SAGC Seminar Series and Bioinformatics Workshops
We host a monthly seminar series promoting local and national genomics excellence in research
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Reports and Summaries from Past Meetings
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Instructor: Daniel Thomson
Approximately 30 participants attended our full-day RNA-seq Analysis Workshop at the stunning new Flinders City Campus. The workshop aimed to provide a comprehensive overview of RNA-seq applications and a step-by-step guide to conducting RNA-seq analysis for mRNA differential expression, with in-depth explanations on both executing the analysis and interpreting the results. Additionally, participants were given hands-on experience with Nextflow and nf-core pipelines, familiarizing themselves with these powerful tools for RNA-seq data processing.
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Speaker: Stefano Mangiola
Dr. Stefano Mangiol, Group Leader of Computational Cancer Immunogenomics, at SAiGENCI/The University of Adelaide, gave of a fantastic talk discussing the mammoth undertaking in developing a comprehensive immune system single cell atlas by integrating data from nearly 13,000 single-cell RNA sequencing samples across 45 anatomical sites. He covered the novel methods (tidyomics) and software infrastructure used to model this large-scale data, providing a foundational resource for advancing precision medicine.
Instructors: Cathal King and John Salamon
Led by Cathal King and John Salamon, this workshop focused on data analysis techniques surrounding spatial omic experiments. Attendees got the opportunity to analyse and handle data outputs from 3 main spatial omic technologies namely 10x Visium, 10x Xenium and Stereo-seq (STOmics). Key concepts for analysing spatial omics data were taught including spatially variable gene analysis, cell-type de-convolution and image processing. Dr Davis McCarthy from SVI was also in attendance and gave a talk on his recent work in spatial omics and bioinformatic method development.
Instructors: Michael Roach, John Salamon, Ziad Al-Bkhetan
In a full-day workshop on bioinformatics workflow management software, a head-to-head comparison was made between two of the most popular solutions, Nextflow and Snakemake. Participants were guided through converting a simple workflow implemented in Bash into a Snakemake workflow in the morning (led by Michael), and a Nextflow workflow in the afternoon (led by John). Finally, Ziad provided a demonstration of the capabilities of Seqera Platform's integration with Nextflow as made available to Australian researchers through BioCommons.
Instructors: Cathal King and Daniel Thomson
26 people attended this bioinformatics workshop located at the Braggs building on the University of Adelaide campus. Attendees got hands on experience in the processing and analysis of single-cell RNA-seq data. The workshop covered the key concepts underpinning single-cell technologies and the appropriate data structures and file formats most commonly used. Mainly focused around the R language, the workshop covered common analyses such as cell clustering, dimensionality reduction, differential gene expression, cell type annotation and data visualisation.