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description: "A module added to the training material made available by EMBL-EBI. Module development was a collaboration between the ASBC community, BioCommons, and EMBL-EBI Protein Data Bank in Europe (PDBe)."
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description: "A module added to the training material made available by EMBL-EBI. Module development was a collaboration between the ASBC community, BioCommons, and EMBL-EBI Protein Data Bank in Europe (PDBe)."
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- name: "17M protein structures added to the AlphaFold Database"
description: "An Australian researcher has recently contributed 17 million protein predictions to the AlphaFold Protein Structure Database, which will have a transformative impact on the international fight to combat antimicrobial resistance."
Copy file name to clipboardExpand all lines: index.md
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@@ -38,20 +38,20 @@ This website is a virtual meeting place and hub for all users of **computing for
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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.
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#### Next meeting is on May 20th
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#### Next meeting is on July 29th
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{% include tiles-simple.html target = "community_meeting" col = "1" %}
| March 11th |**Biswa Prasanna Mishra**<br>(Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system |
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| May 20th |**Cameron Gilchrist**<br>(Korea Basic Science Institute Ochang-center) | Multiple protein structure alignment with FoldMason |
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|29th July | TBA |TBA|
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|16th September |**Tom Goddard**<br>(UCSF) | Predicting atomic structures using OpenFold 3 in ChimeraX |
| March 11th |**Biswa Prasanna Mishra**<br>(Griffith University) | Molecular Characterisation of the *Bacillus subtilis SpbK* antiphage defence system |
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| May 20th |**Cameron Gilchrist**<br>(Korea Basic Science Institute Ochang-center) | Multiple protein structure alignment with FoldMason |
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| July 29th |**Roland Dunbrack**<br>(Fox Chase Cancer Center)|Structural bioinformatics and AlphaFold modeling of the human kinome and its interactions|
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| September 16th |**Tom Goddard**<br>(UCSF)| Predicting atomic structures using OpenFold 3 in ChimeraX |
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| November 12th | TBA| TBA |
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{% include callout.html type="note" content="These dates may change depending on other community events and the availability of speakers. " %}
description: Porting software prioritised by the community to AMD to allow software execution at Pawsey Supercomputing Research Centre and other centres operating AMD GPUs.
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type: Activity_in_progress
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roadmap: A shared platform, or platforms (Roadmap D3Ab)
- title: "Visit the software resources page to see the tools ported to AMD GPUs"
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url: /software
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---
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{% include tiles-simple.html target = "tiles" col = "1" %}
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## Details
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- Deep Learning models work natively with NVIDIA hardware.
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- Setonix at Pawsey contains a large number of AMD GPUs.
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- Models can be made to work with AMD hardware available at Pawsey.
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- This ongoing activity is specifically for the identification, prioritisation, and porting of structural biology software from NVIDIA to AMD GPUs.
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### Completed
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-[AMD compatible containers for nf-core proteinfold](nfcore_proteinfold_pawsey).
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### In Progress
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### Future
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- Continue to port software to AMD that has been prioritised by the community.
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### Acknowledgements
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This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.
- Adapt containers for compatibility with nf-core proteinfold.
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- Test nfcore proteinfold workflow at Pawsey.
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### In Progress
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- ProteinFold config optimized for Pawsey.
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### Future
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- Port software to AMD that has been prioritised by the community.
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### Acknowledgements
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This work was supported by Australian BioCommons and the Pawsey Supercomputing Research Centre (https://ror.org/04f2f0537). Australian BioCommons receives NCRIS funding through Bioplatforms Australia. Pawsey Supercomputing Research Centre receives funding from the Australian Government and the Government of Western Australia.
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page_id: contributing
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toc: false
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#type: resources
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toc: false
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redirect_from: /website/contributing
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---
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{% include callout.html type="important" content="Contributing guidelines will be available soon." %}
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A key aim of the community is to enable sharing of knowledge, methods (i.e. software and workflows), and expertise: to accelerate progress across the community, foster collaborations, and reduce replication of effort.
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Here, we outline an initial set of contribution mechanisms that are intended to allow for community sharing, and
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attribution of credit to those who have created the work being shared.
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{% include callout.html type="important" content="Additional contribution guidelines will be added as they are prioritised by the community." %}
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## Sharing computational workflows
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{% include callout.html type="important" content="Workflows from a [ASBC community collection on the WorkflowHub registry](https://workflowhub.eu/collections/40) will be automatically imported and displayed on a dedicated software page soon. Additional instructions will be available soon. For now, if you would like your workflows listed on the website when the integration with WorkflowHub is ready, please follow the instructions below." %}
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#### 1. [Register as a WorkflowHub user and either set up, or join, a Team](https://about.workflowhub.eu/docs/organising-and-setup/)
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#### 2. [Register your workflow(s) on WorkflowHub](https://about.workflowhub.eu/docs/registering_workflows/registering-a-workflow/)
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#### 3. Annotate these workflows by adding the minimum metadata highlighted here
| Workflow title | Make sure the title is descriptive and highlights what the workflow does.|
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| Creator(s) | If you have included a `CITATION.cff` file in your GitHub repository, WorkflowHub can parse this and automatically populate the creator field. |
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| Description | Note that descriptions included in GitHub repository README files will be automatically parsed by WorkflowHub. |
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| Maturity | Indicate if the workflow is `mature` or a `work-in-progress`. |
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| License | Note that if a license file is included in your GitHub repository it will be automatically parsed by WorkflowHub. |
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| EDAM Topics and Operations | Add concepts from [EDAM](https://github.com/edamontology/edamontology) as standardised short descriptions of workflow domain, purpose, and function. You can search for EDAM terms within the WorkflowHub workflow registration wizard. You can also use [EDAM browser](https://edamontology.github.io/edam-browser/) to explore and search the EDAM ontology for appropriate concepts. |
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The metadata included above is based on a BioCommons [example available here](https://australianbiocommons.github.io/how-to-workflowhub-space/new_workflow#add-minimum-metadata).
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