@article {1162, title = {Jenkins-{CI}, an {Open}-{Source} {Continuous} {Integration} {System}, as a {Scientific} {Data} and {Image}-{Processing} {Platform}}, journal = {Journal of Biomolecular Screening}, year = {2016}, 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}, issn = {1552-454X}, doi = {10.1177/1087057116679993}, author = {Moutsatsos, Ioannis K. and Hossain, Imtiaz and Agarinis, Claudia and Harbinski, Fred and Abraham, Yann and Dobler, Luc and Zhang, Xian and Wilson, Christopher J. and Jenkins, Jeremy L. and Holway, Nicholas and Tallarico, John and Parker, Christian N.} } @article {975, title = {"Just Another Tool for Online Studies" (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0130834}, abstract = {

We present here "Just Another Tool for Online Studies" (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS{\textquoteright} main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0130834}, author = {Lange, Kristian and K{\"u}hn, Simone and Filevich, Elisa} } @article {10.1371/journal.pone.0014094, title = {JULIDE: A Software Tool for 3D Reconstruction and Statistical Analysis of Autoradiographic Mouse Brain Sections}, journal = {PLoS ONE}, volume = {5}, number = {11}, year = {2010}, month = {11}, pages = {e14094}, publisher = {Public Library of Science}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, doi = {10.1371/journal.pone.0014094}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J. and Thiran, Jean-Philippe} } @article {1042, title = {JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.}, journal = {PLoS One}, volume = {5}, year = {2010}, month = {2010}, pages = {e14094}, abstract = {

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

}, keywords = {Animals, Autoradiography, Brain, Carbon Radioisotopes, Deoxyglucose, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Male, Maze Learning, Mice, Mice, Inbred C57BL, Reproducibility of Results, Software}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014094}, author = {Ribes, Delphine and Parafita, Julia and Charrier, R{\'e}mi and Magara, Fulvio and Magistretti, Pierre J and Thiran, Jean-Philippe} }