Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq

Camila L. Goclowski, Julia Jakiela, Tyler Collins, Saskia Hiltemann, Morgan Howells, Marisa Loach, Jonathan Manning, Pablo Moreno, Alex Ostrovsky, Helena Rasche, Mehmet Tekman, Graeme Tyson, Pavankumar Videm, Wendi Bacon*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Background: 

Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning to code while analyzing data is difficult. The curve may be flattened by separating these two aspects and providing intermediate steps for budding bioinformaticians. Single-cell analysis is in great demand from biologists and biomedical scientists, as evidenced by the proliferation of training events, materials, and collaborative global efforts like the Human Cell Atlas. However, iterative analyses lacking reinstantiation, coupled with unstandardized pipelines, have made effective single-cell training a moving target. 

Findings: 

To address these challenges, we present a Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for single-cell RNA sequencing (scRNA-seq) analysis, which offers parallel analytical methods using a graphical interface (buttons) or code. With clear, interoperable materials, MIGHTS facilitates smooth transitions between environments. Bridging the biologist–programmer gap, MIGHTS emphasizes interdisciplinary communication for effective learning at all levels. Real-world data analysis in MIGHTS promotes critical thinking and best practices, while FAIR data principles ensure validation of results. MIGHTS is freely available, hosted on the Galaxy Training Network, and leverages Galaxy interfaces for analyses in both settings. Given the ongoing popularity of Python-based (Scanpy) and R-based (Seurat & Monocle) scRNA-seq analyses, MIGHTS enables analyses using both. 

Conclusions: 

MIGHTS consists of 11 tutorials, including recordings, slide decks, and interactive visualizations, and a demonstrated track record of sustainability via regular updates and community collaborations. Parallel pathways in MIGHTS enable concurrent training of scientists at any programming level, addressing the heterogeneous needs of novice bioinformaticians.

Original languageEnglish
Article numbergiae107
JournalGigaScience
Volume14
DOIs
Publication statusPublished - 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2025.

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