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    News 2023-08-25

    Success Story: Galaxy Single Cell Training for Researchers project

    The Galaxy Single Cell Training for Researchers project resulted in multiple single-cell analysis workflows and helpful tutorials.

    Three EOSC-Life Training Open Calls were issued from 2020-2023, and a total of 15 projects received funding.

    Success Story: Galaxy Single Cell Training for Researchers project

    In this project, funded in the third Open call, allowed multiple single-cell analysis workflows to be built by using the freely accessible and user-friendly Galaxy project interface. Training materials hosted on the interactive Galaxy training platform were also created that teach users how to perform this analysis.

    Specifically, Julia Jakiela at the University of Edinburgh (supervised by Wendi Bacon, The Open University) built and documented these multiple workflows to expand the open access Galaxy single-cell tutorial suite, creating the first Jupyter Notebook tutorials in the Galaxy environment.

    Responding to user needs

    Jakiela also created parameter iteration workflows and tutorials and trajectory analysis tools. Users can follow these workflows and tutorials to test numerous parameters simultaneously. She also added workflow testing and updates to improve sustainability and best practices across numerous tutorials.

    Using these tutorials effectively

    Users (also non-programmers) can follow these tutorials  to perform multi-language analyses (i.e. by using either Seurat/R-based functions or Scanpy/Python-based functions) and make batch correction comparisons, ensuring usability and accurate application. These resources will help bench biologists and clinicians analyse single-cell data more effectively even if they lack programming skills.

    Spreading the word about project outcomes

    Jakiela delivered these tutorials at an EBI single cell course in early 2023 at the global free Galaxy Smörgasbord (with over 2000 participants!). She also presented on her work (and demonstrated the workflows) at the Galaxy Community Conference in Brisbane, Australia. See a related post from this event here.

    EOSC-Life funding made it possible to create and deliver these training resources, and also allowed Jakiela (an undergraduate student at time the work was completed) to benefit significantly from networking within the Galaxy community.

    Sustainable outcomes

    Read an earlier associated EOSC-Life news story.

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