Single-cell and spatial omics (SPO) technologies advance precision medicine by characterising disease aetiology and resistance at a cellular level, enabling more precise treatment predictions, drug development, and diagnostics (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645080/). Public data initiatives have led to over 390 petabytes of data stored in the European Bioinformatics Institute (https://www.ebi.ac.uk/about/our-impact) and over 62 million single cells in the Human Cell Atlas data portal (https://data.humancellatlas.org/). SPO analysis is difficult, requiring numerous subjective decisions with no unified pipeline. SPO analysis remains the purview of computationally trained scientists - a significant and growing skills shortage. The Galaxy Project enables non-programmers to perform free analysis in a graphical user interface with embedded FAIR (findable, accessible, interoperable and reproducible) features. The Galaxy Single-cell and sPatial Omics Community (SPOC) of practice (https://galaxyproject.org/community/sig/singlecell/) has built a wealth of tools, tutorials, and slide decks to support non-programmers to learn and apply SPO analyses in Galaxy. We spearheaded the development of unified subdomains (https://singlecell.usegalaxy.eu/), created community development training for other communities, and pushed feature development for our extensive training site (https://training.galaxyproject.org/training-material/topics/single-cell/) within the Galaxy Training Network, using expertise in both bioinformatics and STEM education best practices.
However, the ‘publish or perish’ pressures within academia leads to “feature creep”, the proliferation of new tools, software and training that are not maintained after their initial publications. Resources become quickly out of date, which can lead to frustration or even completely block scientists trying to learn to analyse, access, or use this critical data.
SPOC has committed to both expanding and, importantly, maintaining its offerings. We therefore propose a Hackathon project to check, test, update, import, and improve the SPO resources in Galaxy. Contributors can range from Galaxy enthusiasts to people new to Github, as we have low-level (fixing typos across pages; testing tutorials); mid-level (updating slide-decks and best practices; updating workflows); and high-level (adding workflow-testing; converting documents and workflows to tutorials) options for contributors depending on time and expertise.
Wendi Bacon, Morgan Howells