title: Considerations for the use of cellular electrophysiology models within cardiac tissue simulations.
abstract: The use of mathematical models to study cardiac electrophysiology has a long history, and numerous cellular scale models are now available, covering a range of species and cell types. Their use to study emergent properties in tissue is also widespread, typically using the monodomain or bidomain equations coupled to one or more cell models. Despite the relative maturity of this field, little has been written looking in detail at the interface between the cellular and tissue-level models. Mathematically this is relatively straightforward and well-defined. There are however many details and potential inconsistencies that need to be addressed, in order to ensure correct operation of a cellular model within a tissue simulation. This paper will describe these issues and how to address them. Simply having models available in a common format such as CellML is still of limited utility, with significant manual effort being required to integrate these models within a tissue simulation. We will thus also discuss the facilities available for automating this in a consistent fashion within Chaste, our robust and high-performance cardiac electrophysiology simulator. It will be seen that a common theme arising is the need to go beyond a representation of the model mathematics in a standard language, to include additional semantic information required in determining the model's interface, and hence to enhance interoperability. Such information can be added as metadata, but agreement is needed on the terms to use, including development of appropriate ontologies, if reliable automated use of CellML models is to become common.
authors.affiliation: Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford OX13QD, UK. jonathan.cooper@comlab.ox.ac.uk
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cooper
authors.forename: Alberto
authors.initials: A
authors.lastname: Corrias
authors.forename: David
authors.initials: D
authors.lastname: Gavaghan
authors.forename: Denis
authors.initials: D
authors.lastname: Noble
mesh_terms: D055724:Electrophysiological Phenomena; D006321:Heart / Q000502:physiology*; D008954:Models, Biological; D009206:Myocardium / Q000166:cytology*; D012984:Software