Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction.
Scientific endeavour is reliant upon the extension and reuse of previous knowledge. The formalization of this process for computational 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 formalized 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 Pandit-Hinch-Niederer et al. 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.
Terkildsen
Jonna R
JR
Computing Laboratory, University of Oxford, Oxford OX1 3QD, UK.
Niederer
Steven
S
Crampin
Edmund J
EJ
Hunter
Peter
P
Smith
Nicolas P
NP
D000818:Animals; D002118:Calcium / Q000378:metabolism; D054849:Cardiac Electrophysiology / Q000379:methods*; D002478:Cells, Cultured; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008954:Models, Biological; D009200:Myocardial Contraction / Q000502:physiology*; D032383:Myocytes, Cardiac / Q000166:cytology / Q000502:physiology*; D051381:Rats; D012984:Software
D002118:Calcium