Single Cell Omics Update: Meeting Cancelled, Spatial Omics Events & Lab Call-Out

[Tiffanie Nelson]

Dear colleagues,

Please note that today's meeting is cancelled due to the unavailability of a speaker. We will reconvene on Wednesday, November 19th, at 13:00 AEDT.

At our next meeting, Cabiria Liang, a PhD candidate from the Sydney Precision Data Science group at The University of Sydney, will present BenchHub, a framework for discovering curated datasets for methodology benchmarking. We welcome any other presentations or topic suggestions. You can view the meeting agenda here.

I also have two upcoming event announcements and a call-out for involvement:

Event Announcement - Webinar: Getting started with spatial omics

• Spatial omics offers unprecedented opportunities to understand cells, tissues, and systems by integrating omics and imaging technologies. This webinar will provide an introduction to the evolving field of spatial omics and its various methods. We will begin with an overview of spatial omics and how it differs from other omics methods, then explore considerations for data analysis, compare and contrast available tools, and delve into some of the bioinformatics theory.

• When: September 10, 2025, 12pm AEST

• More information and registrations: https://www.biocommons.org.au/events/spatial-omics-webinar-2025

Event Announcement - Workshop: Spatial omics

• This hands-on workshop will teach you how to analyze data from in situ spatial experiments (e.g., CosMx, Xenium) using Seurat in R to visualize gene expression within tissue samples. Using real experimental data, we will go through the process of data import, quality control, filtering, dimensionality reduction, visualization, and differential expression analysis. We will discuss the rationale behind each step and essential best practices for designing and running spatial omics experiments.

• When: October 28-29, 2025 (Applications close October 10)

• More information and applications: https://www.biocommons.org.au/events/spatial-omics-workshop-2025

Call-out for help to curate the Single Cell Omics Analysis Lab

As you may know, we are developing a Single Cell Analysis Lab on Galaxy Australia, and we'd love your input! What tools and workflows would you find most useful? Would it be beneficial to include Spatial Omics tools?

I am looking for interested individuals to join in a working group to discuss how to make this Single Cell Analysis Lab user-friendly with relevant tools and workflows. If you are interested in joining, please let me know.

If you are new to the Galaxy platform, here are some Single Cell Omics Analysis tutorials you can access now:

• Inferring single cell trajectories with Scanpy

• Pre-processing of 10X Single-Cell ATAC-seq Datasets

• Multi-sample batch correction with Harmony and SnapATAC2

If you are interested in joining the Single Cell Lab Galaxy working group or have other topic ideas, please get in touch.

Regards,
Tiff

NB: You can join this Single Cell and Spatial Omics Google Group from any email address (without the need for a Google Account) by emailing singlecellom...@biocommons.org.au

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Tiff Nelson, PhD (she/her)

Genomics Research Community Engagement Lead
Australian BioCommons

The University of Melbourne

M: +61 (0) 476 985 154

W: biocommons.org.au

I work flexibly. If I am sending this message outside of normal business hours it is because it suits me. There is no expectation on my part that you will respond outside of your working hours.

My position is funded by Bioplatforms Australia and hosted by The University of Melbourne.

I acknowledge the Traditional Owners of the lands upon which I work and pay my respects to their Elders, both past and present.