diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 69932c5..1dcf30c 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -27,13 +27,13 @@ Keiran Rowell: git: keiran-rowell-unsw email: k.rowell@unsw.edu.au orcid: 0000-0001-6955-1167 - affiliation: Computational Scientist, Structural Biology Facility UNSW + affiliation: Computational Scientist, Structural Biology Facility, UNSW -Kate Michie: +Katharine Michie: git: katemichie email: k.michie@unsw.edu.au orcid: 0000-0002-2133-2237 - affiliation: Chief Scientist, Structural Biology Facility UNSW + affiliation: Chief Scientist, Structural Biology Facility, UNSW James Lingford: git: jlingford @@ -57,7 +57,7 @@ Thomas Litfin: git: tlitfin-unsw email: t.litfin@unsw.edu.au orcid: 0000-0002-4863-3865 - affiliation: Senior Research Associate, Structural Biology Facility UNSW + affiliation: Senior Research Associate, Structural Biology Facility, UNSW Ziad Al-Bkhetan: git: ziadbkh @@ -159,4 +159,18 @@ Farah Zaib Khan: Sehrish Kanwal: affiliation: Senior Research Fellow (Bioinformatics), The University of Melbourne git: skanwal - orcid: https://orcid.org/0000-0002-5044-4692 \ No newline at end of file + orcid: https://orcid.org/0000-0002-5044-4692 + +Paulyna Magaña: + affiliation: Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) + git: paulynamagana + orcid: https://orcid.org/0009-0004-1524-2966 + +Kristina Gagalova: + affiliation: Curtin University and Centre for Crop and Disease Management (CCDM), Perth, Australia + git: KristinaGagalova + orcid: https://orcid.org/0000-0002-5975-0805 + +Jennifer Fleming: + affiliation: Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) + orcid: https://orcid.org/0000-0003-4016-8740 \ No newline at end of file diff --git a/_data/events.yml b/_data/events.yml index acdda39..8cad6a1 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -8,6 +8,7 @@ # location: Cyberspace - name: BioMolecular Horizons startDate: 2024-09-22 + endDate: 2024-09-22 description: "Launch of the website at BioMolecular Horizons 2024" url: https://www.bmh2024.com/ - name: Australian Structural Biology Computing community meeting diff --git a/_data/news.yml b/_data/news.yml index ed0dc0a..1101faa 100644 --- a/_data/news.yml +++ b/_data/news.yml @@ -1,6 +1,8 @@ -- name: "Script for Alphafold output validation metrics!" - date: 2024-11-01 - description: "Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen ()" -- name: "Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)" - date: 2024-11-01 - description: "MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen ()" +- name: "View the webinar series for protein design" + date: 2025-11-11 + url: https://youtube.com/playlist?list=PL3KeWF8P6MjzKtxXLp83w78K_AGUskL0a&si=eMvuLoQzcg9sIws5 + description: "A limited series webinar from 2025 that shared strategies to get the best outcomes from protein design projects. Speakers included: Richard Birkinshaw, Rhys Grinter, Josh Hardy, Joel Mackay, and Cyntia Taveneau." +- name: "NCI Data Collection now available!" + date: 2026-02-23 + url: https://dx.doi.org/10.25914/q48c-9a86 + description: "This collection replicates key reference databases used for protein structure prediction and analysis. These resources enable NCI users to leverage deep learning models for molecular structure prediction. The datasets support AlphaFold3, AlphaFold2, Boltz, RoseTTaFold-All-Atom, ESMFold and HelixFold3 structure prediction tools." \ No newline at end of file diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 9ce69d6..33c2e5f 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -11,11 +11,11 @@ subitems: url: /contributors - title: Community library subitems: - - title: Community resources + - title: General resources url: /community_resources - title: How-to Guides url: /guides - - title: Community workflows + - title: Workflows url: /workflows - title: External resources subitems: diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 1964e0e..06fd6b0 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -312,7 +312,22 @@ URL: https://cluster.foldseek.com/ - Description: Reference data to support AI structural biology prediction models Tag: Community resource - Title: NCI Structural Biology AI Reference Collection + Title: NCI Structural Biology AI Reference Collection Type: - Reference database - URL: https://dx.doi.org/10.25914/q48c-9a86 \ No newline at end of file + URL: https://dx.doi.org/10.25914/q48c-9a86 + DOI: https://dx.doi.org/10.25914/q48c-9a86 +- Description: Online tutorial covering the principles of protein architecture and function + Tag: Community resource + Title: Foundations of protein structure tutorial + Type: + - Online tutorial + URL: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ + DOI: https://doi.org/10.6019/tol.foundations-protein-structure-t.2026.00001.1 +- Description: A limited series of webinars from 2025 that shared strategies to get the best outcomes from protein design projects. + Tag: Community resource + Title: Protein design webinar series + Type: + - Webinar series + URL: protein_design_seminars + DOI: https://doi.org/10.5281/zenodo.17626498 \ No newline at end of file diff --git a/_includes/events.html b/_includes/events.html index d557ff0..0d96c47 100644 --- a/_includes/events.html +++ b/_includes/events.html @@ -93,30 +93,7 @@

{{ event.name | escape }}

.events-category:last-child { margin-bottom: 0; } - - .category-title { - font-size: 1.3rem; - font-weight: 600; - color: #012152; - margin-bottom: 20px; - text-transform: uppercase; - letter-spacing: 0.1em; - position: relative; - padding-left: 20px; - } - - .category-title::before { - content: ''; - position: absolute; - left: 0; - top: 50%; - transform: translateY(-50%); - width: 4px; - height: 18px; - background: #012152; - border-radius: 2px; - } - + .events-list { display: grid; grid-template-columns: 1fr 1fr; diff --git a/_includes/news.html b/_includes/news.html new file mode 100644 index 0000000..75524e7 --- /dev/null +++ b/_includes/news.html @@ -0,0 +1,237 @@ +
+
+
+ {%- assign current_date = "now" | date: "%s" -%} +
+ {%- assign news = site.data.news | sort: "date" | reverse %} + {%- assign count = 0 -%} +
+ {%- for item in news -%} +
+
+
+
{{ item.date | date: "%d" | escape }}
+
{{ item.date | date: "%b" | escape }}
+
{{ item.date | date: "%Y" | escape }}
+
+
+

{{ item.name | escape }}

+

{{ item.description | markdownify }}

+
+
→
+
+
+ {%- assign count = count | plus: 1 -%} + {%- if include.limit and count == include.limit -%} + {%- break -%} + {%- endif -%} + {%- endfor -%} +
+
+
+
+ + + + +
diff --git a/_includes/resource-table-category.html b/_includes/resource-table-category.html index 68e22a1..f07dbb3 100644 --- a/_includes/resource-table-category.html +++ b/_includes/resource-table-category.html @@ -16,6 +16,7 @@ {%- endif %} Description + DOI Type @@ -35,6 +36,11 @@ {{tool.Title}} {%- endif %} {{tool.Description}} + {% if tool.DOI%} + DOI + {%- else %} + + {%- endif %} {% if tool.Type %} {%- for type in tool.Type %} diff --git a/_sass/_custom_classes.scss b/_sass/_custom_classes.scss index a6c4c8a..bbf1798 100644 --- a/_sass/_custom_classes.scss +++ b/_sass/_custom_classes.scss @@ -69,5 +69,15 @@ margin-bottom: $spacer * 3; #content { margin-bottom: 0 !important; + + // Allow long Markdown code lines to wrap instead of overflowing. + pre { + white-space: pre-wrap; + word-break: break-word; + } + + pre code { + white-space: inherit; + } } } diff --git a/index.md b/index.md index ee18fa3..a241e58 100644 --- a/index.md +++ b/index.md @@ -8,39 +8,57 @@ redirect_from: /website/ tiles: - title: "Join the mailing list, meetings etc." url: /join_conversation + - title: "Read the community infrastructure roadmap" + url: https://doi.org/10.5281/zenodo.15786982 - title: "See activities that are in progress" url: /activities - title: "Share your work with the community" url: /contributing +community_meeting: + - title: "Click to visit the rolling agenda and find out more." + url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi --- This website is a virtual meeting place and hub for all users of **computing for structural biology research in Australia**. This is a collective community effort. It can be what we make it! + ## Getting involved -{% include tiles-simple.html target = "tiles" col = "3" %} +{% include tiles-simple.html target = "tiles" col = "2" %} + + +## News + +{% include news.html limit = 2 %} + + +## Community talk series for 2026 + +Starting this year, speakers from across the structural biology community will be invited to present their work at the regular community meetings. The current plan is for there to be five of these meetings every year. + + +#### Next meeting is on May 20th + +{% include tiles-simple.html target = "community_meeting" col = "1" %} -## Protein design seminar series - watch the recordings +#### All meeting dates -| 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) | +- **11th March 2026** +- **20th May 2026** +- **29th July 2026** +- **16th September 2026** +- **4th November 2026** -## Upcoming Events -{% include events.html event_type="upcoming_event" limit=4 %} +{% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %} ## Acknowledgements -This website represents a joint effort by many people at multiple Australian institutions. +This community represents a joint effort by people at multiple Australian institutions. A list of contributors is [available here](contributors). {% include affiliation-tiles-selection.html %} diff --git a/pages/activities/ebi_module_dev.md b/pages/activities/ebi_module_dev.md new file mode 100644 index 0000000..774ff8d --- /dev/null +++ b/pages/activities/ebi_module_dev.md @@ -0,0 +1,28 @@ +--- +title: EMBL-EBI Foundations of Protein Structure module development +description: Developing the content for an online EMBL-EBI tutorial covering the principles of protein architecture and function. +type: Activity_in_progress +roadmap_category: Global-connections +contributors: [Jennifer Fleming, Kristina Gagalova, Johan Gustafsson, Michael Healy, Thomas Litfin, Paulyna Magaña, Katharine Michie] +toc: false +tiles: + - title: "View the Foundations of Protein Structure module" + url: https://www.ebi.ac.uk/training/online/courses/foundations-protein-structure/ +--- + + +{% include tiles-simple.html target = "tiles" col = "1" %} + + +## Details + +A collaboration developing the content for a `Foundations of Protein Structure` module that will be +added to the training material made available by EMBL-EBI. The development of the module is a +collaboration between members of the Australian Structural Biology Computing community, and the +team from [Protein Data Bank in Europe (PDBe)](https://www.ebi.ac.uk/pdbe/). + + +## Future + +- Development of additional modules +- Contributions from additional community members diff --git a/pages/activities/infrastructure_roadmap.md b/pages/activities/infrastructure_roadmap.md index d8f7efe..72593ee 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -7,12 +7,20 @@ roadmap: Community co-authored document roadmap_category: No-category toc: false redirect_from: /website/infrastructure_roadmap +tiles: + - title: "Read the Australian Structural Biology Deep-Learning Infrastructure Roadmap" + url: https://doi.org/10.5281/zenodo.15786982 --- -## Citation -> Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. [https://doi.org/10.5281/zenodo.15786982](https://doi.org/10.5281/zenodo.15786982) +{% include tiles-simple.html target = "tiles" col = "1" %} + + +## Citation +``` +Michie, K. A., Litfin, T., Beecroft, S. J., Collins, B., Czabotar, P., Downton, M., Doyle, M. T., Ghosal, D., Grinter, R., Knott, G. J., Samaha, G., Christiansen, J. H., & Gustafsson, O. J. R. (2025). Australian Structural Biology Deep-Learning Infrastructure Roadmap. Zenodo. https://doi.org/10.5281/zenodo.15786982 +``` ## Executive Summary from roadmap @@ -77,4 +85,4 @@ included in D3. Globe image: Clker-Free-Vector-Images, CC0, via Wikimedia Common ### Contributors - Australian Structural Biology Computing Community -- Australian BioCommons and infrastructure partners \ No newline at end of file +- Australian BioCommons and infrastructure partners diff --git a/pages/activities/nci_data_collections.md b/pages/activities/nci_data_collections.md index d27e134..fb9b765 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -7,12 +7,14 @@ roadmap_category: Shared-platform contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] toc: false redirect_from: /website/nci_data_collections +tiles: + - title: "Access the data collection at NCI" + url: https://dx.doi.org/10.25914/q48c-9a86 --- -## Availability -The data collection is currently available here: ****. -The collection has also been added to the **[community resources list](community_resources)**. +{% include tiles-simple.html target = "tiles" col = "1" %} + ## Details @@ -23,7 +25,8 @@ The collection has also been added to the **[community resources list](community This activity aims to create a stable release of up-to-date reference data (with DOI) to support reproducible structure prediction workflows. -### Completed + +## Completed - Catalog latest version of reference data. - Harmonize data across different structure prediction models (AlphaFold2, AlphaFold3, Boltz, ColabFold, HelixFold3, RosettaFold-AA). diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index 71f7353..6ab40c2 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -7,16 +7,21 @@ roadmap_category: Training contributors: [Rhys Grinter, Gavin Knott, Cyntia Taveneau, Josh Hardy, Joel Mackay, Kate Michie, Johan Gustafsson, Melissa Burke] toc: false redirect_from: /website/protein_design_seminars +tiles: + - title: "View the 2025 Protein Design Seminar Series" + url: https://youtube.com/playlist?list=PL3KeWF8P6MjzKtxXLp83w78K_AGUskL0a&si=eMvuLoQzcg9sIws5 --- +{% include tiles-simple.html target = "tiles" col = "1" %} + + ## Details - Computational protein design can produce synthetic proteins that disrupt the function of a target protein. - Australian community members are actively using protein design technology to solve biological problems. - Community members will host a monthly seminar series to share knowledge on protein design strategies to get the best outcomes from protein design projects. - Registration is **[available here](https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator)**. | Date | Time | Speaker(s) | Topic | Recording | Presentation | |---------------|------------|--------------------|-------|-----------|----------| diff --git a/pages/join_conversation.md b/pages/join_conversation.md index bfbaf79..9395344 100644 --- a/pages/join_conversation.md +++ b/pages/join_conversation.md @@ -1,28 +1,26 @@ --- -title: Join the conversation +title: Ways to join the conversation description: page_id: join toc: false redirect_from: /website/join_conversation tiles: - - title: "Attend the regular community meetings" + - title: "View the rolling agenda for the community meetings" url: https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi - - title: "Attend events" + - title: "View the events page" url: /events - - title: "Join the mailing list" - url: /join_conversation#mailing-list --- +If you would like to, there are multiple ways to join the conversation. -### Ways to join -If you would like to, there are multiple ways to join the conversation. +### Attend the regular community meetings and other events -{% include tiles-simple.html col = "3" target = "tiles" %} +{% include tiles-simple.html col = "2" target = "tiles" %} -### Mailing list +### Join the mailing list If you join the mailing list (subscribe below), you will receive community updates and notifications, including information