update participants

_data/sidebars/main.yml

@@ -6,8 +6,8 @@ subitems:
     url: /processes
   - title: Available resources
     url: /resources
-  - title: Existing projects
-    url: /projects
+  - title: ABLeS Participants
+    url: /participants
   - title: Shared software and reference data
     url: /if89
   - title: Acknowledging ABLeS

faq.md

@@ -29,19 +29,19 @@ toc: false
         </h2>
         <div id="collapse-faq-2" class="accordion-collapse collapse" aria-labelledby="heading-faq-2" data-bs-parent="#accordion-faq">
           <div class="accordion-body">
-            The allocation of SUs is on a quarterly basis. At the beginning of each quarter, BioCommons will allocate 100 kSU of computational resources to each community. Additional resources will be allocated according to the quarterly plan proposed by the community, as well as the resources still available in that quarter. 
-            <br/>Communities should utilise the allocated SUs:
+            The allocation of SUs is on a quarterly basis. At the beginning of each quarter, BioCommons will allocate 100 kSU of computational resources to each participant. Additional resources will be allocated according to the quarterly plan proposed by the participant, as well as the resources still available in that quarter. 
+            <br/>Groups should utilise the allocated SUs:
             <ol>
                 <li>For projects approved by the steering committee.</li> 
-                <li>Using the tools, methods and/or workflows that are suited to their community requirements.</li>
-                <li>While making sure to consider that the allocation is a shared resource for their community (if in doubt, consult with your community bioinformatics lead, or the BioCommons)</li>
+                <li>Using the tools, methods and/or workflows that are suited to their participant requirements.</li>
+                <li>While making sure to consider that the allocation is a shared resource for their participant (if in doubt, consult with your participant bioinformatics lead, or the BioCommons)</li>
             </ol>
             <blockquote>
                 <strong>Note:</strong>
                 <ul>
-                    <li>Communities can request additional resources when needed through the <a href="https://docs.google.com/forms/d/e/1FAIpQLSfzHJajEKTnGuYWb1gLRR2nlUExLIRM7qSGy_hhbiCKB3KX2Q/viewform?usp=sf_link"><strong>GoogleForm</strong></a>, if the quarterly plan did not accurately predict resource requirements.</li>
+                    <li>Groups can request additional resources when needed through the <a href="https://docs.google.com/forms/d/e/1FAIpQLSfzHJajEKTnGuYWb1gLRR2nlUExLIRM7qSGy_hhbiCKB3KX2Q/viewform?usp=sf_link"><strong>GoogleForm</strong></a>, if the quarterly plan did not accurately predict resource requirements.</li>
                     <li>Unused SUs **can NOT** be rolled-over to the next quarter. </li>
-                    <li>As ABLeS is a shared resource covering many communities, it is expected that each community will adopt a best-effort approach to firstly estimate their computational requirement realistically and accurately, and also actively manage the allocations which are provided (i.e. don’t waste your allocation, as the resource is still finite). </li>
+                    <li>As ABLeS is a shared resource covering many participants, it is expected that each participant will adopt a best-effort approach to firstly estimate their computational requirement realistically and accurately, and also actively manage the allocations which are provided (i.e. don’t waste your allocation, as the resource is still finite). </li>
                 </ul>                
                 </blockquote>
           </div>

if89-technical.md

@@ -6,7 +6,7 @@ title: ABLeS - Application Installation Guidelines
 
 The following documentation describes the installation procedures for bioinformatics software at the National Computational Infrastructure (NCI project allocation if89) enabled by the Australian BioCommons and included in Tools and Workflows repository.
 
-The maintenance process is purposely standardised using scripts to allow for sustainability. These scripts were developed to be similar to the NCI software management scripts to enable transferability. NCI staff, AusARG bioinformatics community, and bioinformatics/computational biology leads for the Australian BioCommons Leadership Share (ABLeS) program contributed to these scripts.
+The maintenance process is purposely standardised using scripts to allow for sustainability. These scripts were developed to be similar to the NCI software management scripts to enable transferability. NCI staff, AusARG bioinformatics participant, and bioinformatics/computational biology leads for the Australian BioCommons Leadership Share (ABLeS) program contributed to these scripts.
 
 >* All software on if89 should be installed into `/g/data/if89/apps directory`. 
 >* One directory for each software, then a subdirectory for each version of this software. 
@@ -22,7 +22,7 @@ This script should be added to the repository of all scripts and patches, which
 In order to contribute to `if89`, you need to satisfy the following conditions:
 
 1. **Obtain access to the `if89` project**: Everyone can request access to `if89` if they have a user account on GADI. Simply, request to join at this [link](https://my.nci.org.au/mancini/project/if89).
-2. **Request to join the writer group under `if89`**: request to join at this [link](https://my.nci.org.au/mancini/project/if89_w)
+2. **Request to join the writer participant under `if89`**: request to join at this [link](https://my.nci.org.au/mancini/project/if89_w)
 3. **Request access to `ables-software-installations` repository**: The repository link is [https://git.nci.org.au/dsr900/ables-software-installations](https://git.nci.org.au/dsr900/ables-software-installations). Access is managed through your Gadi username and password.
 
    If you do not have access, please contact one of the following repository maintainers and they will add you:

if89.md

@@ -3,9 +3,9 @@ title: Shared repository of tools and software (`project if89` on NCI)
 toc: false
 ---
 
-ABLeS communities have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This
-is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user community. Anyone
-from an NCI community can contribute to if89 and add more tools that will be shared with others.
+ABLeS participants have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This
+is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user participant. Anyone
+from an NCI participant can contribute to if89 and add more tools that will be shared with others.
 
 # Software
 

index.md

@@ -18,7 +18,7 @@ toc: false
 
 The ABLeS (Australian BioCommons Leadership Share) program was established in April 2021 to more readily support data-driven bioinformatics. This effort is supported by the [Australian BioCommons](https://www.biocommons.org.au/) in partnership with Bioplatforms Australia, the [National Computational Infrastructure (NCI, Canberra)](https://nci.org.au/), and the [Pawsey Supercomputing Research Centre (Pawsey, Perth)](https://pawsey.org.au/). 
 
-ABLeS targets established groups and communities that are focused on a common research theme, create reference data and/or software, and have the ability to plan and prioritise a computational research program.
+ABLeS targets established participants and participants that are focused on a common research theme, create reference data and/or software, and have the ability to plan and prioritise a computational research program.
 
 ABLeS projects broadly align with the following three principles:
 
@@ -28,7 +28,7 @@ ABLeS projects broadly align with the following three principles:
 
 3. Resources are planned and approached with a level of care appropriate to their status as limited and consumable resources.
 
-The support available includes access to computational and data infrastructure, specialist expertise, support to adopt best practices and share outputs effectively, and a community led and shared repository of bioinformatics software (i.e. tools and workflows).
+The support available includes access to computational and data infrastructure, specialist expertise, support to adopt best practices and share outputs effectively, and a participant led and shared repository of bioinformatics software (i.e. tools and workflows).
 
 More details are available in the ABLeS publication:
 
@@ -39,11 +39,11 @@ More details are available in the ABLeS publication:
 
 ### Creation of reference data assets
 
-ABLeS reference data allocations support research groups and consortia within the life sciences to access the dedicated compute capacity required to efficiently construct reference data.
+ABLeS reference data allocations support research participants and consortia within the life sciences to access the dedicated compute capacity required to efficiently construct reference data.
 
 ### Production bioinformatics
 
-Institutes, consortia and core facilities are increasingly facing issues scaling their in-house compute and data infrastructure to the questions, sample sizes, and data set sizes they are addressing as part of their research programs. ABLeS production allocations support these groups to implement and run their computational workflow approaches for omics data analysis *at scale*.
+Institutes, consortia and core facilities are increasingly facing issues scaling their in-house compute and data infrastructure to the questions, sample sizes, and data set sizes they are addressing as part of their research programs. ABLeS production allocations support these participants to implement and run their computational workflow approaches for omics data analysis *at scale*.
 
 ### Software accelerator
 

projects.md → participants.md

@@ -1,5 +1,5 @@
 ---
-title: ABLeS projects
+title: ABLeS Participants
 toc: false
 ---
 
@@ -27,5 +27,5 @@ toc: false
 
 ## ABLeS projects
 
-{% include section-navigation-tiles.html type="projects" search=true col="4" %}
+{% include section-navigation-tiles.html type="ABLeS Participant" search=true col="4" %}
 

projects/ausARG.md → participants/ausARG.md

@@ -1,17 +1,25 @@
 ---
-title: Australian Amphibian and Reptile Genomics (AusARG)
+title: Workspace for the Australian Amphibian and Reptile Genomics (AusARG)
 description: Bioinformatics analyses for the Australian Amphibian and Reptile Genomics initiative.
 toc: false
-type: projects
+type: ABLeS Participant
 ---
 
-## Bioinformatics leads
+
+## Project title
+
+Workspace for the Australian Amphibian and Reptile Genomics (AusARG)
+
+## Collaborators and funding
+
+
+## Contact(s)
 
 - Hardip Patel <[email protected]>
 - Terry Bertozzi <[email protected]>
 
 
-## Details
+## Project description and aims
 
 The [Australian Amphibian and Reptile Genomics Initiative (AusARG)](https://ausargenomics.com/) is a national collaborative project that will facilitate research using genomics approaches towards a more thorough understanding of evolution and conservation of Australia’s unique native amphibians and reptiles that are now under threat, through climate, disease or habitat modification.
 
@@ -21,4 +29,15 @@ AusARG's mission is to build genomic resources to understand and protect Austral
 + Phylogenomics
 + Conservation and Taxonomy genomics
 
-### [GitHub link](https://github.com/AusARG)
+[GitHub link](https://github.com/AusARG)
+
+
+## How is ABLeS supporting this work?
+
+This work is supported through the reference data asset creation scheme provided by ABLeS. The support includes 135 TB long term storage, 1 TB temoprary storage on scratch and 100 KSUs per quarter.
+
+## Expected outputs enabled by participation in ABLeS
+
+<br/>
+
+> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.*

projects/awri.md → participants/awri.md

@@ -1,17 +1,35 @@
 ---
-title: Australian Wine Research Institute
+title: Workspace for Australian Wine Research Institute
 description: Genetic diversity of Australian wine grapevine germplasm.
 toc: false
-type: projects
+type: ABLeS Participant
 ---
 
-## Bioinformatics leads
+## Project title
 
-Markus Herderich <[email protected]>
+Workspace for Australian Wine Research Institute
 
+## Collaborators and funding
 
-## Details
+
+## Contact(s)
+
+- Markus Herderich <[email protected]>
+
+## Project description and aims
 
 Grapevine cultivars can be unequivocally typed by both physical differences (ampelography) and genetic tests. However, due to their very similar characteristics, the identification of clones within a cultivar relies on the accurate tracing of supply records to the point of origin. Such records are not always available or reliable, particularly for older accessions. 
 
 Whole genome sequencing (WGS) provides the most highly detailed methodology for defining grapevine cultivars and more importantly, this can be extended to differentiating clones within those cultivars. The [AWRI](https://www.awri.com.au/) has developed a world-first clonal sequencing pipeline that has been successfully used to define grapevine clones as true-to-sequence. This information will underpin investments in replanting, facilitate vineyard recovery and improve income for Australian grape grower and wine producers.
+
+
+## How is ABLeS supporting this work?
+
+This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 1 TB permenant storage  and 50 KSUs per quarter.
+
+
+## Expected outputs enabled by participation in ABLeS
+
+<br/>
+
+> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.*

projects/benchmarking.md → participants/benchmarking.md

@@ -2,15 +2,25 @@
 title: Benchmarking life science software on national and institutional HPC platforms.
 description: A benchmarking project across multiple research organisations.
 toc: false
-type: projects
+type: ABLeS Participant
 ---
 
-## Bioinformatics leads
+## Project title
 
-Johan Gustafsson <[email protected]>, Ziad Al Bkhetan <[email protected]>, Edward Yang <[email protected]>, Julie Iskander <[email protected]>
+Benchmarking life science software on national and institutional HPC platforms.
 
+## Collaborators and funding
 
-## Details
+
+## Contact(s)
+
+- Johan Gustafsson <[email protected]>
+- Ziad Al Bkhetan <[email protected]>
+- Edward Yang <[email protected]>
+- Julie Iskander <[email protected]>
+
+
+## Project description and aims
 
 The goal of this project is to benchmark software that is commonly used throughout the life sciences on Australia’s national HPC facilities. The software benchmarked will span research areas such as bioinformatics and molecular dynamics, as well as general software that is commonly used such as [`NumPy`](https://bio.tools/numpy) and [`R`](https://bio.tools/r). The benchmarks also aim to test a variety of workloads, such as machine learning & artificial intelligence (ML/AI), traditional HPC (on a small to moderate scale), I/O dependent software (latency and bandwidth), and high throughput workloads.
 
@@ -22,3 +32,18 @@ Life science researchers will benefit from this as it will:
 - Establish an easy-to-setup benchmarking pipeline – facilitated by [`Nextflow`](https://bio.tools/nextflow).
 
 All results and the pipeline will be made publicly available via GitHub.
+
+
+
+## How is ABLeS supporting this work?
+
+This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes 1 TB temprary storage, 1 TB long term storage and 10 KSUs per quarter.
+
+## Expected outputs enabled by participation in ABLeS
+
+Sharing benchmarking results with the broader bioinformatics comunity in Australia.
+
+
+<br/>
+
+> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.*

participants/csbn.md

@@ -0,0 +1,56 @@
+---
+title: Computational Structural Biology Node
+description: explore software and hardware efficiencies in the current deep learning revolution in computational structural biology.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Computational Structural Biology Node
+
+## Collaborators and funding
+
+
+- [Structural Biology Facility, The University of New South Wales](https://www.analytical.unsw.edu.au/facilities/sbf)
+
+- [The Australian BioCommons](https://www.biocommons.org.au/)
+
+- [Pawsey Supercomputing Centre](https://pawsey.org.au/)
+
+## Contact(s)
+
+- Keiran Rowell - Scientific Officer - UNSW, Structural Biology Facility - <[email protected]>
+- Kate Michie - Chief Scientist - UNSW, Structural Biology Facility - <[email protected]>
+
+## Project description and aims
+
+Computational techniques applicable to all species, the focus is optimised and exploratory computation rather than investigation of any particular species. But we have local expertise in: 
+
+- Fundamental evolutionary biology: archeal protein development and divergence into eukaryotes  
+
+- Biomedical therapies in human genetic disorders:  cardiomyopathy implicated protein mutations 
+
+
+The structural biology node will explore software and hardware efficiencies in the current deep learning revolution in computational structural biology. 
+These findings will be shared with local and national HPC facilities, the steering committee, and scientific advisory board in order to formulate best-practice in this new style of compute for biomolecules and drive widespread adoption by biochemical/medical researchers in Australia.   
+
+
+Aims:  
+-  Benchmarking AlphaFold variants (e.g. OpenFold, FastFold) and optimising their use on HPC facilities 
+- Apply protein generative AI (e.g. RFDiffusion, EvoDiff, ProteinMPNN) for generation of novel protein designs in fundamental biology (molecular motors) and antibodies therapeutics  
+- Validating compilation of CUDA code of the above software onto AMD GPUs.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the production bioinformatics scheme provided by ABLeS. The supports includes unlimited temporary storage on scratch, 5 TB permenant storage and 150 KSUs per quarter.
+
+
+## Expected outputs enabled by participation in ABLeS
+
+This project is to support the Structural Biology Node being responsive to the deep learning developments in structural biology compute, which is producing pre-print code at a rapid which, many of which find eventual publication in top-rank journals. This is the beginning of software explosion in this ecosystem, and so we will be continually validating new code as the leading-edge validators for wide use by the biological research participant.  
+
+
+<br/>
+
+> *These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.*