update participants

participants.md

@@ -9,21 +9,21 @@ toc: false
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participants/FHMRI.md

@@ -16,14 +16,13 @@ Flinders Health and Medical Research Institute, College of Medicine and Public H
 
 ## Contact(s)
 
--   Michael Roach, Flinders, <michael.roach@flinders.edu.au>
--   Clarice Harker, Flinders, <clarice.cram@flinders.edu.au>
+- Michael Roach, Flinders, <michael.roach@flinders.edu.au>
+- Clarice Harker, Flinders, <clarice.cram@flinders.edu.au>
 
 ## Project description and aims
 
 FHMRI Bioinformatics aims to support Flinders research groups with bioinformatics analyses, ranging from preprocessing large datasets with established pipelines through to hands-on analyses requiring custom software and tool development. We use where possible established nf-core pipelines or published and well-maintained pipelines preferably built using a workflow manager. We develop tools mostly with Snakemake to support custom applications for research groups. Aims and analyses are therefore quite varied, but impact is considerable as not all research groups can support a full time bioinformatician so having access to bioinformatics support when needed is greatly beneficial.
 
-
 ## How is ABLeS supporting this work?
 
 This work is supported through the Production Bioinformatics scheme provided by ABLeS.

participants/aus-biocommons.md

@@ -0,0 +1,43 @@
+---
+title: Australian BioCommons
+description: There are a wide range of applications of agentic AI that are emerging but questions of deployment, security and value are common amongst all types of users. This project seeks to investigate a number of applications of agentic AI in bioinformatics, understand the value of this applications to the end user compared to more manual alternatives and in the process understand the technical challenges and limitations of running these via locally deployable models.  
+toc: false
+type: ABLeS Participant
+page_id: aus-biocommons
+---
+
+## Project title
+
+Understanding the role and complexities of agentic workflows and local models in life-science applications
+
+## Collaborators and funding
+
+Australian BioCommons
+
+## Contact(s)
+
+Benjamin Goudey <benjamin@biocommons.org.au>
+
+## Project description and aims
+
+We will be using this project to:
+
+1) critically compare and contrast existing benchmarks of agentic systems in AI
+
+2) contrast the performance of  local and frontier models on these datasets across distinct metrics 
+
+3) understand how the different components of the system (model, reasoning budget, SKILLs and other setup configuration) influence performance in the syste, and how we can measure and optimise this.
+
+4) understand the strengths and limitations of the outputs and processes in these agentic workflows for users of different technical skill levels.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS.
+
+## Expected outputs enabled by participation in ABLeS
+
+We expect to produce research and whitepapers for this explored area. This wil be released as preprints and al source code will be made public.
+
+<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/ccdm.md

@@ -0,0 +1,47 @@
+---
+title: Centre for Crop and Disease Management - Curtin University
+description: AAGI and CCDM are advancing crop resilience and disease management by integrating genomics, pangenomics, structural bioinformatics, and advanced omics technologies to uncover genetic and molecular mechanisms underlying adaptation, virulence, and host defence in crops, pathogens, and pests.
+toc: false
+type: ABLeS Participant
+page_id: ccdm
+---
+
+## Project title
+
+Advancing bioinformatics, pangenomics and structural proteomics for plant pathology and improvement
+
+## Collaborators and funding
+
+- University of Western Australia - Prof Dave Edwards
+
+- Adelaide University - A. Prof Julian Taylor
+
+- [https://grdc.com.au/grdc-investments/investments/investment?code=CUR2210-005OPX](https://grdc.com.au/grdc-investments/investments/investment?code=CUR2210-005OPX)
+
+## Contact(s)
+
+Kristina Gagalova, CCDM, Curtin University, <kristina.gagalova@curtin.edu.au>
+
+## Project description and aims
+
+Our project investigates structural variation, gene presence–absence patterns, and evolutionary dynamics to understand traits such as disease resistance and environmental adaptation in Australian crops. We integrate with structural bioinformatics and protein modelling (e.g. AlphaFold and ESMFold) to predict how natural variants affect protein structure, stability, and interactions, revealing molecular mechanisms underlying plant–pathogen interactions and stress adaptation. 
+
+To support dissemination and accessibility, we also aim to develop interactive structure visualisation tools and a scalable database initially hosting 2,000–5,000 protein and protein–protein interaction models, with future expansion towards >50,000 structures. This platform will include a web application enabling users to explore and interact with pre-generated structural models, alongside integration of a locally hosted large language model (LLM) to facilitate natural-language querying and interpretation of the data.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS.
+
+## Expected outputs enabled by participation in ABLeS
+
+1) Development and release of curated datasets for protein–protein interaction analysis and querying. To be released through the web app described in the project.
+
+2) Comparative evaluation of structural bioinformatics and pangenomics tools, targeting high-impact Q1 journal publications.
+
+3) Development, release, and dissemination of open-source software and computational workflows with Nextflow.
+
+4) The project also supports HDR training outcomes, with an HDR student currently dedicated to the structural bioinformatics component; over the next stages of the project, this work is expected to generate publication-quality analyses leading to 2–3 research papers.
+
+<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/mel-latrobe.md

@@ -0,0 +1,40 @@
+---
+title: Molecular Ecology Lab, La Trobe University.
+description: Develop scalable nanopore DNA barcoding and phylogenetic workflows capable of processing thousands of Australian invertebrate specimens for biodiversity, conservation, and invasive species research.
+toc: false
+type: ABLeS Participant
+page_id: mel-latrobe
+---
+
+## Project title
+
+Scalable Nanopore DNA Barcoding and Phylogenetic Workflows for High-Throughput Australian Invertebrate Biodiversity Research
+
+## Collaborators and funding
+
+- La Trobe University
+- Deakin University
+- ARC Linkage
+- Christmas Island National Parks
+
+## Contact(s)
+
+Nick Murphy, La Trobe University. <n.murphy@latrobe.edu.au>
+
+## Project description and aims
+
+This project will develop scalable nanopore sequencing workflows for high-throughput DNA barcoding and phylogenetic analysis of Australian terrestrial invertebrates. The workflows will support the analysis of thousands of specimens for studies of short-range endemism, cryptic biodiversity, and ecological interactions associated with invasive yellow crazy ants, while providing reproducible and user-friendly pipelines that can be adopted by a broader research community.
+
+The project will deliver reproducible and user-friendly pipelines that enable routine analysis by non-specialist researchers on national computational infrastructure.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS.
+
+## Expected outputs enabled by participation in ABLeS
+
+Expected outputs include DNA barcode and phylogenetic sequence datasets for thousands of Australian terrestrial invertebrate specimens, peer-reviewed publications on short-range endemism and invasive species ecology, and reproducible nanopore analysis workflows for high-throughput biodiversity research. Sequence data will be deposited in public repositories such as NCBI GenBank and the Sequence Read Archive (SRA), while associated metadata, workflows, and documentation will be made available through GitHub and appropriate institutional or public data repositories to support reuse by the broader research community.
+
+<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/thekids-3.md

@@ -0,0 +1,52 @@
+---
+title: Translational Intelligence, The Kids Research Institute Australia
+description: The project involves development of agentic workflows to autonomously test bioinformatic tools, and subsequently construct novel agentic workflows to answer unexplored biomedical questions.
+toc: false
+type: ABLeS Participant
+page_id: thekids-3
+---
+
+## Project title
+
+Developing agentic systems autonomously using public biomedical data to accelerate and enrich research workflows.
+
+## Collaborators and funding
+
+- The Kids Research Institute Australia - https://www.thekids.org.au/
+
+- The University of Western Australia - https://www.uwa.edu.au
+
+## Contact(s)
+
+Kevin Chen, The Kids Research Institute Australia, kevin.chen@thekids.org.au
+
+## Project description and aims
+
+A large volume of bioinformatic tools are available to researchers, with new tools regularly released. While these offer potential, the process of using and evaluating these is challenging. For example, sufficient bioinformatic expertise is needed to understand how these tools could be used, with the process of understanding documentation, testing, and evaluating results being time-consuming. As a consequence, researchers will preference tools they are familiar with rather than those that will produce the most accurate results, and there are tools which have unexplored potential. Agentic workflows offer an opportunity to overcome these limitations - by designing tools that emulate the manual workflow used to test tools, it becomes possible to autonomously investigate the capabilities of these tools, systemtically benchmarking them to determine the strenghts and limitations of each one.
+
+This project aims to develop agentic workflows that will autonomously identify and test tools, including downloading appropriate testing and benchmarking data and metrics. The findings from this will then be used to autonomously consturct agentic workflows that are tailored to a user's use case, allowing for analyses where no established pipeline exists.
+
+Upon completion, it is envisaged that the project will:
+- assist researchers in determining which tools are most appropriate for their use case
+- help standardise benchmarking/testing procedures in domains where it is currently heterogeneous
+- provide a means for researchers, including those with little or no bioinformatic expertise, to use bioinformatic tools for their desired analyses
+
+Downstream, these are expected to assist researchers with analysing their data more efficiently, to uncover findings such as mechanisms underpinning diseases or drug targets. 
+
+The following analyses are planned:
+    - following development of the basic tool testing agentic workflow, this will be tested against a shortlist of 50 tools with a varying level of hardware/software requirements (e.g. those that could be run on a laptop, to those requiring GPUs)
+    - the capacity of the agentic workflow to a) correctly determine parameters, necessary hardware, b) generate biologically correct results against ground truths will be quantified.
+    - the performance of these agentic workflows against general coding agents, such as Claude Code and Codex, will be investigated
+
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS.
+
+## Expected outputs enabled by participation in ABLeS
+
+Findings are intended to be published via a manuscript - the target journal is Nature Methods. Furthermore, the code repository will be made publicly available via 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._

participants/thekids-4.md

@@ -0,0 +1,42 @@
+---
+title: Breastfeeding and immunology group, the Kids Reseach Institute Australia
+description: MicrobialExplorer is an interactive R Shiny web application for exploratory analysis and visualisation of microbiome sequencing data, supporting researchers without bioinformatics expertise to interrogate their own datasets.
+
+toc: false
+type: ABLeS Participant
+page_id: thekids-4
+---
+
+## Project title
+
+MicrobialExplorer
+
+## Collaborators and funding
+
+Breastfeeding and immunology group, the Kids Reseach Institute Australia
+
+## Contact(s)
+
+Patricia.AgudeloRomero <Patricia.AgudeloRomero@thekids.org.au>
+
+## Project description and aims
+
+MicrobialExplorer is a modular R Shiny application designed to make microbiome data analysis accessible to researchers without programming experience. The app provides an interactive interface for quality control, taxonomic composition, alpha and beta diversity, differential abundance, and functional analysis of 16S rRNA datasets.
+
+The aim of this project is to host MicrobialExplorer on a dedicated VM so that it can be deployed as a publicly accessible web application for the research community at The Kids Research Institute Australia and collaborating institutions. This will allow researchers to upload their own processed microbiome data and generate publication-quality visualisations and statistics without needing to write code, lowering the barrier to entry for microbiome data interpretation.
+
+The app is currently under active development, with modules for QC, composition, alpha diversity, beta diversity, and differential abundance completed, and a functional analysis module in progress. The broader impact includes supporting reproducible, standardised analysis workflows across multiple cohorts and projects at TKI, and forms part of a planned methods publication.
+
+## How is ABLeS supporting this work?
+
+This work is supported through the Production Bioinformatics scheme provided by ABLeS.
+
+## Expected outputs enabled by participation in ABLeS
+
+A publicly hosted instance of MicrobialExplorer, accessible via a web URL for use by researchers at The Kids Research Institute Australia and external collaborators. The application and its source code will be maintained on GitHub (agudeloromero/MicrobialExplorer) for transparency and reproducibility. A methods publication describing the application is also planned (target journal TBC).
+
+Hosting MicrobialExplorer through ABLeS will also support upcoming funding applications, including an ARC Future Fellowship and WA Department of Health grant opportunities.
+
+<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._