Received December 19, 2007
Revised January 17, 2008
Accepted after revision March 4, 2008
Computational Physiology [320]
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Using Physiome standards to couple cellular functions for cardiac excitation contraction
Jonna R Terkildsen 1,
Steven A Niederer 2,
Edmund J Crampin 1,
Peter J Hunter 1,
Nicolas P Smith 2*
1 University of Auckland
2 University of Oxford
* To whom correspondence should be addressed. E-mail: nic.smith{at}comlab.ox.ac.uk.
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Abstract |
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Scientific endeavour is reliant upon the extension and reuse of previous knowledge. The formalisation of this process for mathematical modelling is facilitated by the use of accepted standards with which to describe and simulate models, ensuring consistency between the models and thus reducing the development and propagation of errors. CellML 1.1, an XML-based programming language, has been designed as a modelling standard which, by virtue of its import and grouping functions, facilitates model combination and reuse. Using CellML 1.1, we demonstrate the process of formalised model reuse by combining three separate models of rat cardiomyocyte function (an electrophysiology model, a model of cellular calcium dynamics, and a mechanics model) which together make up the Niederer and Smith cell model. Not only is this integrative model of rat electromechanics a useful tool for cardiac modelling, but it is also an ideal framework with which to demonstrate both the power of model reuse, and the challenges associated with this process. We highlight and classify a number of these issues associated with combining models, and provide some suggested solutions.
Key Words:
Calcium transient, Cardiac cell, Electrophysiology
