update release

_config.yml

@@ -2,7 +2,7 @@
 title: ABLeS
 topnav_title: ABLeS
 description: ABLeS
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@2.4.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@5.0.0
 permalink: pretty
 gtag: G-T8GWK081T9
 

acknowledgements.md

@@ -9,11 +9,29 @@ The ABLeS program should be both cited and acknowledged in any publication, pres
 
 1. Use the following citation:
 
-> Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (2023). *Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share (3.0).* Zenodo. [https://doi.org/10.5281/zenodo.10139651](https://doi.org/10.5281/zenodo.10139651)
+```
+Gustafsson, Ove Johan Ragnar, Al Bkhetan, Ziad, Francis, Rhys & Manos, Steven. (2023). *Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share (3.0).* Zenodo. [https://doi.org/10.5281/zenodo.10139651](https://doi.org/10.5281/zenodo.10139651)
+```
+```
+@misc{gustafsson_2023_10139651,
+  author       = {Gustafsson, Ove Johan Ragnar and Al Bkhetan, Ziad and Francis, Rhys and Manos, Steven},
+  title        = {Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share},
+  month        = Nov,
+  year         = 2023,
+  publisher    = {Zenodo},
+  version      = {3.0},
+  doi          = {10.5281/zenodo.10139651},
+  url          = {https://doi.org/10.5281/zenodo.10139651},
+}
+```
+
+{:start="2"}
 
 2. Use the following acknowledgement statement:
 
->"The authors acknowledge the provision of computing and data resources provided by the Australian BioCommons Leadership Share (ABLeS) program. This program is co-funded by Bioplatforms Australia (enabled by NCRIS), the National Computational Infrastructure and Pawsey Supercomputing Research Centre."
+```
+"The authors acknowledge the provision of computing and data resources provided by the Australian BioCommons Leadership Share (ABLeS) program. This program is co-funded by Bioplatforms Australia (enabled by NCRIS), the National Computational Infrastructure and Pawsey Supercomputing Research Centre."
+```
 
 ## ABLeS co-authorship policy
 

if89.md

@@ -122,7 +122,7 @@ The list of tools available through the Australian BioCommons Shared Tools and W
 Some of the databases required by different bioinformatics software tools are made available through the if89 project.  
 They are located at <code>/g/data/if89/data_library</code>. You can request other databases to be included by [contacting us](https://australianbiocommons.github.io/ables/contact-us/).
 
-A list of the currently available (`as of 25 Jan 2023`) databases is included below:
+A list of the currently available (`as of 25 Aug 2025`) databases is included below:
 
 <div class="accordion" id="accordion-if89-ds">
       <div class="accordion-item">
@@ -221,6 +221,28 @@ A list of the currently available (`as of 25 Jan 2023`) databases is included be
                  <td>Kraken2 pre-built index for RefSeq database (archaea, bacteria, viral, plasmid, human, protozoa & fungi) plus UniVec_Core.
                  </td>
                </tr>
+               <tr>
+                  <td>Kraken2</td>
+                  <td><a href="https://benlangmead.github.io/aws-indexes/k2"> Kraken 2, KrakenUniq and Bracken indexes </a></td>
+                  <td> 9 Jun 2025 </td>
+                  <td><code>kraken2/09062025/k2_core_nt</code></td>
+                  <td>Kraken2 Very large collection, inclusive of GenBank, RefSeq, TPA and PDB.</td>
+                </tr>
+                <tr>
+                  <td>Kraken2</td>
+                  <td><a href="https://benlangmead.github.io/aws-indexes/k2"> Kraken 2, KrakenUniq and Bracken indexes </a></td>
+                  <td> 9 Jun 2025 </td>
+                  <td><code>kraken2/09062025/k2_standard</code></td>
+                  <td>Kraken2 pre-built "standard" database, includes RefSeq archaea, bacteria, viral, plasmid, human, plus UniVec_Core.</td>
+                </tr>
+               <tr>
+                 <td>Dfam</td>
+                 <td><a href="https://www.dfam.org/home"> Dfam </a></td>
+                 <td> 04 Aug 2025 </td>
+                 <td><code>dfam/04082025/dfam39</code></td>
+                 <td>Dfam 3.9; FamDB Format 2.0; Partition 7 [dfam39_full.7.h5]: Mammalia (57 GB) More info - https://www.dfam.org/releases/Dfam_3.9/families/FamDB/README.txt. Available with RepeatMasker/4.2.0 (if89 module)
+                 </td>
+               </tr>
               </tbody>
             </table>
           </div>
@@ -234,3 +256,4 @@ A list of the currently available (`as of 25 Jan 2023`) databases is included be
 ## if89 Contributors
 
 {% include contributor-tiles-all.html custom="Hardip Patel, Ziad Al Bkhetan, J King Chang, Andre Martins Reis, Hasindu Gamaarachchi, Kyle Drover, Tim Amos, Kisaru Liyanage, Terry Bertozzi, Javed Shaikh, Kirat Alreja, Leah Kemp, Andrey Bliznyuk, Hyungtaek Jung, Wenjing Xue, Johan Gustafsson, Dale Roberts" sort=false%}
+

participants/bpa.md

@@ -0,0 +1,42 @@
+---
+title: Bioplatforms Australia
+description: The Avian Genomics Initiative will fill genomic data gaps for investigating and managing unique Australian bird species.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Australian Avian Genomics Initiative
+
+## Collaborators and funding
+
+Funding led by Bioplatforms Australia, additional funding and collaboration from the Australian research community.
+
+## Contact(s)
+
+-   Sophie Mazard, Bioplatforms Australia, <smazard@bioplatforms.com>
+-   Anna Kearns, CSIRO, <Anna.Kearns@csiro.au>
+
+## Project description and aims
+
+Australia is home to approximately 830 species of birds, of which 43% are endemics found nowhere else. Despite substantial international efforts in avian genomics and phylogenomics, significant gaps remain in reference data for Australian bird species.
+An audit of existing data found 687 reference genomes for Australian birds. Out of the 107 families of birds found in Australia, 41 families of native or endemic birds lack Australian representative reference genomes. Filling these gaps in referential data would significantly enhance our understanding of genomics, ecology, and behaviour for species and functional traits unique to Australia.
+
+The Australian Avian Genomics Initiative, established in 2023, aims to:
+
+- Build genomic data for bird conservation: develop data on phylogenomics, reference genomes, and population genetics to support the understanding and conservation of Australia’s unique bird species.
+- Advance fundamental bird genomics research: explore key species traits relevant to Australia, including migration, nectarivory, drought tolerance, cooperative breeding, and more.
+- Address critical biodiversity needs: use genomics to complement fundamental research and meet the needs identified by society, government, and industry."
+
+## How is ABLeS supporting this work?
+
+This project is supported by the Reference Data Generation scheme provided by ABLeS, providing access to compute and storage resources at the National Computational Infrastructure (NCI) and the Pawsey Supercomputing Research Centre.
+
+## Expected outputs enabled by participation in ABLeS
+
+Datasets (Umbrella Bioproject ID: PRJNA1098052, [https://data.bioplatforms.com/organization/aus-avian](https://data.bioplatforms.com/organization/aus-avian)) publications ([https://doi.org/10.25953/740m-0320](https://doi.org/10.25953/740m-0320)).
+
+<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/minderoo.md

@@ -0,0 +1,38 @@
+---
+title: Bioplatforms Australia, Minderoo Foundation, Fish Genomics Consortium
+description: The Australian Fish Genomics Initiative seeks to address critical deficiencies in available genomic data for Australian fishes. By generating high-quality genomic data, this work will provide a foundation for improved population monitoring, environmental assessment, and the sustainable management of fisheries and aquatic ecosystems.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Australian Fish Genomics Initiative
+
+## Collaborators and funding
+
+-   Bioplatforms Australia
+-   Minderoo Foundation
+
+## Contact(s)
+
+-   Amy Tims, UniMelb, <amy.tims@unimelb.edu.au>
+-   Sophie Mazard, Bioplatforms Australia, <smazard@bioplatforms.com>
+-   Luciano Beheregaray, Flinders University, <luciano.beheregaray@flinders.edu.au> 
+-   Shannon Corrigan, Minderoo Foundation, <scorrigan@minderoo.org>
+
+## Project description and aims
+
+[https://bioplatforms.com/project/australian-fish-genomics-initiative/](https://bioplatforms.com/project/australian-fish-genomics-initiative/)
+
+## How is ABLeS supporting this work?
+
+This project is supported by the Reference Data Generation scheme provided by ABLeS, providing access to compute and storage resources at the National Computational Infrastructure (NCI) and the Pawsey Supercomputing Research Centre.
+
+## Expected outputs enabled by participation in ABLeS
+
+Reference genomes for ~80 species, transcriptomes, short read data for population genetics. Raw data stored on Bioplatforms data portal.
+
+<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/platypus.md

@@ -0,0 +1,44 @@
+---
+title: Australian Proteome Analysis Facility, Macquarie University
+description: We will use protein mass spectrometry and transcriptomics to identify the constituent proteins of platypus venom. Candidate proteins identified will then be analysed and screened in assays, to determine their function, associated envenomation symptoms, and potential as novel therapeutics.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Characterization of the Platypus Venom Proteome for Novel Proteins and Therapeutic Candidates
+
+## Collaborators and funding
+
+Australasian Wildlife Genomics Group, University of Sydney
+
+## Contact(s)
+
+-   Adele Gonsalvez, Australasian Wildlife Genomics Group, <adele.gonsalvez@sydney.edu.au>
+-   Emma Peel, Australasian Wildlife Genomics Group, <emma.peel@sydney.edu.au>
+-   Carolyn Hogg, Australasian Wildlife Genomics Group, <carolyn.hogg@sydney.edu.au>
+-   Sophie Mazard, Bioplatforms Australia, <smazard@bioplatforms.com>
+-   Meena Mikhael, Australian Proteome Analysis Facility, <meena.mikhael@mq.edu.au> 
+-   Natalie Saez, Institute for Molecular Bioscience, <n.saez@imb.uq.edu.au>
+
+## Project description and aims
+
+This project will employ a comprehensive proteogenomic strategy to identify and evaluate novel therapeutic proteins from platypus venom. We will integrate RNA sequencing (RNA-seq) data with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to create a detailed map of the venom's protein composition. Venom-derived RNA from this study, supplemented with 61 publicly available platypus tissue samples, will be assembled against the high-quality reference genome to generate a custom, tissue-specific protein database. This database will enable high-confidence identification of proteins from LC-MS/MS analysis of venom fluid. 
+
+The aims include: 
+1) *Develop a Platypus Proteome Database*: To assemble transcript sequences from both novel and publicly available RNA-seq data and generate a comprehensive protein sequence database using the Pawsey Setonix cluster. 
+2) *Identify Venom Proteins*: To analyze platypus venom fluid using LC-MS/MS and identify its constituent proteins by searching against the custom-generated proteome database. This proteomic database aims to provide novel insights into platypus venom composition, and our understanding of the platypus venom system. 
+3) *Evaluate Functionality and Therapeutic Potential*: To clone, express, and purify the identified venom proteins for use in functional assays, to attribute their functionality, associated envenomation symptoms,  and suitability for therapeutic development.
+
+## How is ABLeS supporting this work?
+
+This project is supported by the Production Bioinformatics scheme provided by ABLeS, providing access to compute and storage resources at the Pawsey Supercomputing Research Centre.
+
+## Expected outputs enabled by participation in ABLeS
+
+It is expected that novel platypus venom proteins will be identified through this proteogenomic strategy, and results will subsequently be published in a peer-reviewed academic journal.
+
+<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/pmcc.md

@@ -0,0 +1,35 @@
+---
+title: Transcriptome Methods Development at Peter MacCallum Cancer Centre
+description: The dysregulation of splicing is a hallmark of cancer. Comparing local RNA-seq cohort data to large-scale global splicing databases remains challenging due to incompatible and specialised processing pipelines. This project aims to uniformly process local reference cohort data to allow efficient comparison with major international pre-computed datasets.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Standardised processing of cancer cohort RNA-seq data for streamlined analysis and discovery
+
+## Collaborators and funding
+
+-   [Peter MacCallum Cancer Centre](https://www.petermac.org/)
+-   [Children’s Cancer Institute](https://www.ccia.org.au/)
+
+## Contact(s)
+
+Andrew Lonsdale, Peter MacCallum Cancer Centre, <andrew.lonsdale@petermac.org>
+
+## Project description and aims
+
+Leveraging these summarised databases effectively with patient and research cohorts requires private RNA-seq samples to be processed using the same pipelines. The Snapcount and Recount3 common backend workflow differs from clinical and standard pipelines, and requires raw data to be reanalyzed and processed to directly comparable with the pre-computed public databases. The goal of this project is to develop a systematic method to: transfer files to national compute, process private samples using a common workflow, summarise at cohort level, and export results back for analysis. 
+
+## How is ABLeS supporting this work?
+
+This project is supported by the Production Bioinformatics scheme provided by ABLeS, providing access to compute and storage resources at the Pawsey Supercomputing Research Centre.
+
+## Expected outputs enabled by participation in ABLeS
+
+The major outcome of this project would be a Snapcount3 compatible resource via a Snaptron server. This will give an API for querying splicing and metadata across across. paediatric caner cohorts for researchers to use. This will result in both a web accessible database for querying, and an associated paper disseminating key findings.  A Snaptron web service running under Docker will be deployed on institutional virtual machines  to store and disseminate the data.
+
+<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/scu.md

@@ -0,0 +1,40 @@
+---
+title: Tobias Kretzschmar, Southern Cross University
+description: This project aims to contribute to the improvement of hemp as a crop, particularly in terms of seed production, through quantitative genetic and functional genomic techniques. 
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Determination of genetic basis of sex expression in hemp (Cannabis sativa)
+
+## Collaborators and funding
+
+This project is funded by the Australian Research Council (ARC) Linkage project LP240200616 (Swinging both ways – the genetic control of sex expression in hemp)
+
+## Contact(s)
+
+-   Stephen Siazon, Southern Cross University, <s.siazon.10@student.scu.edu.au>
+-   Locedie Mansueto, Southern Cross University, <locedie.mansueto@scu.edu.au> 
+-   Tobias Kretzschmar, Southern Cross University, <Tobias.Kretzschmar@scu.edu.au>
+
+## Project description and aims
+
+Hemp (low THC Cannabis sativa) is an emerging Australian crop that produces high-quality edible oils and plant-based protein from seeds. Hemp typically has separate male and female plants, with 50% of the crop being males that don’t produce seed, causing low and variable yields.
+
+This project will characterize novel sex-determining genetic factors in hemp, using quantitative genetic and functional genomic approaches. This includes Quantitative Trait Locus (QTL) mapping, Bulk Segregant Analysis via sequencing (BSAseq), transcriptomic analysis via RNA sequencing, DNA resequencing and potentially de-novo assemblies of Cannabis genomes.
+
+Project outcomes include enhanced knowledge on hemp sex expression, novel hemp crop technologies and associated germplasm that will deliver significant increases to seed yields.
+
+## How is ABLeS supporting this work?
+
+This project is supported by the Production Bioinformatics scheme provided by ABLeS, providing access to compute and storage resources at the National Computational Infrastructure (NCI).
+
+## Expected outputs enabled by participation in ABLeS
+
+Outputs will be published in peer-reviewed journals and genomics data will be submitted in appropriate public repositories. 
+
+<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/thyroid-cancer.md

@@ -1,13 +1,14 @@
 ---
 title: Thyroid Cancer Research Group, The University of Sydney
-description:
+description: Applying single cell RNA sequencing to understand the immune landscape of thyroid cancer, with the goal of identifying therapeutic targets and biomarkers.
 toc: false
 type: ABLeS Participant
 ---
 
 ## Project title
 
-Applying single cell RNA sequencing to understand the immune landscape of thyroid cancer, with the goal of identifying therapeutic targets and biomarkers.
+Thyroid Autoimmunity and the Immune Landscape in Thyroid Cancer
+
 
 ## Collaborators and funding
 

participants/tsi.md

@@ -2,7 +2,7 @@
 title: Threatened Species Initiative
 description: Bioinformatics analyses for the Threatened Species Initiative.
 toc: false
-type: ABLeS Participant
+type: ABLeS Participant - Completed
 ---
 
 ## Project title