diff --git a/Gemfile b/Gemfile index 47909af..6624e0d 100644 --- a/Gemfile +++ b/Gemfile @@ -1,5 +1,7 @@ source "https://rubygems.org" +gem "openssl", "~> 3.3.1" + group :jekyll_plugins do gem "github-pages" end diff --git a/_config.yml b/_config.yml index 2dfa4b8..80b0a21 100644 --- a/_config.yml +++ b/_config.yml @@ -55,9 +55,9 @@ theme_variables: # toc: # min_headings: 2 # headings: 'h2' - # topnav: + topnav: # theme: light - # brand_logo: assets/img/main_logo.svg + brand_logo: assets/img/aus-struct-bio-computing-2.png # github: true # twitter: false # theme_color: 0d6efd diff --git a/_data/events.yml b/_data/events.yml index 6ff9a35..4a7634a 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -70,6 +70,12 @@ 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: 51st Lorne Conference on Protein Structure and Function + startDate: 2026-02-08 + endDate: 2026-02-12 + description: "Click to visit the conference website." + url: https://www.lorneproteins.org/ + location: Online - name: ABACBS 2025 workshop startDate: 2025-11-27 endDate: 2025-11-27 diff --git a/_data/footer.yml b/_data/footer.yml index c4dd028..5c86315 100644 --- a/_data/footer.yml +++ b/_data/footer.yml @@ -1,4 +1,4 @@ -copyright: A collaborative effort by the Australian Structural Biology community. All rights are reserved by the respective contributors. +copyright: A collaborative effort by the Australian Structural Biology Computing community. All rights are reserved by the respective contributors. #extra_line: #columns: # - type: image diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 1c5965c..32f377f 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -3,29 +3,29 @@ subitems: url: /index - title: Join the conversation url: /join_conversation - - title: Activities - url: /activities - - title: How-to Guides - url: /guides - - title: External resources - subitems: - - 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: Activities + url: /activities - title: Contributors url: /contributors + - title: Community library + subitems: + - title: How-to Guides + url: /guides + - title: Community workflows + url: /workflows + - title: External resources + subitems: + - title: Structure Prediction + url: /structure_prediction + - title: Protein Design + url: /protein_design + - title: Protein Search + url: /protein_search + - title: Molecular Dynamics + url: /molecular_dynamics + - title: Infrastructure + url: /infrastructure - title: Events url: /events - - title: News - url: /news diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 776894d..e49304c 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -1,261 +1,312 @@ -- Description: Access a full version of AlphaFold2 supported by the Australian Biocommons +- Description: Free AlphaFold2 service supported by the Australian Biocommons + Tag: Structure Prediction Title: Australian AlphaFold Service Type: - - Webservers and computing resources + - Service URL: https://www.biocommons.org.au/alphafold -- Description: Free access to a high-performance computing network through a simple - web interface for Australian Researchers - Title: Galaxy Australia - Type: - - Webservers and computing resources - URL: https://usegalaxy.org.au -- Description: Structure prediction notebooks available to run for free on Google - Colab platform +- Description: Free structure prediction notebooks available to run on Google Colab + platform + Tag: Structure Prediction Title: ColabFold Notebooks Type: - - Webservers and computing resources + - Service URL: https://github.com/sokrypton/ColabFold?tab=readme-ov-file#making-protein-folding-accessible-to-all-via-google-colab -- Description: Multiple Structure Alignment in a browser +- Description: Structure Alignment in a browser + Tag: Search Title: FoldSeek web server Type: - - Webservers and computing resources + - Service URL: https://search.foldseek.com/ - Description: Freemium service for deep learning structural biology software + Tag: Structure Prediction Title: Tamarind Bio Type: - - Webservers and computing resources + - Service URL: https://www.tamarind.bio/ - Description: Freemium service for deep learning structural biology software + Tag: Protein Design + Title: Tamarind Bio + Type: + - Service + URL: https://www.tamarind.bio/ +- Description: Freemium service for deep learning structural biology software + Tag: Structure Prediction Title: NeuroSnap Type: - - Webservers and computing resources + - Service URL: https://neurosnap.ai/ -- Description: AlphaFold3 provided by Google's webserver to their compute infrastructure. - NON-COMMERICAL USE! +- Description: Freemium service for deep learning structural biology software + Tag: Protein Design + Title: NeuroSnap + Type: + - Service + URL: https://neurosnap.ai/ +- Description: Free Google service to run AlphaFold3. NON-COMMERICAL USE! + Tag: Structure Prediction Title: AlphaFold3 Server Type: - - Webservers and computing resources + - Service URL: https://alphafoldserver.com/about - Description: Peak academic Australian Research Computing Facility + Tag: Infrastructure Title: National Computing Infrastructure Type: - - Webservers and computing resources + - Infrastructure URL: https://nci.org.au/users/how-access-nci - Description: Peak academic Australian Research Computing Facility + Tag: Infrastructure Title: Pawsey Supercomputing Centre Type: - - Webservers and computing resources + - Infrastructure URL: https://pawsey.org.au/support/ -- Description: 'Curated search list of computational biology tools around the world ' - Title: BioTools - Type: - - Webservers and computing resources - URL: https://bio.tools/ -- Description: NVIDIA web server and API for running protein design and structure - prediction software (e.g. RFDiffusion, ESMFold, etc.) - Title: NVIDIA Biology - Type: - - Webservers and computing resources - URL: https://build.nvidia.com/explore/biology?ncid=em-prod-179751 -- Description: The best way to get up to competency with using an interpreting AlphaFold. - Should be done by all grad students using AF +- Description: Australian BioCommons Leadership Share (ABLeS) + Tag: Infrastructure + Title: ABLeS + Type: + - Infrastructure + URL: https://www.biocommons.org.au/ables +- Description: Free access to a high-performance computing network through a simple + web interface for Australian Researchers + Tag: Infrastructure + Title: Galaxy Australia + Type: + - Infrastructure + URL: https://usegalaxy.org.au +- Description: EBI Guide to using AlphaFold and interpreting model outputs + Tag: Structure Prediction Title: EMBL-EBI AlphaFold Guide Type: - - Computational structural bio guides and tutorials + - Technical Guide URL: https://www.ebi.ac.uk/training/online/courses/alphafold/ -- Description: A visual walkthrough of the AlphaFold3 architecture, with more details - and diagrams than you were probably looking for. +- Description: A visual walkthrough of the AlphaFold3 architecture + Tag: Structure Prediction Title: AlphaFold3 explainer Type: - - Computational structural bio guides and tutorials + - Technical Guide URL: https://elanapearl.github.io/blog/2024/the-illustrated-alphafold/ - Description: Lists state-of-the-art and emerging tools for Biomolecular Structure Prediction. + Tag: Structure Prediction Title: Biomolecular Structure Prediction Tools Type: - - Computational structural bio guides and tutorials + - Tool Registry URL: https://abeebyekeen.com/biomodes-biomolecular-structure-prediction/ -- Description: User guide for running MMseqs from the command line - Title: MMseqs2 tutorial - Type: - - Computational structural bio guides and tutorials - URL: https://github.com/soedinglab/MMseqs2/wiki/Tutorials -- Description: User guide for running Hiden Markov Models of protein sequences on - the command line - Title: HH-suite tutorial - Type: - - Computational structural bio guides and tutorials - URL: https://github.com/soedinglab/hh-suite/wiki -- Description: User guide for running HMMER on the command line - Title: HMMER tutorial - Type: - - Computational structural bio guides and tutorials - URL: http://hmmer.org/documentation.html -- Description: Walkthrough guide on running RFDiffusion - Title: RFDiffusion - Type: - - Computational structural bio guides and tutorials - URL: https://github.com/RosettaCommons/RFdiffusion -- Description: User guide on protein design with Rosetta - Title: Rosetta tutorial - Type: - - Computational structural bio guides and tutorials - URL: https://docs.rosettacommons.org/docs/latest/Home -- Description: Collection of how-to guides for protein design - Title: Pyrosetta tutorials - Type: - - Computational structural bio guides and tutorials - URL: https://github.com/ProteinDesignLab/protein-design-tutorials -- Description: Google Colab notebooks for running protein design - Title: ColabDesign notebooks - Type: - - Computational structural bio guides and tutorials - URL: https://github.com/sokrypton/ColabDesign +- Description: Lists state-of-the-art and emerging tools for Biomolecular Structure + Prediction. + Tag: Protein Design + Title: Biomolecular Structure Prediction Tools + Type: + - Tool Registry + URL: https://abeebyekeen.com/biomodes-biomolecular-structure-prediction/ +- Description: A collection of software for protein structure prediction and design, + with a focus on new deep learning and transformer based tools. + Tag: Structure Prediction + Title: Awesome Protein Structure Prediction and Design Software List + Type: + - Tool Registry + URL: https://github.com/pansapiens/awesome-protein-design-software +- Description: A collection of software for protein structure prediction and design, + with a focus on new deep learning and transformer based tools. + Tag: Protein Design + Title: Awesome Protein Structure Prediction and Design Software List + Type: + - Tool Registry + URL: https://github.com/pansapiens/awesome-protein-design-software - Description: Molecular Dynamics simulation tutorials + Tag: Molecular Dynamics Title: GROMACS tutorials Type: - - Computational structural bio guides and tutorials + - Tutorial URL: http://www.mdtutorials.com/gmx/ - Description: Molecular Dynamics simulation tutorials + Tag: Molecular Dynamics Title: GROMACS tutorials Type: - - Computational structural bio guides and tutorials + - Tutorial URL: https://gromacstutorials.github.io/ - Description: Molecular Dynamics simulation tutorials + Tag: Molecular Dynamics Title: LAMMPS tutorials Type: - - Computational structural bio guides and tutorials + - Tutorial URL: https://lammpstutorials.github.io/ - Description: Molecular Dynamics simulation tutorials + Tag: Molecular Dynamics Title: Amber tutorial Type: - - Computational structural bio guides and tutorials + - Tutorial URL: https://ambermd.org/tutorials/ -- Description: Short how-to guide on using BLAST from the command line - Title: BLAST tutorial - Type: - - Computational structural bio guides and tutorials - URL: https://docs.tinybio.cloud/docs/blast-tutorial -- Description: Three short tutorials for running ColabFold - Title: ColabFold tutorial - Type: - - Computational structural bio guides and tutorials - URL: https://protocolexchange.researchsquare.com/article/pex-2490/v1 - Description: Covers basics of ssh and jupyter notebooks on a HPC + Tag: Structure Prediction Title: Running ColabFold notebook on a HPC Type: - - Computational structural bio guides and tutorials + - Tutorial URL: https://www.jameslingford.com/blog/colabfold-hpc-ssh-howto/ - Description: Protein visualisation guides for UCSF ChimeraX + Tag: Visualization Title: ChimeraX recipes Type: - - Protein viz guides and tutorials + - Tutorial URL: https://rbvi.github.io/chimerax-recipes/ - Description: ChimeraX how-to + Tag: Visualization Title: ChimeraX cavity visualisation Type: - - Protein viz guides and tutorials + - Tutorial URL: https://www.jameslingford.com/blog/chimerax-cavity-surfaces/ - Description: ChimeraX how-to + Tag: Visualization Title: ChimeraX outline selected area Type: - - Protein viz guides and tutorials + - Tutorial URL: https://www.jameslingford.com/blog/chimerax-outlines/ - Description: ~1hr talks by method developers on recent breakthroughs in protein modelling + Tag: Structure Prediction Title: Boston Protein Design and Modeling Club Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/@bpdmc -- Description: 100 second videos on how to use various protein tools. Guides are with - their clean proprietary interface +- Description: ~1hr talks by method developers on recent breakthroughs in protein + modelling + Tag: Protein Design + Title: Boston Protein Design and Modeling Club + Type: + - Presentation + URL: https://www.youtube.com/@bpdmc +- Description: 100 second videos on how to use various protein tools. + Tag: Protein Design Title: NeuroSnap protein design videos Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/@NeurosnapInc/videos - Description: Talks focused on CryoEM but also computational structural biology and protein design + Tag: CryoEM Title: Structural Biology Grid Consortium Talk Series Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/@SBGridTV/videos - Description: Overview of the AlphaFold pipeline by the New England Journal of Medicine - Title: AlphaFold 5 minute explainer - Medical Journal + Tag: Structure Prediction + Title: AlphaFold 5 minute explainer Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/watch?v=7q8Uw3rmXyE -- Description: Detailed and lucid talk on understanding the machine learning concepts - behind AI protein structure prediction methods - Title: ' AlphaFold2, OpenFold, Protein Language Models and Beyond | Nazim Bouatta ' +- Description: Detailed description of the machine learning concepts behind AI protein + structure prediction methods + Tag: Structure Prediction + Title: AlphaFold2, OpenFold, Protein Language Models and Beyond Type: - - YouTube talks and tutorials + - Presentation URL: https://youtu.be/ON1ltprZKPo?si=WkZ3Y8eZfVusWUvo - Description: Blender tutorials for protein animations + Tag: Visualization Title: Brady Johnston Blender tutorials Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/@BradyJohnston - Description: Blender tutorials for protein animations + Tag: Visualization Title: Luminous Lab Blender tutorials Type: - - YouTube talks and tutorials + - Presentation URL: https://www.youtube.com/@LuminousLab - Description: Playlist of tutorials on how to use ChimeraX with command lines + Tag: Visualization Title: ChimeraX tutorials Type: - - YouTube talks and tutorials + - Presentation URL: https://youtube.com/playlist?list=PL4eF1KHNgDfIYSKCS3_S0PTRYtYTV9Myi&si=gBWxBbzifFmF32ln - Description: Talks focused on molecular dynamics simulations and computational chemistry + Tag: Molecular Dynamics Title: European Centre of Excellence for Computational Biomolecular Research Type: - - YouTube talks and tutorials + - Presentation URL: https://youtube.com/@bioexcelcoe?si=5jSzsDzpBKwGQThr - Description: European community for structural bioinformatics research + Tag: Structure Prediction + Title: ELIXIR 3D-BioInfo + Type: + - Community + URL: https://elixir-europe.org/communities/3d-bioinfo +- Description: European community for structural bioinformatics research + Tag: Protein Design Title: ELIXIR 3D-BioInfo Type: - - Online communities + - Community URL: https://elixir-europe.org/communities/3d-bioinfo - Description: A discord channel for asking questions related to the various Colab documents that are available + Tag: Structure Prediction Title: ColabBio Discord Type: - - Online communities + - Community + URL: https://discord.gg/M8BCm5WV +- Description: A discord channel for asking questions related to the various Colab + documents that are available + Tag: Protein Design + Title: ColabBio Discord + Type: + - Community URL: https://discord.gg/M8BCm5WV - Description: A slack channel to discuss developments of Boltz + Tag: Structure Prediction Title: Boltz Slack Type: - - Online communities + - Community URL: https://join.slack.com/t/boltz-community/shared_invite/zt-34qg8uink-V1LGdRRUf3avAUVaRvv93w -- Description: 'Social media posting platform ' - Title: Bluesky - Type: - - Online communities - URL: https://bsky.app/ -- Description: 'Social media posting platform ' - Title: Mastodon +- Description: '200 million AF2 predicted protein structures, with AlphaMissense etc + included ' + Tag: Structure Prediction + Title: AlphaFold Protein Structure database Type: - - Online communities - URL: https://joinmastodon.org/ + - Reference database + URL: https://alphafold.ebi.ac.uk/ - Description: '200 million AF2 predicted protein structures, with AlphaMissense etc included ' + Tag: Search Title: AlphaFold Protein Structure database Type: - - Reference databases + - Reference database URL: https://alphafold.ebi.ac.uk/ - Description: 770 million ESMFold predicted structures -- much faster calculations as the don't relying on explicity co-evolutionary multiple sequence alignments + Tag: Structure Prediction Title: Evolutionary Scale Modelling Atlas of structures Type: - - Reference databases + - Reference database URL: https://esmatlas.com/ +- Description: 770 million ESMFold predicted structures -- much faster calculations + as the don't relying on explicity co-evolutionary multiple sequence alignments + Tag: Search + Title: Evolutionary Scale Modelling Atlas of structures + Type: + - Reference database + URL: https://esmatlas.com/ +- Description: Database of UniProt and Metagenome predicted structures clustered with + foldseek + Tag: Structure Prediction + Title: AFESM Clusters Database + Type: + - Reference database + URL: https://afesm.foldseek.com/ - Description: Database of UniProt and Metagenome predicted structures clustered with foldseek + Tag: Search Title: AFESM Clusters Database Type: - - Reference databases + - Reference database URL: https://afesm.foldseek.com/ - Description: Database of UniProt predicted structures clustered with foldseek + Tag: Structure Prediction + Title: AFDB Clusters Database + Type: + - Reference database + URL: https://cluster.foldseek.com/ +- Description: Database of UniProt predicted structures clustered with foldseek + Tag: Search Title: AFDB Clusters Database Type: - - Reference databases + - Reference database URL: https://cluster.foldseek.com/ diff --git a/_includes/events.html b/_includes/events.html index afff52b..d557ff0 100644 --- a/_includes/events.html +++ b/_includes/events.html @@ -53,14 +53,6 @@

{{ event.name | escape }}

box-sizing: border-box; } - body { - font-family: 'Inter', -apple-system, BlinkMacSystemFont, sans-serif; - background: #ffffff; - color: #1a1a1a; - line-height: 1.4; - min-height: 100vh; - } - .events{ display: block; }; diff --git a/_includes/resource-table-category-new.html b/_includes/resource-table-category-new.html new file mode 100644 index 0000000..0c6adfe --- /dev/null +++ b/_includes/resource-table-category-new.html @@ -0,0 +1,42 @@ +{%- 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 %} + + {% if tool.URL %} + + {%- else %} + + {%- endif %} + + + + {%- endfor %} + +
ResourceDescriptionType
{{tool.Title}}{{tool.Title}}{{tool.Description}} + {% if tool.Type %} + {%- for type in tool.Type %} + + {%- endfor %} + {%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/resource-table-category.html b/_includes/resource-table-category.html index f9484b1..68e22a1 100644 --- a/_includes/resource-table-category.html +++ b/_includes/resource-table-category.html @@ -16,12 +16,13 @@ {%- endif %} Description + Type {%- for tool in tools %} {% assign found = false %} - {% for desc in tool.Type %} + {% for desc in tool.Tag %} {% if desc == include.category %} {% assign found = true %} {% endif %} @@ -33,17 +34,14 @@ {%- else %} {{tool.Title}} {%- endif %} - {{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 %} -
+ {{tool.Description}} + + {% if tool.Type %} + {%- for type in tool.Type %} + + {%- endfor %} {%- endif %} diff --git a/_includes/section-navigation-tiles_mod.html b/_includes/section-navigation-tiles_mod.html index b1003d8..58d72e9 100644 --- a/_includes/section-navigation-tiles_mod.html +++ b/_includes/section-navigation-tiles_mod.html @@ -11,8 +11,11 @@ {%- for page in pages_to_add_as_tiles -%} {%- if page.type == include.type %} -
+
+ {%- if page.roadmap_category -%} +
{{ page.roadmap_category }}
+ {%- endif -%}

{{ page.title }}

{% if page.description %}

{{ page.description }}

@@ -28,68 +31,81 @@

{{ page.title }}

\ No newline at end of file diff --git a/_includes/tiles-simple.html b/_includes/tiles-simple.html index e9ef7db..4c521c1 100644 --- a/_includes/tiles-simple.html +++ b/_includes/tiles-simple.html @@ -5,13 +5,13 @@ {%- endif %}
-
+
{%- for item in tiles %} {%- if item.title %}
-

{{ item.title }}

+

{{ item.title }}

 @@ -26,30 +26,32 @@ .simple-tile-link { text-decoration: none; - color: inherit; + color: #012152; display: flex; } .simple-tile-item { - border: 1px solid #e0e0e0; border-radius: 12px; padding: 25px; transition: all 0.3s ease; - background: #012152;; + background: #f0f3fa; width: 100%; display: flex; flex-direction: column; justify-content: space-between; + color: #012152; } .simple-tile-item:hover { transform: translateY(-4px); box-shadow: 0 8px 25px rgba(0,0,0,0.1); border-color: #012152; + background: #012152; + color: #fff; } .simple-tile-title { - color: #ffffff; + color: inherit; font-weight: 400; margin-top: 0px; margin-bottom: 0px; diff --git a/_sass/_bootstrap_variables.scss b/_sass/_bootstrap_variables.scss index 56055fc..786bc07 100644 --- a/_sass/_bootstrap_variables.scss +++ b/_sass/_bootstrap_variables.scss @@ -1,11 +1,16 @@ /*-----Theme colors-----*/ $primary: #012152; $secondary: #6c757d; -$light: #f8f9fa; +$light: #f0f3fa; $dark: #212529; +$white: #fff; /*-----Custom values for Bootstrap variables-----*/ $link-decoration: none; $navbar-light-hover-color: $light; +$body-bg: $light; +$card-bg: $white; +$border-radius: 20px; +$link-color: blue; // 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 c0afd33..a6c4c8a 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -60,4 +60,14 @@ color: $primary; padding: 7px 11px; } -} \ No newline at end of file +} + +#main { + background-color: $white; + border-radius: $border-radius; + padding: $spacer * 3; + margin-bottom: $spacer * 3; + #content { + margin-bottom: 0 !important; + } +} diff --git a/_sass/_custom_variables.scss b/_sass/_custom_variables.scss index 541e50e..ed38b4e 100644 --- a/_sass/_custom_variables.scss +++ b/_sass/_custom_variables.scss @@ -5,7 +5,8 @@ $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: $primary; \ No newline at end of file + +$nav-card-bg: $light; +$nav-card-color: $primary; +$nav-card-bg-hover: $primary; +$nav-card-color-hover: $white; \ No newline at end of file diff --git a/assets/img/aus-struct-bio-computing-2.png b/assets/img/aus-struct-bio-computing-2.png new file mode 100644 index 0000000..f5683dc Binary files /dev/null and b/assets/img/aus-struct-bio-computing-2.png differ diff --git a/index.md b/index.md index 1bff306..ee18fa3 100644 --- a/index.md +++ b/index.md @@ -6,22 +6,32 @@ toc: false #sidebar: true redirect_from: /website/ tiles: - - title: "Join the conversation" + - title: "Join the mailing list, meetings etc." url: /join_conversation - - title: "Read the Australian 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" + url: /contributing --- 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 = "2" %} +## Getting involved -## Protein design seminar series +{% include tiles-simple.html target = "tiles" col = "3" %} + + +## Protein design seminar series - watch the recordings + +| 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 video-list-columns.html - video_id="tKqH8WlkIX4" - list="The protein design seminar series included 5 presentations from Australian structural biologists utilising the latest developments in de novo protein design to develop protein binders to various therapeutic targets.|Watch Prof Joel Mackay share a recent project describing baby steps in the AI-guided design of proteins to modulate gene transcription.|The full series schedule, seminar registration link and recordings of completed seminars are available here.|" %} ## Upcoming Events diff --git a/pages/activities.md b/pages/activities.md index 5fa5670..2bbb711 100644 --- a/pages/activities.md +++ b/pages/activities.md @@ -6,55 +6,42 @@ toc: false redirect_from: /website/activities --- -
-
-

Roadmap deliverable 1: An Australian Structural Biology community space capable of fostering collaboration and knowledge sharing

+Community activities are organised based on the four major deliverables described in the [Australian Structural Biology Deep-Learning Infrastructure Roadmap](/infrastructure_roadmap). + +
+
+

1. Community space: deliverable 1 is an Australian Structural Biology community space (e.g. this website) that is capable of fostering collaboration and knowledge sharing.

-
-
-

Roadmap deliverable 2: A computational structural biology training program, developed in conjunction with the community

+ +
+
+

2. Training program: deliverable 2 is a computational structural biology training program, developed in conjunction with the community.

-
-
-

Roadmap deliverable 3: A shared platform, or platforms, for computational structural biology

+ +
+
+

3. Shared platform(s): deliverable 3 is a shared platform, or platforms, for computational structural biology.

-
-
-

Roadmap deliverable 4: Alignment, adoption and contribution to global best-practice efforts

+ +
+
+

4. Global connections: deliverable 4 is the alignment, adoption and contribution to global best-practice efforts.

+ ## In progress -{% include section-navigation-tiles_mod.html type ="activity_in_progress" %} +{% include section-navigation-tiles_mod.html type ="Activity_in_progress" %} ## Completed -{% include section-navigation-tiles_mod.html type ="activity_completed" %} +{% include section-navigation-tiles_mod.html type ="Completed_activity" %} diff --git a/pages/activities/abacbs_workshop.md b/pages/activities/abacbs_workshop.md index 363de8b..b421807 100644 --- a/pages/activities/abacbs_workshop.md +++ b/pages/activities/abacbs_workshop.md @@ -1,9 +1,9 @@ --- title: ABACBS 2025 workshop description: Leveraging peak Australian compute to enable workflows for predictive structural biology at scale -type: activity_in_progress +type: Completed_activity roadmap: A computational structural biology training program (Roadmap D2) -roadmap_category: D2 +roadmap_category: Training contributors: [Johan Gustafsson, Ziad Al-Bkhetan, Thomas Litfin, Sarah Beecroft, Georgie Samaha, Mitchell O'Brien, Farah Zaib Khan, Sehrish Kanwal] toc: false redirect_from: /website/abacbs25_workshop diff --git a/pages/activities/batch_structure_prediction.md b/pages/activities/batch_structure_prediction.md index d52acf1..2e9c437 100644 --- a/pages/activities/batch_structure_prediction.md +++ b/pages/activities/batch_structure_prediction.md @@ -1,9 +1,9 @@ --- title: Batch Structure Prediction Workflows description: Developing optimized batch workflows for structure prediction. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3A) -roadmap_category: D3 +roadmap_category: Shared-platform contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Cameron Hyde, Thomas Litfin] toc: false redirect_from: /website/batch_structure_prediction diff --git a/pages/activities/bindcraft_access.md b/pages/activities/bindcraft_access.md index c077694..8f8718c 100644 --- a/pages/activities/bindcraft_access.md +++ b/pages/activities/bindcraft_access.md @@ -1,9 +1,9 @@ --- title: Community Access to BindCraft description: Increasing community access to an end-to-end solution for protein binder design. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3Ac) -roadmap_category: D3 +roadmap_category: Shared-platform contributors: [Ziad Al-Bkhetan, Thomas Litfin] toc: false redirect_from: /website/bindcraft_access diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md index bc61b5d..d8f7efe 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -1,10 +1,10 @@ --- title: Infrastructure Roadmap description: Draft and publish an Australian infrastructure roadmap for addressing computational challenges facing structural biology. -type: activity_completed +type: Completed_activity contributors: [Kate Michie, Thomas Litfin, Sarah Beecroft, Brett Collins, Matthew Downton, Rhys Grinter, Gavin Knott, Johan Gustafsson, Charlie Bond, Joel Mackay, Michael Parker, Craig Morton, Begoña Heras, Fiona Whelan] roadmap: Community co-authored document -roadmap_category: none +roadmap_category: No-category toc: false redirect_from: /website/infrastructure_roadmap --- diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md index ec2c51b..7232557 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -1,9 +1,9 @@ --- title: NCI Data Collection description: Create a stable release of up-to-date reference data (with DOI) at the NCI. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3F) -roadmap_category: D3 +roadmap_category: Shared-platform contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] toc: false redirect_from: /website/nci_data_collections diff --git a/pages/activities/nci_ood_proteinfold.md b/pages/activities/nci_ood_proteinfold.md index 8c8238d..d76aea6 100644 --- a/pages/activities/nci_ood_proteinfold.md +++ b/pages/activities/nci_ood_proteinfold.md @@ -1,9 +1,9 @@ --- title: OpenOnDemand GUI ProteinFold app description: Create and adapt a pilot ProteinFold app for OpenOnDemand. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3Ac) -roadmap_category: D3 +roadmap_category: Shared-platform contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] toc: false redirect_from: /website/nci_ood_proteinfold diff --git a/pages/activities/nfcore_proteinfold.md b/pages/activities/nfcore_proteinfold.md index f7c8c11..9c7fe0b 100644 --- a/pages/activities/nfcore_proteinfold.md +++ b/pages/activities/nfcore_proteinfold.md @@ -1,9 +1,9 @@ --- title: nf-core ProteinFold v2.0 Release description: Contribute towards, and locally deploy, v2.0 of nf-core ProteinFold workflow. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3A) -roadmap_category: D3 +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 diff --git a/pages/activities/nfcore_proteinfold_pawsey.md b/pages/activities/nfcore_proteinfold_pawsey.md index 633513d..6318f4f 100644 --- a/pages/activities/nfcore_proteinfold_pawsey.md +++ b/pages/activities/nfcore_proteinfold_pawsey.md @@ -1,9 +1,9 @@ --- title: nf-core ProteinFold at Pawsey description: Deploy nf-core ProteinFold workflow at Pawsey Supercomputing Research Centre. -type: activity_in_progress +type: Activity_in_progress roadmap: A shared platform, or platforms (Roadmap D3Ab) -roadmap_category: D3 +roadmap_category: Shared-platform contributors: [Sarah Beecroft, Joshua Storm Caley] toc: false redirect_from: /website/nfcore_proteinfold_pawsey diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index 45caeff..71f7353 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -1,9 +1,9 @@ --- title: Protein Design Seminar Series (2025) description: Community members will host a monthly seminar series to share knowledge on protein design strategies. -type: activity_completed +type: Completed_activity roadmap: A computational structural biology training program (Roadmap D2) -roadmap_category: D2 +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 diff --git a/pages/guides.md b/pages/guides.md index 9c70bc1..c05c80d 100644 --- a/pages/guides.md +++ b/pages/guides.md @@ -2,11 +2,10 @@ title: How-to Guides description: How-to Guides for the use of deep learning methods in structural biology. page_id: guides -toc: false #type: resources datatable: true toc: false redirect_from: /website/guides --- -{% include section-navigation-tiles.html type="guide"%} +{% include section-navigation-tiles.html type="Guide"%} diff --git a/pages/guides/protein_struct_pred/AlphaFold2_how_to_guide.md b/pages/guides/protein_struct_pred/AlphaFold2_how_to_guide.md index fb91c74..896d47f 100644 --- a/pages/guides/protein_struct_pred/AlphaFold2_how_to_guide.md +++ b/pages/guides/protein_struct_pred/AlphaFold2_how_to_guide.md @@ -1,6 +1,6 @@ --- title: AlphaFold2 How-to Guide -type: guide +type: Guide contributors: [Michael Healy] description: Practical guide for working with real AlphaFold data affiliations: [University of Queensland] diff --git a/pages/guides/protein_struct_pred/best-practices-alphafold.md b/pages/guides/protein_struct_pred/best-practices-alphafold.md index 6b9e3da..82b7b11 100644 --- a/pages/guides/protein_struct_pred/best-practices-alphafold.md +++ b/pages/guides/protein_struct_pred/best-practices-alphafold.md @@ -1,7 +1,7 @@ --- title: Best practices for presenting and sharing AlphaFold models in a paper description: Have you recently started using AlphaFold and want to include its structural predictions in your paper, but don't know the best way to do so? In this short guide, we clarify what you should include so that your work is clear and reproducible for the reader. -type: guide +type: Guide contributors: [James Lingford] affiliations: [Monash University] toc: true diff --git a/pages/join_conversation.md b/pages/join_conversation.md index 838c088..bfbaf79 100644 --- a/pages/join_conversation.md +++ b/pages/join_conversation.md @@ -6,22 +6,28 @@ toc: false redirect_from: /website/join_conversation tiles: - - title: "Quarterly community meetings" + - title: "Attend the regular community meetings" url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi - - title: "Events" + - title: "Attend events" 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: -{% include tiles-simple.html col = "2" target = "tiles" %} +### Ways to join -
+If you would like to, there are multiple ways to join the conversation. + +{% include tiles-simple.html col = "3" target = "tiles" %} -If you join the mailing list (below), you will receive community updates and automatic community meeting invitations. ### Mailing list +If you join the mailing list (subscribe below), you will receive +community updates and notifications, including information +about scheduled community meetings and events. +