ ] De-duplicate reference datasets across different methods. \ No newline at end of file diff --git a/pages/activities/nfcore_proteinfold_pawsey.md b/pages/activities/nfcore_proteinfold_pawsey.md new file mode 100644 index 0000000..d6b1e35 --- /dev/null +++ b/pages/activities/nfcore_proteinfold_pawsey.md @@ -0,0 +1,24 @@ +--- +title: nf-core ProteinFold at Pawsey +type: activity_inprogress +contributors: [Sarah Beecroft, Joshua Storm Caley] +--- + +### 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: +- [x] Build AMD compatible container for AlphaFold2. +- [x] Build AMD compatible container for Boltz-1. +- [x] Build AMD compatible container for ESMFold. + +### In Progress: +- [ ] Adapt containers for compatibility with nfcore proteinfold. +- [ ] Test nfcore proteinfold workflow at Pawsey. + +### Future: +- [ ] Build AMD compatible container for Boltz-2. +- [ ] ProteinFold config optimized for Pawsey. \ No newline at end of file diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md new file mode 100644 index 0000000..f75eb31 --- /dev/null +++ b/pages/activities/protein_design_seminars.md @@ -0,0 +1,23 @@ +--- +title: Protein Design Seminar Series (2025) +type: activity_inprogress +contributors: [Rhys Grinter, Gavin Knott, Cyntia Taveneau, Josh Hardy, Kate Michie, Johan Gustafsson, Melissa Burke] +--- + + +### 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 | +|---------------|------------|--------------------|-------| +| 15 July | 12pm AEST | Rhys Grinter | Using AI protein design to design binding proteins to challenging bacterial transporters | +| 12 August | 12pm AEST | Cyntia Taveneau | Icrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors | +| 16 September | 12pm AEST | Richard Birkinshaw | Using in silico design methods to create de novo proteins that selectively modulate apoptosis | +| 7 October | 12pm AEST* | Josh Hardy | Introducing ProteinDJ: A modular and open-source framework for protein design workflows | +| 11 November | 12pm AEST* | TBC | TBC | +| *Affected by daylight savings | \ No newline at end of file diff --git a/pages/contributors.md b/pages/contributors.md new file mode 100644 index 0000000..cdca331 --- /dev/null +++ b/pages/contributors.md @@ -0,0 +1,10 @@ +--- +title: Community contributors +page_id: contributors +type: resources +--- + +The projects included here represent a joint effort by the following people at multiple Australian institutions: + +{% include contributor-tiles-all.html %} + diff --git a/pages/events.md b/pages/events.md new file mode 100644 index 0000000..3a05db8 --- /dev/null +++ b/pages/events.md @@ -0,0 +1,16 @@ +--- +title: Events +description: Announcements for relevant courses, meetings, and information about structural biology. +page_id: events +--- + + +## Upcoming events + +{% include events.html event_type="upcoming_event" truncate=true %} + + +## Past events + +{% include events.html event_type="past_event" truncate=true %} + diff --git a/pages/example_page.md b/pages/example_page.md deleted file mode 100644 index 940c6bf..0000000 --- a/pages/example_page.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -title: Example page ---- - -This page serves as an example page. - - -Keiran is adding content to the example pages - -Pushing a change with GitHub actions diff --git a/pages/external_resources.md b/pages/external_resources.md new file mode 100644 index 0000000..46e9dc8 --- /dev/null +++ b/pages/external_resources.md @@ -0,0 +1,8 @@ +--- +title: External Resources +page_id: external_resources +#datatable: true +type: resources +--- + + diff --git a/pages/guides.md b/pages/guides.md new file mode 100644 index 0000000..9029cab --- /dev/null +++ b/pages/guides.md @@ -0,0 +1,9 @@ +--- +title: How-to Guides +description: How-to Guides for the use of deep learning methods in structural biology. +page_id: guides +type: resources +datatable: true +--- + +{% include section-navigation-tiles.html type="guide"%} diff --git a/pages/join_conversation.md b/pages/join_conversation.md new file mode 100644 index 0000000..9070df1 --- /dev/null +++ b/pages/join_conversation.md @@ -0,0 +1,52 @@ +--- +title: Join the conversation +description: +page_id: join + +tiles: + - title: "Quarterly community meetings" + url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi + - title: "Events" + url: /events +--- + +If you would like to, there are multiple ways to join the conversation: + +{% include tiles-simple.html col = "2" target = "tiles" %} + +If you join the mailing list (below), you will receive community updates and automatic community meeting invitations. + +### Mailing list + +
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