Overview
BioShell supports nationally delivered training events and research projects across Australia.
Training
The following training has been delivered using BioShell as the computational environment. All training run by Australian BioCommons are openly available via Zenodo.
Unlocking nf-core: customising workflows for your research
Samaha G, Willet C, Hakkaart C, Beecroft S, Stott A, Ip A, Cooke S (2023)
RNASeq: reads to differential genes and pathways
Samaha G, Deshpande N, Lu C-Y, Chung J, Stott A, Ip A (2023)
Genetic Outlier Analysis
Stuart K, Samaha G, Barugahare A, Miller S, Deshpande N, Lu C-Y (2024)
Nextflow for the life sciences
Jaya F, Geaghan M, Xue W, Antczak M, Gauthier M-E, Beecroft S, O'Brien M, et al (2025)
Spatial omics
Jaya F, Williams S, O'Brien MJ, Matigian N, Thind AS, Wang C, Mori G (2025)
Introduction to the Linux Command Line Workshop
Allan J, Merce C, Kadolsky U, Zhang A (2026)
Unlocking nf-core: customising workflows for your research
Willet C, Geaghan M, Gagalova K, Antczak M, Samaha G, O'Brien M (2026)
Nextflow for the life sciences (Peter Mac rerun)
Lupat R and Li S (2026)
Single cell RNAseq analysis in R (QCIF rerun)
Matigan N, Williams S (2026)
Single cell RNAseq analysis in R
Williams S, Jaya F, Barugahare A, Harrison P (2026)
Spatial omics (QCIF rerun)
Williams S, Matigan N (2026)
Spatial omics sampler
Williams S (2026)
Supported research
BioShell has supported research projects across a range of molecular life sciences disciplines. This section highlights projects that have used BioShell as part of their research.
Mapping the co-aggregation proteome of TDP-43 in models of ALS/FTD
We aim to understand the molecular and cellular causes of amyotrophic lateral sclerosis (ALS)/motor neuron disease (MND) and frontotemporal dementia (FTD). To this end we employ various genetically engineered in vitro and in vivo model systems, advanced microscopy and biochemistry techniques to develop and test potential therapeutics in proof-of-concept pre-clinical studies.
Sequence-specific targeting of retroviral RNAs
This project will deliver a versatile, scalable RNA-targeting workflow applicable to difficult or repetitive sequences. By exploiting the therapy-ready humanised CRISPR-Cas-Inspired RNA Targeting System (CIRTS) technology, this project will generate a validated toolbox for the design and screening of targeting RNAs at scale, primed for translation.
Functional dissection of a conserved systemic block governing seed nitrogen quality in soybean
Identify and characterise amino acid transporter genes associated with nitrogen transport and redistribution in soybean. Bioshell will be used to perform computationally intensive analyses including comparative genomics, RNA-sequencing data analysis, phylogenetic reconstruction and genome-wide functional annotation
Analysis of data for prediction of cancer patient response to checkpoint therapy
This project investigates multi-omic biomarkers that provide robust, reproducible prediction of a cancer patient's likelihood of responding to immune checkpoint blockade. By integrating bulk RNA-seq and ATAC-seq with flow-cytometric immune subset profiling, we aim to uncover the transcriptomic and epigenetic determinants of primary immunotherapy resistance across lung cancer and melanoma cohorts.
Fungicide Sensitivity in Cereal Rust Pathogens
This project investigates variation in fungicide sensitivity among cereal rust pathogens and explores factors associated with reduced sensitivity. The research aims to improve understanding of fungicide responses and support effective management of cereal rust diseases.
Human Cardiac Regeneration
Investigating omics datasets of human cardiomyocytes in health and disease. We will use published data to investigate drivers of cardiomyocyte mitosis.
Fields of research
BioShell is equipped to support bioinformatics across a broad range of disciplines. The projects above span the following fields of research.