From ff642b5d3990d3eef82ce817d6fd6347832f15f6 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Thu, 26 Jun 2025 17:42:57 +0930 Subject: [PATCH 1/2] add join_conversation to nav bar --- _data/sidebars/main.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 4ec2e90..1c5965c 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -1,6 +1,8 @@ subitems: - title: Home url: /index + - title: Join the conversation + url: /join_conversation - title: Activities url: /activities - title: How-to Guides From fcd1ec5b1da9357460a4295d52f93f2f70ef0e18 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 4 Jul 2025 09:24:19 +0930 Subject: [PATCH 2/2] content updates --- _data/CONTRIBUTORS.yml | 1 - contributing/contributing.md | 2 +- pages/activities.md | 4 +-- .../activities/batch_structure_prediction.md | 24 ++++++------- pages/activities/bindcraft_access.md | 36 ++++++++++--------- pages/activities/binder_access.md | 2 +- pages/activities/infrastructure_roadmap.md | 29 ++++++++------- pages/activities/nci_data_collections.md | 15 ++++---- pages/activities/nci_ood_proteinfold.md | 19 +++++----- pages/activities/nfcore_proteinfold.md | 26 +++++++------- pages/activities/nfcore_proteinfold_pawsey.md | 27 +++++++------- pages/activities/protein_design_seminars.md | 6 ++-- pages/contributors.md | 2 +- pages/external_resources.md | 2 +- pages/guides.md | 2 +- pages/resources/external_communities.md | 2 +- pages/resources/external_databases.md | 2 +- pages/resources/external_guides.md | 2 +- pages/resources/external_servers.md | 2 +- pages/resources/external_videos.md | 2 +- pages/resources/external_viz.md | 2 +- 21 files changed, 111 insertions(+), 98 deletions(-) diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 3681820..b465075 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -79,7 +79,6 @@ Mitchell O'Brien: Matthew Downton: git: mattdton - orcid: 0000-0002-4693-1965 affiliation: Associate Director - Performance Optimisation, National Computational Infrastructure (NCI) Kisaru Liyanage: diff --git a/contributing/contributing.md b/contributing/contributing.md index 52d6f65..fc3b878 100644 --- a/contributing/contributing.md +++ b/contributing/contributing.md @@ -1,7 +1,7 @@ --- title: Contributing page_id: contributing -type: resources +#type: resources --- {% include callout.html type="important" content="Contributing guidelines will be available soon." %} diff --git a/pages/activities.md b/pages/activities.md index e9dc0d4..f866718 100644 --- a/pages/activities.md +++ b/pages/activities.md @@ -1,13 +1,13 @@ --- title: Community Activities page_id: activities -type: resources +#type: resources toc: false --- ## In progress -{% include section-navigation-tiles-simple.html col = "2" type="activity_inprogress" except="binder_access.md" %} +{% include section-navigation-tiles-simple.html col = "2" type="activity_in_progress" except="binder_access.md" %} ## Future diff --git a/pages/activities/batch_structure_prediction.md b/pages/activities/batch_structure_prediction.md index 1293d2c..a327941 100644 --- a/pages/activities/batch_structure_prediction.md +++ b/pages/activities/batch_structure_prediction.md @@ -1,10 +1,10 @@ --- title: Batch Structure Prediction Workflows -type: activity_inprogress +type: activity_in_progress contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Cameron Hyde, Thomas Litfin] --- -### Details: +## Details - Structure prediction software often natively supports single predictions. - Specific workflows can re-use MSA input to massively improve efficiency over naive implementation. @@ -15,18 +15,18 @@ contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Row This activity involves developing optimized batch workflows for structure prediction. -### Completed: +### Completed -- [x] Add support for re-using MSAs to Galaxy Australia AlphaFold2 service. +- Add support for re-using MSAs to Galaxy Australia AlphaFold2 service. -### In Progress: +### 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. +- 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: +### 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 +- 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 index e122a3f..fe88461 100644 --- a/pages/activities/bindcraft_access.md +++ b/pages/activities/bindcraft_access.md @@ -1,31 +1,35 @@ --- title: Community Access to BindCraft -type: activity_inprogress +type: activity_in_progress contributors: [Ziad Al-Bkhetan, Thomas Litfin] --- -### Details + +## 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. +- 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. +- BindCraft tool is available within a NextFlow **[workflow](https://github.com/Australian-Structural-Biology-Computing/bindflow)** to support portable deployment. + +{% include callout.html type="warning" content="Native BindCraft tool requires PyRosetta as a filter with non-commercial license." %} + + +### Completed -:warning: Native BindCraft tool requires PyRosetta as a filter with non-commercial license +- Wrap the BindCraft tool in a Nextflow workflow (**[bindflow](https://github.com/Australian-Structural-Biology-Computing/bindflow)**). +- Add support for parallel execution across multiple GPUs. +- Negotiate PyRosetta license for non-commercial use at NCI. +- Output partial results when HPC scheduler jobs time out. -### 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 -### In Progress: +- Install workflow at NCI. +- Release BindCraft fork without PyRosetta dependency. +- Release BindCraft fork with open-source replacements for PyRosetta filters. -- [ ] Install workflow at NCI. -- [ ] Release BindCraft fork without PyRosetta dependancy. -- [ ] Release BindCraft fork with open-source replacements for PyRosetta filters. -### Future: +### Future -- [ ] OpenOnDemand app for running BindCraft from a graphical web interface. \ No newline at end of file +- 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 index 38e9c11..6b32948 100644 --- a/pages/activities/binder_access.md +++ b/pages/activities/binder_access.md @@ -1,6 +1,6 @@ --- title: Exploring how to increase access to RFdiffusion -type: activity_inprogress +type: activity_in_progress --- 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 index c62eb0b..90f87f9 100644 --- a/pages/activities/infrastructure_roadmap.md +++ b/pages/activities/infrastructure_roadmap.md @@ -1,26 +1,29 @@ --- title: Infrastructure Roadmap -type: activity_inprogress +type: activity_in_progress --- -### Details: +## 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: +### 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. +- Initial draft of infrastructure roadmap. +- Initial community feedback incorporated, content updated, implementation section added. +- Review and updates based on feedback from co-authors and academic panel. +- Review and updates based on feedback from community and BioCommons infrastructure partners. +- Review and updates based on feedback from international experts. -### In Progress: -- [ ] Addressing final review comments. +### In Progress -### Future: -- [ ] Publication to Zenodo. +- Addressing final review comments. + +### Future + +- Publication to Zenodo. + +### Contributors -### 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 index df566db..3432401 100644 --- a/pages/activities/nci_data_collections.md +++ b/pages/activities/nci_data_collections.md @@ -1,10 +1,10 @@ --- title: NCI Data Collection -type: activity_inprogress +type: activity_in_progress contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Thomas Litfin] --- -### Details +## 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. @@ -13,10 +13,11 @@ contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley This activity aims to create a stable release of up-to-date reference data (with DOI) to support reproducible structure prediction workflows. -### Completed: +### Completed -- [x] Catalog latest version of reference data. -- [x] Harmonize data across different structure prediction models (AlphaFold2, AlphaFold3, Boltz, ColabFold, HelixFold3, RosettaFold-AA). +- Catalog latest version of reference data. +- 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 +### 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 index 86b4511..d438866 100644 --- a/pages/activities/nci_ood_proteinfold.md +++ b/pages/activities/nci_ood_proteinfold.md @@ -1,24 +1,27 @@ --- title: OpenOnDemand GUI ProteinFold app -type: activity_inprogress +type: activity_in_progress contributors: [Matthew Downton, Kisaru Liyanage, Wenjing Xue, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] --- -### Details: +## 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). +- Several institutional HPCs have an OpenOnDemand deployment (e.g. KOD @ UNSW, ARE @ NCI). -### Completed: -- [x] Pilot app developed and hosted on Katana at UNSW. +### Completed + +- 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. +- Adapt pilot ProteinFold app for ARE at NCI. + +### Future + +- Add support for more optional settings in web form interface.
KOD-proteinfold diff --git a/pages/activities/nfcore_proteinfold.md b/pages/activities/nfcore_proteinfold.md index e6aa8bc..5ebd23a 100644 --- a/pages/activities/nfcore_proteinfold.md +++ b/pages/activities/nfcore_proteinfold.md @@ -1,10 +1,10 @@ --- title: nf-core ProteinFold v2.0 Release -type: activity_inprogress +type: activity_in_progress contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Rowell, Thomas Litfin] --- -### Details: +## 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. @@ -14,17 +14,17 @@ contributors: [Ziad Al-Bkhetan, Mitchell O'Brien, Joshua Storm Caley, Keiran Row ### 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. +- Config optimized for efficient utilization for Gadi at NCI. +- Add RosettaFold-All-Atom. +- Add HelixFold3. +- Add Boltz-1. +- Add AlphaFold3 (BYO weights). +- Add support for local MSA search for Boltz-1. +- Add standardized reporting with visualisation. +- Add support for quality metrics in output reporting. +- 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 +- 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 index d6b1e35..353a99d 100644 --- a/pages/activities/nfcore_proteinfold_pawsey.md +++ b/pages/activities/nfcore_proteinfold_pawsey.md @@ -1,24 +1,27 @@ --- title: nf-core ProteinFold at Pawsey -type: activity_inprogress +type: activity_in_progress contributors: [Sarah Beecroft, Joshua Storm Caley] --- -### Details: +## 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. +### Completed -### In Progress: -- [ ] Adapt containers for compatibility with nfcore proteinfold. -- [ ] Test nfcore proteinfold workflow at Pawsey. +- Build AMD compatible container for AlphaFold2. +- Build AMD compatible container for Boltz-1. +- Build AMD compatible container for ESMFold. -### Future: -- [ ] Build AMD compatible container for Boltz-2. -- [ ] ProteinFold config optimized for Pawsey. \ No newline at end of file +### In Progress + +- Adapt containers for compatibility with nf-core 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 index f75eb31..a28835a 100644 --- a/pages/activities/protein_design_seminars.md +++ b/pages/activities/protein_design_seminars.md @@ -1,17 +1,17 @@ --- title: Protein Design Seminar Series (2025) -type: activity_inprogress +type: activity_in_progress contributors: [Rhys Grinter, Gavin Knott, Cyntia Taveneau, Josh Hardy, Kate Michie, Johan Gustafsson, Melissa Burke] --- -### Details +## 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) + 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 | |---------------|------------|--------------------|-------| diff --git a/pages/contributors.md b/pages/contributors.md index cdca331..69c6b57 100644 --- a/pages/contributors.md +++ b/pages/contributors.md @@ -1,7 +1,7 @@ --- title: Community contributors page_id: contributors -type: resources +#type: resources --- The projects included here represent a joint effort by the following people at multiple Australian institutions: diff --git a/pages/external_resources.md b/pages/external_resources.md index 46e9dc8..15682bd 100644 --- a/pages/external_resources.md +++ b/pages/external_resources.md @@ -2,7 +2,7 @@ title: External Resources page_id: external_resources #datatable: true -type: resources +#type: resources --- diff --git a/pages/guides.md b/pages/guides.md index 9029cab..8b13d1b 100644 --- a/pages/guides.md +++ b/pages/guides.md @@ -2,7 +2,7 @@ title: How-to Guides description: How-to Guides for the use of deep learning methods in structural biology. page_id: guides -type: resources +#type: resources datatable: true --- diff --git a/pages/resources/external_communities.md b/pages/resources/external_communities.md index ef10f51..f4275a4 100644 --- a/pages/resources/external_communities.md +++ b/pages/resources/external_communities.md @@ -2,7 +2,7 @@ title: External Communities page_id: external_resources_communities datatable: true -type: resources +#type: resources --- {% include resource-table-communities.html %} diff --git a/pages/resources/external_databases.md b/pages/resources/external_databases.md index 7b067d1..c5a377a 100644 --- a/pages/resources/external_databases.md +++ b/pages/resources/external_databases.md @@ -2,7 +2,7 @@ title: External Databases page_id: external_resources_dbs datatable: true -type: resources +#type: resources --- {% include resource-table-dbs.html %} diff --git a/pages/resources/external_guides.md b/pages/resources/external_guides.md index cadec2b..2512656 100644 --- a/pages/resources/external_guides.md +++ b/pages/resources/external_guides.md @@ -2,7 +2,7 @@ title: External Guides page_id: external_resources_guides datatable: true -type: resources +#type: resources --- {% include resource-table-guides.html %} diff --git a/pages/resources/external_servers.md b/pages/resources/external_servers.md index 248e7fd..d236eff 100644 --- a/pages/resources/external_servers.md +++ b/pages/resources/external_servers.md @@ -2,7 +2,7 @@ title: External Resources & Servers page_id: external_resources_servers datatable: true -type: resources +#type: resources --- {% include resource-table-servers.html %} diff --git a/pages/resources/external_videos.md b/pages/resources/external_videos.md index a49d784..99c8a26 100644 --- a/pages/resources/external_videos.md +++ b/pages/resources/external_videos.md @@ -2,7 +2,7 @@ title: External Videos page_id: external_resources_videos datatable: true -type: resources +#type: resources --- {% include resource-table-videos.html %} diff --git a/pages/resources/external_viz.md b/pages/resources/external_viz.md index 103b940..0173a67 100644 --- a/pages/resources/external_viz.md +++ b/pages/resources/external_viz.md @@ -2,7 +2,7 @@ title: External Visualization page_id: external_resources_viz datatable: true -type: resources +#type: resources --- {% include resource-table-viz.html %}