title: Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.
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.
authors.affiliation: 1 Developmental and Molecular Pathways, NIBR, Cambridge, MA, USA.
authors.forename: Ioannis K
authors.initials: IK
authors.lastname: Moutsatsos
authors.affiliation: 2 Centre for Proteomic Chemistry, NIBR, Postfach, Basel, Switzerland.
authors.forename: Imtiaz
authors.initials: I
authors.lastname: Hossain
authors.affiliation: 3 Developmental and Molecular Pathways, NIBR, Postfach, Basel, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Agarinis
authors.affiliation: 4 Editas Medicine, Cambridge, MA, USA.
authors.forename: Fred
authors.initials: F
authors.lastname: Harbinski
authors.affiliation: 5 The Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Vlaanderen, Belgium.
authors.forename: Yann
authors.initials: Y
authors.lastname: Abraham
authors.affiliation: 6 République et Canton du Jura, Switzerland.
authors.forename: Luc
authors.initials: L
authors.lastname: Dobler
authors.affiliation: 2 Centre for Proteomic Chemistry, NIBR, Postfach, Basel, Switzerland.
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: 4 Editas Medicine, Cambridge, MA, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Wilson
authors.affiliation: 1 Developmental and Molecular Pathways, NIBR, Cambridge, MA, USA.
authors.forename: Jeremy L
authors.initials: JL
authors.lastname: Jenkins
authors.affiliation: 7 Scientific Computing, NIBR Informatics, Novartis, Postfach, Basel, Switzerland.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Holway
authors.affiliation: 1 Developmental and Molecular Pathways, NIBR, Cambridge, MA, USA.
authors.forename: John
authors.initials: J
authors.lastname: Tallarico
authors.affiliation: 3 Developmental and Molecular Pathways, NIBR, Postfach, Basel, Switzerland.
authors.forename: Christian N
authors.initials: CN
authors.lastname: Parker
mesh_terms: D000465:Algorithms; D000818:Animals; D002460:Cell Line; D005786:Gene Expression Regulation; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D020407:Internet; D057054:Molecular Imaging / Q000379:methods / Q000706:statistics & numerical data*; D010750:Phosphoproteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface; D057188:Workflow
chemical_list: D010750:Phosphoproteins; D034741:RNA, Small Interfering
keywords: CellProfiler; continuous integration; high-content screening; high-performance computing