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Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}

Submitted by karopka on Sun, 2016/12/11 - 19:48
TitleJenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}
Publication TypeJournal Article
Year of Publication2016
AuthorsMoutsatsos, IK, Hossain, I, Agarinis, C, Harbinski, F, Abraham, Y, Dobler, L, Zhang, X, Wilson, CJ, Jenkins, JL, Holway, N, Tallarico, J, Parker, CN
JournalJournal of Biomolecular Screening
KeywordsCellProfiler, continuous integration, high-content screening, high-performance computing

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.

PubMed ID27899692
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