Interactive Workflows in a Virtual Laboratory for e-Bioscience: The SigWin-Detector Tool for Gene Expression Analysis

  • Authors:

  • Marcia A. Inda;Adam S. Z. Belloum;Marco Roos;Dmitry Vasunin;Cees de Laat;L. O. Hertzberger;Timo M. Breit

  • Affiliations:

  • University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands;University of Amsterdam, the Netherlands

  • Venue:
  • E-SCIENCE '06 Proceedings of the Second IEEE International Conference on e-Science and Grid Computing
  • Year:
  • 2006

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Abstract

Explorative research is a vital part of biological sciences. Biologists frequently have to examine and compare multiple (large) sets of biological data in an interactive and explorative manner. Exploring alternative ways of examining the data and managing the necessary resources often require substantial (manual) effort and time. In this paper, we present a concrete example of how VLAM, a grid-based workflow management system, can enhance experimentation. We discuss in detail the process of developing the SigWin-detector, an application in the domain of bioinformatics. We show that SigWin-detector can promptly identify regions of increased gene expression in transcriptome maps and periodicity in weather data. We also show that the workflow can be extended or partially modified. The individual modules can also be used to compose different experiments. SigWin-detector fulfills the requirements of interactive and explorative experimentation.