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SPIM workflow manager for HPC
J. Kožusznik, P. Bainar, J. Klímová, M. Krumnikl, P. Moravec, V. Svatoň, P. Tomančák,
Language English Country Great Britain
Document type Journal Article, Research Support, Non-U.S. Gov't
NLK
Free Medical Journals
from 1996 to 1 year ago
PubMed Central
from 2007
Open Access Digital Library
from 1996-01-01
Medline Complete (EBSCOhost)
from 1998-01-01
Oxford Journals Open Access Collection
from 1985-01-01 to 2022-09-30
Oxford Journals Open Access Collection
from 1985-01-01
ROAD: Directory of Open Access Scholarly Resources
from 1998
- MeSH
- Microscopy MeSH
- Image Processing, Computer-Assisted MeSH
- Workflow * MeSH
- Software * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The code is distributed free and open source under the MIT license. Source code: https://github.com/fiji-hpc/hpc-workflow-manager/, documentation: https://imagej.net/SPIM_Workflow_Manager_For_HPC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
References provided by Crossref.org
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- $a SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The code is distributed free and open source under the MIT license. Source code: https://github.com/fiji-hpc/hpc-workflow-manager/, documentation: https://imagej.net/SPIM_Workflow_Manager_For_HPC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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- $a Krumnikl, Michal $u Department of Computer Science, FEECS VSB-Technical University of Ostrava, Ostrava, Czech Republic. IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic.
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