Moutsatsos, Ioannis, Hossain, Imtiaz, Agarinis, Claudia, Harbinski, Fred, Abraham, Yann, Dobler, Luc, Zhang, Xian, Wilson, Chris, Jenkins, Jeremy, Holway, Nicholas, Myer, Vic, Tallarico, John, Mickanin, Craig and Parker, Christian (2016) Jenkins-CI, an open source continuous integration system, as a scientific data and image processing platform. Journal of Biomolecular Screening, publis (2016 N). pp. 1-24. ISSN PMID: 27899692

Abstract

Image based screening assays generate large volumes of heterogeneous data, requiring a plethora of computational tools for processing and analysis. Building robust, scalable workflows for such applications is a major undertaking; requiring collaboration between scientists and engineers with their own specialized area of expertise.
Jenkins-CI, is an open source continuous integration system, which has been used to build an analysis platform for processing high content screening results (HCS). The availability of over 800 plugins for Jenkins-CI enables numerous standard computing tasks and allows the robust integration of specialized applications designed high throughput screening.
CellProfiler is an open source resource that has become one of the preferred tools for the analysis and quantification of biological images. Jenkins-CI has made it possible to configure CellProfiler for high performance, parallel processing on Linux clusters deployed at two distant locations. This ability to deploy, at scale, and to parallelize the use of CellProfiler greatly facilitates its use in high throughput screening applications.
The Jenkins-CI platform described here is accessible via an internet web interface facilitating sharing, annotating and reuse of protocols and results. Image processing pipelines developed using the CellProfiler desktop client can be deployed and shared through a centralized Jenkins repository. Centralized monitoring of the system allows operational issues to be quickly identified, facilitating user support. Limitations in the user interface of Jenkins were addressed using plugins from the Jenkins-CI community. Examples showing how Jenkins-CI can be used to run CellProfiler for the analysis of HCS assays is presented.

Item Type:	Article
Keywords:	CellProfiler, Continuous Integration, High Content Screening, High Performance Computing
Date Deposited:	07 Dec 2016 00:45
Last Modified:	07 Dec 2016 00:45
URI:	https://oak.novartis.com/id/eprint/29802