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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Field Markup Language: biological field representation in XML.

David Chang1, Nigel H Lovell, Socrates Dokos

  • 1Graduate School of Biomedical Engineering, University of New South Wales, Sydney 2052, Australia.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
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Summary

A new Field Markup Language (FML) standardizes biological model data exchange. This framework integrates with CellML to build complex tissue models, demonstrated with a cardiac pacemaker example.

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Biophysics

Background:

  • The proliferation of biological models online necessitates standardized frameworks for data access and visualization.
  • Existing frameworks lack comprehensive support for describing and exchanging field information crucial for biological modeling.

Purpose of the Study:

  • To introduce the Field Markup Language (FML) as a standardized framework for biological model description and data exchange.
  • To demonstrate the integration of FML with CellML for constructing multi-scale biological models.
  • To present a practical application of FML and CellML in modeling cardiac electrophysiology.

Main Methods:

  • Development of the Field Markup Language (FML) based on the Physiome Modeling Framework.
  • Implementation of a supporting application framework for FML.
  • Integration of CellML models within the FML framework.
  • Construction and simulation of a spatially-heterogeneous cardiac pacemaker model using FML and CellML.

Main Results:

  • FML provides a standardized method for describing and exchanging biological field information.
  • The FML framework successfully incorporates CellML models to build tissue-scale models.
  • A cardiac pacemaker model was successfully constructed and solved using FML and CellML, demonstrating electrical activation and propagation.

Conclusions:

  • FML offers a standardized solution for managing and integrating diverse biological models.
  • The integration of FML and CellML enables the development of complex, multi-scale biological simulations.
  • This approach facilitates the study of physiological processes like cardiac electrical activity.