Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model.
CellML 1.1 was released as a formal specification in February 2006 with the first release of a complete implementation of the CellML API following in December. The combination of these two developments paves the way for a powerful new paradigm in mathematically modeling cardiac cellular electrophysiology. In this article we explore the practical application of this paradigm using the example of integrating new mechanisms into a well known model of human ventricular myocyte electrophysiology. Through practical application of the CellML 1.1 paradigm we demonstrate the advantages inherent in such an approach and contrast them to more traditional methods of model description, exchange, and publication. This work has also provided the impetus for some recent developments in regard to CellML metadata specifications. The development of the tools and techniques used in this work has helped define some guidelines that should prove useful in future developments in this field. By following these guidelines model authors can increase the usability of their work by other scientists. This work presents the first attempt to utilize annotated CellML models to present not only the underlying mathematical models but also specify the numerical simulations and graphical outputs in an interchangeable, machine readable format. By doing so, all simulations are able to be duplicated by anyone with access to a capable tool. Similarly, identical graphical representations of the numerical simulation results can be produced.
Nickerson
David
D
Division of Bioengineering, Faculty of Engineering, National University of Singapore, Singapore. biendp@nus.edu.sg
Buist
Martin
M
D000255:Adenosine Triphosphate / Q000737:chemistry; D002118:Calcium / Q000737:chemistry*; D015220:Calcium Channels / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006325:Heart Atria / Q000473:pathology*; D006801:Humans; D008954:Models, Biological; D008962:Models, Theoretical; D017202:Myocardial Ischemia / Q000473:pathology; D032383:Myocytes, Cardiac / Q000166:cytology* / Q000378:metabolism; D011188:Potassium / Q000737:chemistry*; D019831:Sodium-Calcium Exchanger / Q000737:chemistry; D012984:Software
D015220:Calcium Channels; D019831:Sodium-Calcium Exchanger; D000255:Adenosine Triphosphate; D011188:Potassium; D002118:Calcium