Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform
| Autor: | Imtiaz Hossain, Jeremy L. Jenkins, Yann Abraham, Nicholas Holway, Xian Zhang, John A. Tallarico, Christine D. Wilson, Fred Harbinski, Christian N. Parker, Ioannis Moutsatsos, Claudia Agarinis, Luc Dobler |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Computer science Reuse computer.software_genre Bioinformatics high-content screening Biochemistry Analytical Chemistry Cell Line Workflow 03 medical and health sciences User-Computer Interface continuous integration Computer cluster CellProfiler Image Processing Computer-Assisted Animals Humans Plug-in RNA Small Interfering Original Research Data processing Internet business.industry high-performance computing Phosphoproteins Molecular Imaging 030104 developmental biology Gene Expression Regulation Scalability Molecular Medicine User interface Software engineering business computer Algorithms Biotechnology Data integration |
| Zdroj: | Slas Discovery |
| ISSN: | 2472-5560 2472-5552 |
| Popis: | High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. |
| Databáze: | OpenAIRE |
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