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Publication Detail
Addressing the challenges of multiscale model management in systems biology
  • Publication Type:
    Conference
  • Authors:
    Hetherington J, Bogle IDL, Saffrey P, Margoninski O, Li L, Varela Rey M, Yamaji S, Baigent S, Ashmore J, Page K, Seymour RM, Finkelstein A, Warner A
  • Publisher:
    Pergamon-Elsevier Science Ltd
  • Publication date:
    15/08/2007
  • Place of publication:
    Glasgow, Scotland
  • Pagination:
    962, 979
  • Published proceedings:
    Computers and Chemical Engineering
  • Volume:
    31
  • Issue:
    8
  • Print ISSN:
    0098-1354
  • Keywords:
    modelling, systems, biology, metadata, middleware, SOFTWARE, ENVIRONMENT, OSCILLATIONS, INFORMATION, SIMULATION, GENES, CELLS
  • Notes:
    2007/08/15/ 281 10.1016/j.compchemeng.2006.10.004 Mathematical and computational modelling are emerging as important techniques for studying the behaviour of complex biological systems. We argue that two advances are necessary to properly leverage these techniques: firstly, the ability to integrate models developed and executed on separate tools, without the need for substantial translation and secondly, a comprehensive system for storing and man-ageing not only the models themselves but also the parameters and tools used to execute those models and the results they produce. A framework for modelling with these features is described here. We have developed of a suite of XML-based services used for the storing and analysis of models, model parameters and results, and tools for model integration. We present these here, and evaluate their effectiveness using a worked example based on part of the hepatocyte glycogenolysis system. (c) 2006 Elsevier Ltd. All rights reserved.
Abstract
Mathematical and computational modelling are emerging as important techniques for studying the behaviour of complex biological systems. We argue that two advances are necessary to properly leverage these techniques: firstly, the ability to integrate models developed and executed on separate tools, without the need for substantial translation and secondly, a comprehensive system for storing and man-ageing not only the models themselves but also the parameters and tools used to execute those models and the results they produce. A framework for modelling with these features is described here. We have developed of a suite of XML-based services used for the storing and analysis of models, model parameters and results, and tools for model integration. We present these here, and evaluate their effectiveness using a worked example based on part of the hepatocyte glycogenolysis system.
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