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CellML and associated tools and techniques.

Alan Garny1, David P Nickerson, Jonathan Cooper

  • 1Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK. alan.garny@dpag.ox.ac.uk

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
|June 27, 2008
PubMed
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The CellML markup language facilitates sharing biological models. This review assesses tools and techniques available for CellML, aiding the scientific modeling community.

Area of Science:

  • Computational Biology
  • Physiology
  • Biophysics

Background:

  • Increasing complexity of biological models presents development challenges.
  • Sharing and reusing computational biological models is problematic due to insufficient information.
  • The Physiome Project aims to standardize human body modeling.

Purpose of the Study:

  • To review and discuss tools and techniques for the CellML markup language.
  • To assess the current state of CellML adoption and resources.
  • To identify future directions for biological modeling languages.

Main Methods:

  • Introduction to the CellML markup language.
  • Review of existing CellML editors and validators.
  • Discussion of online repositories, code generators, and simulation environments.

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  • Examination of the CellML Application Program Interface (API).

    • Main Results:

    • CellML provides a framework for sharing physiological models.
    • A range of tools and techniques now support CellML.
    • Future directions include the need for additional markup languages.

    Conclusions:

    • CellML has advanced the standardization of biological models.
    • The availability of tools has improved the usability of CellML.
    • Further development is needed to enhance model sharing and reuse.