Abstract:
CellML (http://www.cellml.org) is an XML standard for encoding differential-algebraic equation (DAE) models and facilitating the building of model repositories and general purpose software tools. The CellML 1.1 standard (available at http://www.cellml.org/specifications/cellml_1.1) supports public and private interfaces that enable encapsulation hierarchies and provide mechanisms for information hiding and abstraction. Model reuse is facilitated by the import element, enabling new models to be constructed by combining existing models into model hierarchies. The process of importing models, developed by different research groups, into a more complex integrated model will be illustrated with three cardiac myocyte models. The 1st is the Pandit et al model [1] of cardiac excitability, the 2nd is the Hinch et al model [2] of calcium dynamics and the 3rd is the Niederer et al model [3] of myofilament mechanics. The resulting coupled electromechanics model is reported in Terkildsen et al [4]. We will also discuss the decomposition of these three models into a library of separate modular components (e.g. individual ion channel models). 1. http://www.cellml.org/models/pandit_clark_giles_demir_2001_version07 2. http://www.cellml.org/models/hinch_greenstein_tanskanen_xu_winslow_2004_version01 3. http://www.cellml.org/models/niederer_hunter_smith_2006_version01 4. Terkildsen, J.R., Niederer, S., Crampin E.J., Hunter, P.J., and Smith N.P. Using Physiome standards to couple cellular functions for cardiac excitation contraction. Exp Physiol; 93, pp919-929, 2008. http://www.cellml.org/models/terkildsen_niederer_crampin_hunter_smith_2008_version01