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Reverse-Engineering Gene-Regulatory Networks using Evolutionary Algorithms and Grid Computing

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Abstract

Objective. Living organisms regulate the expression of genes using complex interactions of transcription factors, messenger RNA and active protein products. Due to their complexity, gene-regulatory networks are not fully understood.However, by building computational models it is possible to gain insight into their function and operation.Methods. Evolutionary algorithms are used to create computational models of gene-regulatory networks based on observed microarray data. These algorithms can be computationally intensive. They will be implemented within an existing grid computing infrastructure, that has been developed for data mining purposes, and which is able to deliver the required compute power.Results. We discuss how models can built achieved using distributed and grid computing technology. In particular we investigate how Condor and JavaSpaces technology is suited to the requirements of our modeling approach.Conclusions. Determining network models of gene-regulatory networks using evolutionary algorithms not only requires considerable computational power, but also a modeling formalism that can explain the underlying dynamics.

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Authors and Affiliations

  1. School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland

    Martin Swain (Dr.), Thomas Hunniford (Dr.) & Werner Dubitzky (Prof. Dr.)

  2. School of Biomedical Sciences, Weihenstephan University of Applied Sciences, Feising, Germany

    Johannes Mandel & Niall Palfreyman (Dr.)

Authors
  1. Martin Swain
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  2. Thomas Hunniford
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  3. Werner Dubitzky
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  4. Johannes Mandel
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  5. Niall Palfreyman
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Corresponding author

Correspondence to Martin Swain.

Additional information

Based on “Modeling Gene-Regulatory Networks using Evolutionary Algorithms and Distributed Computing”, by M. Swain, T. Hunniford, W. Dubitzky, J. Mandel and N. Palfreyman which appeared in the Third International Workshop on Biomedical Computations on the Grid © 2005 IEEE.

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Swain, M., Hunniford, T., Dubitzky, W. et al. Reverse-Engineering Gene-Regulatory Networks using Evolutionary Algorithms and Grid Computing. J Clin Monit Comput 19, 329–337 (2005). https://doi.org/10.1007/s10877-005-0678-x

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  • DOI: https://doi.org/10.1007/s10877-005-0678-x

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