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SLAS Discov. 2017 Mar;22(3):238-249. doi: 10.1177/1087057116679993. Epub 2016 Dec 13.

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

Author information

1
1 Developmental and Molecular Pathways, NIBR, Cambridge, MA, USA.
2
2 Centre for Proteomic Chemistry, NIBR, Postfach, Basel, Switzerland.
3
3 Developmental and Molecular Pathways, NIBR, Postfach, Basel, Switzerland.
4
4 Editas Medicine, Cambridge, MA, USA.
5
5 The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Vlaanderen, Belgium.
6
6 République et Canton du Jura, Switzerland.
7
7 Scientific Computing, NIBR Informatics, Novartis, Postfach, Basel, Switzerland.

Abstract

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.

KEYWORDS:

CellProfiler; continuous integration; high-content screening; high-performance computing

PMID:
27899692
PMCID:
PMC5322829
DOI:
10.1177/1087057116679993
[Indexed for MEDLINE]
Free PMC Article

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