Merge pull request #44 from AustralianBioCommons/participants

add ABLeS participants

Author: ziadbkh

participants/bpa.md

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+---
+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, <[email protected]>
+-   Anna Kearns, CSIRO, <[email protected]>
+
+## 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?
+
+Infrastructure choice: Unsure (Pawsey?)
+Quarterly Service Units (estimate): ?
+Storage: requirements for long-term (during the project) and scratch: yes?
+Is access to GPUs required?: Yes?
+Expected number of users: ? 19 projects have been supported through the initiative so far
+Expected duration of the project: 3 years
+
+## 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

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+---
+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, <[email protected]>
+-   Sophie Mazard, Bioplatforms Australia, <[email protected]>
+-   Luciano Beheregaray, Flinders University, <[email protected]> 
+-   Shannon Corrigan, Minderoo Foundation, <[email protected]>
+
+## 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?
+
+Pawsey, ?, ?, ?, ~50 users, 2 years
+
+## 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

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+---
+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, <[email protected]>
+-   Emma Peel, Australasian Wildlife Genomics Group, <[email protected]>
+-   Carolyn Hogg, Australasian Wildlife Genomics Group, <[email protected]>
+-   Sophie Mazard, Bioplatforms Australia, <[email protected]>
+-   Meena Mikhael, Australian Proteome Analysis Facility, <[email protected]> 
+-   Natalie Saez, Institute for Molecular Bioscience, <[email protected]>
+
+## 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?
+
+Infrastructure choice:  Pawsey
+Quarterly Service Units (estimate): 75 kSU
+Storage: 3 Tb storage and 1 Tb long term storage 
+Is access to GPUs required?: No
+Expected number of users: 2
+Expected duration of the project: 4 months
+We are ready to start using the resources
+
+## 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

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+---
+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, <[email protected]>
+
+## 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?
+
+Quarterly allocation of 50000 SU and 5TB of long term storage. 
+
+## 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

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+---
+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, <[email protected]>
+-   Locedie Mansueto, Southern Cross University, <[email protected]> 
+-   Tobias Kretzschmar, Southern Cross University, <[email protected]>
+
+## 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?
+
+NCI; Quarterly Service Units: 20kSUs; 2TB long term storage; 5 TB scratch; GPU: yes; number of users: 2-3; project duration: 6-12 months
+
+## 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/sih.md

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+---
+title: Sydney Informatics Hub (SIH)
+description: Testing and development of exercises for Nextflow for HPC workshop, to demonstrate how beginners can scale their Nextflow pipelines.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Nextflow for HPC Workshop: Testing and Development
+
+## Collaborators and funding
+
+-   Sydney Informatics Hub (SIH)
+-   Australian BioCommons
+-   Pawsey
+-   NCI
+
+## Contact(s)
+
+-   Fred Jaya, SIH, <[email protected]>
+-   Michael Geaghan, SIH, <[email protected]>
+
+## Project description and aims
+
+"The ""Nextflow for HPC"" workshop will be co-delivered in November 2025 on Setonix and Gadi. The workshop will focus on how users can scale and optimise workflows on these systems. The aim of this project is to test and develop follow-along exercises that demonstrate how users can configure Nextflow pipelines to run with an increasing number of samples, and resources (CPU, RAM, wall time). We expect trial and error with different configuration settings, and toy data sets to ensure that the workshop builds upon introduced concepts, and how users can apply these to their own pipelines.
+
+Analyses conducted within this project should not require a lot of walltime or memory, to fit the time restrictions of a workshop. It will require jobs with multiple CPUs to demonstrate parallelisation and scalability of Nextflow. Test data used will be subset RNA-seq paired-end reads.
+
+GitHub repository: [https://github.com/Sydney-Informatics-Hub/nextflow-hpc-workshop](https://github.com/Sydney-Informatics-Hub/nextflow-hpc-workshop)
+
+## How is ABLeS supporting this work?
+
+Both NCI and Pawsey required; 10 kSU/quarter; GPUs not required; Number of users: 5-10; Duration: Until the end of 2025; long term object storage not required, scratch space will be required to store sequencing files (~10 GB) and temporary outputs of nextflow runs (~5GB). 
+
+## Expected outputs enabled by participation in ABLeS
+
+All BioCommons training is archived on Zenodo, and the workshop material will be publicly available on the Sydney Informatics Hub GitHub and GitHub Pages. 
+
+<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/usyd-lo.md

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+---
+title: Nathan Lo, University of Sydney
+description: The proposed project will investigate the genomic architecture, evolutionary history and population structure of multiple Blattodean species. This has substantial implications for our understanding of chromosome evolution, inbreeding and parallel evolution, as well as useful results for the conservation of insect biodiversity in Australia and Japan.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Testing links between life-history and genome evolution
+
+## Collaborators and funding
+
+-   [The University of Sydney](https://meep.sydney.edu.au/)
+-   [The University of Melbourne](https://www.wehi.edu.au/researcher/aaron-jex/)  
+-   Australian Research Council Discovery Project DP240102805; [http://www.arc.gov.au/](http://www.arc.gov.au/)
+
+## Contact(s)
+
+-   Maxim Adams, <[email protected]>
+-   Nathan Lo, <[email protected]>
+
+## Project description and aims
+
+Our aims are to:
+-   Assemble high-quality genomes from species across the subfamily Panesthiinae with which to investigate the presence of genome-wide parallel evolution associated with soil-burrowing behaviour. If detected, this would represent among the first evidence that complex behavioural traits can emerge via parallel molecular trajectories.
+-   Assemble a high-quality reference genome for the Japanese termite Glyptotermes nakajimai against which to align and call genome-wide SNPs in samples across the species’ range. These data will then be used to investigate population structure, inbreeding and genetic diversity in different colonies and populations. When combined with karyotype data, we will novelly test for an association between inbreeding and neo-sex chromosome formation.
+-   Perform maximum-likelihood and Bayesian phylogenetic analyses to contextualise the previous results against the lineages’ evolutionary histories. These methods will also shed light into the biogeographic origins of the species.
+ 
+We request >= 128 GB of RAM (due to the computational demands of these bioinformatic pipelines) and >= 2 TB of storage (due to the large size of raw genomic data). Requested dependencies include: GATK, PLINK, StringTie, Flye, bedtools, samtools, MrBayes, BEAST, IQ-TREE and STRUCTURE.
+
+## How is ABLeS supporting this work?
+
+Infrastructure choice: Pawsey
+Quarterly Service Units (estimate): 100 kSUs
+Storage: >= 2 Tb
+Is access to GPUs required?: Not initially, but we may need them in due course (in a month or so, but it will depend on the approach our new computational specialist wants to use for analyses). 
+Expected number of users: 4
+Expected duration of the project: 3 years
+
+## Expected outputs enabled by participation in ABLeS
+
+Publications in scientific journals such as Current Biology, Molecular Biology and Evolution, PNAS, Evolution.
+
+<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/uwa-hp.md

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+---
+title: Harry Perkins Institute of Medical Research, The University of Western Australia
+description: This project develops a novel approach using high-resolution confocal imaging of chromatin and epigenetics in single cells to derive cell-type-specific signatures of cellular identity and state, such as biological age, and to approximate organ and organism function. The predictive value of these signatures, demonstrated in mice, is now being expanded to human tissues.
+toc: false
+type: ABLeS Participant
+---
+
+## Project title
+
+Biomarkers of Aging and Function
+
+## Collaborators and funding
+
+[FHRIF](https://fhrifund.health.wa.gov.au)
+
+## Contact(s)
+
+-   Dr Kenta Ninomiya, Harry Perkins Institute of Medical Research, The University of Western Australia, <[email protected]>
+-   Dr Alexey Terskikh, Harry Perkins Institute of Medical Research, The University of Western Australia, <[email protected]>
+
+## Project description and aims
+
+This project introduces a novel method to study aging and age-related functional decline by imaging chromatin and epigenetic modifications in single cells. Using high-resolution confocal microscopy, we extract 3D patterns of epigenetic marks to generate cell-type-specific signatures of cellular identity and states, including biological age. We have demonstrated that these signatures can effectively approximate organ and organismal function. Having validated the predictive power of these chromatin and epigenetic signatures in mouse models, our current efforts focus on extending these findings to a diverse range of human tissues and cell types.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS. The support includes 4 TB long term storage and 50 KSUs per quarter.
+
+## Expected outputs enabled by participation in ABLeS
+
+We aim to publish our findings in high-impact journals such as Nature, Nature Aging, or Cell. The research data will be made publicly available through platforms like The Open Science Framework. Developed analysis methods and corresponding codes developed during this project will be shared on GitHub.
+
+<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._