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Automation in Cytomics: A Modern RDBMS Based Platform for Image Analysis and Management in High-Throughput Screening Experiments

  • E. Larios
  • Y. Zhang
  • K. Yan
  • Z. Di
  • S. LeDévédec
  • F. Groffen
  • F. J. Verbeek
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7231)

Abstract

In cytomics bookkeeping of the data generated during lab experiments is crucial. The current approach in cytomics is to conduct High-Throughput Screening (HTS) experiments so that cells can be tested under many different experimental conditions. Given the large amount of different conditions and the readout of the conditions through images, it is clear that the HTS approach requires a proper data management system to reduce the time needed for experiments and the chance of man-made errors. As different types of data exist, the experimental conditions need to be linked to the images produced by the HTS experiments with their metadata and the results of further analysis. Moreover, HTS experiments never stand by themselves, as more experiments are lined up, the amount of data and computations needed to analyze these increases rapidly. To that end cytomic experiments call for automated and systematic solutions that provide convenient and robust features for scientists to manage and analyze their data. In this paper, we propose a platform for managing and analyzing HTS images resulting from cytomics screens taking the automated HTS workflow as a starting point. This platform seamlessly integrates the whole HTS workflow into a single system. The platform relies on a modern relational database system to store user data and process user requests, while providing a convenient web interface to end-users. By implementing this platform, the overall workload of HTS experiments, from experiment design to data analysis, is reduced significantly. Additionally, the platform provides the potential for data integration to accomplish genotype-to-phenotype modeling studies.

Keywords

Graphical User Interface Plate Design Soap Message Computer Cloud User Graphical User Interface 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • E. Larios
    • 1
  • Y. Zhang
    • 2
  • K. Yan
    • 1
  • Z. Di
    • 3
  • S. LeDévédec
    • 3
  • F. Groffen
    • 2
  • F. J. Verbeek
    • 1
  1. 1.Section Imaging and Bioinformatics, LIACSLeiden UniversityLeidenThe Netherlands
  2. 2.Centrum Wiskunde and InformaticaAmsterdamThe Netherlands
  3. 3.Department of Toxicology, LACDRLeiden UniversityLeidenThe Netherlands

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