Interactive Tools (IT) in Galaxy

Combining Synchronous and Asynchronous Workflows

Authors

DOI:

https://doi.org/10.52825/cordi.v1i.419

Keywords:

Interactive Tools, Galaxy, Workflows, Notebooks, Jupyter, R Studio

Abstract

Galaxy [1] is a GUI-based scientific data management and analysis platform that aims to expand the target audience of scientific computing to scientists without advanced computer literacy or access to computing infrastructure. During the operation of a typical asynchronous workflow, the interaction of the user triggers a job submission to a hosted computing system, the results of which are then reported back to the user upon completion of the task. However, such an asynchronous interaction scheme is not compatible with scientific software that require user interaction during the execution itself (synchronous), e.g. many data visualisation software. Interactive Tools on Galaxy (IT; [2]) leverage tool and job components of Galaxy by taking advantage of the latest containerization solutions to provide access to interactive executable software. With ITs, Galaxy is enabling the more and more common use-case of asynchronous workflows while keeping the possibility to bridge at any time to synchronous workflows and reusing all the other Galaxy data management features.

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References

The Galaxy Community - Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update; Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351, https://doi.org/10.1093/nar/gkac247 DOI: https://doi.org/10.1093/nar/gkac610

Gruning, B.A. et al. (2017) Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PLoS Comput Biol, 13, e1005425. https://doi.org/10.1371/journal.pcbi.1005425 DOI: https://doi.org/10.1371/journal.pcbi.1005425

https://training.galaxyproject.org/training-material/topics/admin/tutorials/interactive-tools/tutorial.html (accessed Apr. 24, 2023).

https://realpython.com/jupyter-notebook-introduction/ (accessed Apr. 24, 2023).

https://cfp.jupytercon.com/2020/schedule/presentation/184/climate-jupyterlab-as-an-interactive-tool-in-galaxy/ (accessed Apr. 24, 2023).

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Published

2023-09-07

Conference Proceedings Volume

Section

Poster presentations II (Call for Papers)
Received 2023-04-27
Accepted 2023-06-30
Published 2023-09-07