用于高性能计算的 SPIM 工作流管理器。
SPIM workflow manager for HPC.
机构信息
Department of Computer Science, FEECS VSB-Technical University of Ostrava, Ostrava, Czech Republic.
IT4Innovations, VSB-Technical University of Ostrava, Ostrava, Czech Republic.
出版信息
Bioinformatics. 2019 Oct 1;35(19):3875-3876. doi: 10.1093/bioinformatics/btz140.
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.
摘要
在这里，我们介绍了一个 Fiji 插件，利用了高性能计算即服务的概念，极大地缓解了生命科学家在将复杂的数据密集型处理工作流程委托给高性能计算集群时所面临的挑战。我们以常见的选择性平面照明显微镜图像处理任务为例，展示了在远程超级计算机上执行 Fiji 工作流程可以在数据传输开销的情况下提高周转时间。该插件允许最终用户方便地将图像数据传输到远程高性能计算资源，从 Fiji 图形用户界面管理管道作业并可视化处理结果。
可用性和实现
该代码以 MIT 许可证的形式免费开源分发。源代码：https://github.com/fiji-hpc/hpc-workflow-manager/，文档：https://imagej.net/SPIM_Workflow_Manager_For_HPC。
补充信息
补充数据可在 Bioinformatics 在线获得。
Zotero 插件