From 4c635bbbdd3aa9c30cead32d8b6f602ddde53ecc Mon Sep 17 00:00:00 2001 From: tlitfin Date: Mon, 13 Oct 2025 14:55:48 +1100 Subject: [PATCH 1/5] update landing page with latest seminar --- index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/index.md b/index.md index 858fde3..3d8ddad 100644 --- a/index.md +++ b/index.md @@ -20,8 +20,8 @@ This website is a virtual meeting place and hub for all users of **computing for ## Protein design seminar series {% include video-list-columns.html - video_id="9-3sHy1ybpE" - list="The protein design seminar series includes 6 presentations from Australian structural biologists utilising the latest developments in de novo protein design to develop protein binders to various therapeutic targets.|Watch Dr Richard Birkinshaw share a recent project using in silico design methods to create de novo proteins that selectively modulate apoptosis.|The full series schedule, seminar registration link and recordings of completed seminars are available here.|The next event in the series will be on October 7th and will describe ProteinDJ: A modular and open-source framework for protein design workflows" %} + video_id="xwvF62HxaF0" + list="The protein design seminar series includes 5 presentations from Australian structural biologists utilising the latest developments in de novo protein design to develop protein binders to various therapeutic targets.|Watch Dr Josh Hardy share a recent project describing the development of ProteinDJ: A modular and open-source framework for protein design workflows.|The full series schedule, seminar registration link and recordings of completed seminars are available here.|The final event in the series will be on November 11th and will describe baby steps in the AI-guided design of proteins to modulate gene transcription." %} ## Upcoming Events From 5010333d538257789b253f8c73b5f9c8f581967f Mon Sep 17 00:00:00 2001 From: tlitfin Date: Mon, 13 Oct 2025 14:56:06 +1100 Subject: [PATCH 2/5] update seminar schedule --- _data/events.yml | 8 +------- pages/activities/protein_design_seminars.md | 5 ++--- 2 files changed, 3 insertions(+), 10 deletions(-) diff --git a/_data/events.yml b/_data/events.yml index d133c91..c6e10bd 100644 --- a/_data/events.yml +++ b/_data/events.yml @@ -61,7 +61,7 @@ - name: Protein design seminar series startDate: 2025-11-11 endDate: 2025-11-11 - description: "**Topic:** TBD" + description: "**Topic:** Baby steps in the AI-guided design of proteins to module gene transcription" url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online - name: Australian Structural Biology Computing community meeting @@ -69,10 +69,4 @@ endDate: 2025-11-12 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: Protein design seminar series - startDate: 2025-12-03 - endDate: 2025-12-03 - description: "**Topic:** Baby steps in the AI-guided design of proteins to module gene transcription" - url: https://www.eventbrite.com.au/e/webinar-leveraging-deep-learning-to-design-custom-protein-binding-proteins-tickets-1414347163439?aff=oddtdtcreator location: Online \ No newline at end of file diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index f13d39f..3ac3c9f 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -23,7 +23,6 @@ redirect_from: /website/protein_design_seminars | 15 July | 12pm AEST | Rhys Grinter | Using AI protein design to design binding proteins to challenging bacterial transporters | [YouTube](https://youtu.be/3Ad2gUjeSL8) | [Zenodo](https://doi.org/10.5281/zenodo.16511653) | | 12 August | 12pm AEST | Cyntia Taveneau | AIcrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors | [YouTube](https://www.youtube.com/watch?v=GSoOfyJUYSA) | [Zenodo](https://doi.org/10.5281/zenodo.17033916) | | 16 September | 12pm AEST | Richard Birkinshaw | Using in silico design methods to create de novo proteins that selectively modulate apoptosis | [YouTube](https://youtu.be/9-3sHy1ybpE) | [Zenodo](https://doi.org/10.5281/zenodo.17148914) | -| 7 October | 12pm AEDT* | Josh Hardy | Introducing ProteinDJ: A modular and open-source framework for protein design workflows | | | -| 11 November | 12pm AEDT* | TBC | TBC | | | -| 3 December | 1pm AEDT* | Joel Mackay | Baby steps in the AI-guided design of proteins to module gene transcription | | | +| 7 October | 12pm AEDT* | Josh Hardy | Introducing ProteinDJ: A modular and open-source framework for protein design workflows | [YouTube](https://www.youtube.com/watch?v=xwvF62HxaF0) | | +| 11 November | 12pm AEDT* | Joel Mackay | Baby steps in the AI-guided design of proteins to module gene transcription | | | | *Affected by daylight savings | \ No newline at end of file From 7049cbdae0e6f701881a889265e0eb97bd035052 Mon Sep 17 00:00:00 2001 From: tlitfin Date: Mon, 13 Oct 2025 14:56:21 +1100 Subject: [PATCH 3/5] add abacbs workshop activity --- pages/activities/abacbs25_workshop.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 pages/activities/abacbs25_workshop.md diff --git a/pages/activities/abacbs25_workshop.md b/pages/activities/abacbs25_workshop.md new file mode 100644 index 0000000..6b36494 --- /dev/null +++ b/pages/activities/abacbs25_workshop.md @@ -0,0 +1,23 @@ +--- +title: ABACBS 2025 workshop +description: Leveraging peak Australian compute to enable workflows for predictive structural biology at scale +type: activity_in_progress +roadmap: A computational structural biology training program (Roadmap D2) +roadmap_category: D2 +contributors: [Johan Gustafsson, Ziad Al-Bkhetan, Thomas Litfin, Sarah Beecroft, Georgie Samaha, Mitchell O'Brien, Farah Zaib Khan] +toc: false +redirect_from: /website/abacbs25_workshop +--- + +## Details + +Community members will present a [workshop](https://blackochrelabs.au/abacbs2025_workshops/) at the [ABACBS conference](https://www.abacbs.org/abacbs2025) in Adelaide describing structural biology workflows on national HPC infrastructure. + +### Abstract + +Deep learning for structural biology has numerous applications, ranging from basic research through to clinical application. A key challenge with these approaches is accessibility, and much work is currently being conducted to develop computational workflows to improve this access. However, building, executing, and sharing workflows is challenging. The difficulty only increases when implementing novel approaches like deep learning, and even more so when moving these workflows to national infrastructure to operate at scale. Some of the challenges include knowing how to develop a workflow to optimise use of these large compute systems, how to configure and deploy workflows that can efficiently employ both CPU and GPU, and how to share the workflows created so that others can find, understand, reuse, and ultimately cite the workflow. This workshop will examine these challenges from the perspective of a workflow’s life cycle, and in doing so provide both theory and hands-on activities that will support bioinformaticians to develop, execute, and share computational workflows for structural biology at scale. + +### Content + +- Presentation Slides coming soon +- Workshop content coming soon \ No newline at end of file From bc082d97136ed00305702e47b1ecb321a01a481c Mon Sep 17 00:00:00 2001 From: tlitfin Date: Mon, 13 Oct 2025 16:49:07 +1100 Subject: [PATCH 4/5] Add seminar zenodo link --- pages/activities/protein_design_seminars.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/activities/protein_design_seminars.md b/pages/activities/protein_design_seminars.md index 3ac3c9f..5e7636b 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -23,6 +23,6 @@ redirect_from: /website/protein_design_seminars | 15 July | 12pm AEST | Rhys Grinter | Using AI protein design to design binding proteins to challenging bacterial transporters | [YouTube](https://youtu.be/3Ad2gUjeSL8) | [Zenodo](https://doi.org/10.5281/zenodo.16511653) | | 12 August | 12pm AEST | Cyntia Taveneau | AIcrs: AI-Designed Anti-CRISPRs as Programmable CRISPR Inhibitors | [YouTube](https://www.youtube.com/watch?v=GSoOfyJUYSA) | [Zenodo](https://doi.org/10.5281/zenodo.17033916) | | 16 September | 12pm AEST | Richard Birkinshaw | Using in silico design methods to create de novo proteins that selectively modulate apoptosis | [YouTube](https://youtu.be/9-3sHy1ybpE) | [Zenodo](https://doi.org/10.5281/zenodo.17148914) | -| 7 October | 12pm AEDT* | Josh Hardy | Introducing ProteinDJ: A modular and open-source framework for protein design workflows | [YouTube](https://www.youtube.com/watch?v=xwvF62HxaF0) | | +| 7 October | 12pm AEDT* | Josh Hardy | Introducing ProteinDJ: A modular and open-source framework for protein design workflows | [YouTube](https://www.youtube.com/watch?v=xwvF62HxaF0) | [Zenodo](https://zenodo.org/records/17337232) | | 11 November | 12pm AEDT* | Joel Mackay | Baby steps in the AI-guided design of proteins to module gene transcription | | | | *Affected by daylight savings | \ No newline at end of file From e32d09f19e4dda9ad2a5b7d7d8b8e995f48e4dbd Mon Sep 17 00:00:00 2001 From: tlitfin Date: Tue, 14 Oct 2025 14:01:13 +1100 Subject: [PATCH 5/5] remove abacbs workshop --- pages/activities/abacbs25_workshop.md | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 pages/activities/abacbs25_workshop.md diff --git a/pages/activities/abacbs25_workshop.md b/pages/activities/abacbs25_workshop.md deleted file mode 100644 index 6b36494..0000000 --- a/pages/activities/abacbs25_workshop.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: ABACBS 2025 workshop -description: Leveraging peak Australian compute to enable workflows for predictive structural biology at scale -type: activity_in_progress -roadmap: A computational structural biology training program (Roadmap D2) -roadmap_category: D2 -contributors: [Johan Gustafsson, Ziad Al-Bkhetan, Thomas Litfin, Sarah Beecroft, Georgie Samaha, Mitchell O'Brien, Farah Zaib Khan] -toc: false -redirect_from: /website/abacbs25_workshop ---- - -## Details - -Community members will present a [workshop](https://blackochrelabs.au/abacbs2025_workshops/) at the [ABACBS conference](https://www.abacbs.org/abacbs2025) in Adelaide describing structural biology workflows on national HPC infrastructure. - -### Abstract - -Deep learning for structural biology has numerous applications, ranging from basic research through to clinical application. A key challenge with these approaches is accessibility, and much work is currently being conducted to develop computational workflows to improve this access. However, building, executing, and sharing workflows is challenging. The difficulty only increases when implementing novel approaches like deep learning, and even more so when moving these workflows to national infrastructure to operate at scale. Some of the challenges include knowing how to develop a workflow to optimise use of these large compute systems, how to configure and deploy workflows that can efficiently employ both CPU and GPU, and how to share the workflows created so that others can find, understand, reuse, and ultimately cite the workflow. This workshop will examine these challenges from the perspective of a workflow’s life cycle, and in doing so provide both theory and hands-on activities that will support bioinformaticians to develop, execute, and share computational workflows for structural biology at scale. - -### Content - -- Presentation Slides coming soon -- Workshop content coming soon \ No newline at end of file