SPIM workflow manager for HPC.

Kožusznik, Jan; Bainar, Petr; Klímová, Jana; Krumnikl, Michal; Moravec, Pavel; Svatoň, Václav; Tomančák, Pavel

doi:10.1093/bioinformatics/btz140

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SPIM workflow manager for HPC.

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Tomančák, Pavel
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Kožusznik, J., Bainar, P., Klímová, J., Krumnikl, M., Moravec, P., Svatoň, V., et al. (2019). SPIM workflow manager for HPC. Bioinformatics (Oxford, England), 35(19), 3875-3876. doi:10.1093/bioinformatics/btz140.

Cite as: https://hdl.handle.net/21.11116/0000-0006-7E3A-D

Abstract

Here we introduce a Fiji plugin utilizing the HPC-as-a-Service concept, significantly mitigating the challenges life scientists face when delegating complex data-intensive processing workflows to HPC clusters. We demonstrate on a common Selective Plane Illumination Microscopy image processing task that execution of a Fiji workflow on a remote supercomputer leads to improved turnaround time despite the data transfer overhead. The plugin allows the end users to conveniently transfer image data to remote HPC resources, manage pipeline jobs and visualize processed results directly from the Fiji graphical user interface.