A Specification Language and a Framework for the Execution of Composite Models in Systems Biology

  • Ofer Margoninski
  • Peter Saffrey
  • James Hetherington
  • Anthony Finkelstein
  • Anne Warner
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230)


When modelling complex biological systems it is often desirable to combine a number of distinct sub-models to form a larger composite model. We describe an XML based language that can be used to specify composite models and a lightweight computational framework that executes these models. The language supports specification of structure and implementation details for composite models, along with the interfaces provided by each sub-model. The framework executes each sub-model in its native environment, allowing extensive reuse of existing models. It uses mathematical and computational connectors and translators to unify the models computationally. Unlike other suggested approaches for model integration, our approach does not impose one modeling scheme, composition algorithm or underlying middleware framework. We demonstrate our approach by constructing a composite model describing part of the glucose homeostasis system.


System Biology Composite Model System Biology Markup Language High Level Architecture Model Integration Framework 
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 2006

Authors and Affiliations

  • Ofer Margoninski
    • 1
  • Peter Saffrey
    • 1
  • James Hetherington
    • 1
  • Anthony Finkelstein
    • 1
  • Anne Warner
    • 1
  1. 1.Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, (CoMPLEX)University College LondonLondon

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