Abstract

Reconstruction of biophysically detailed computer models for simulating electrical activities of heart cells provides a powerful tool to systematically investigate the ionic mechanisms underlying the genesis and control of cardiac rhythms. However, the fact that there is no unified or standard architecture for computational cell models, which were built by different research groups with specific purposes, obstructed profound applications of these models. In this study, we employed object-oriented design patterns to redesign and reconstitute the cell models and provided a more flexible, portable, and expansible infrastructure for modeling computational cell models. Meanwhile, using the proposed methods, a simulation platform has been developed for electrical activities of cell models with aims to offer a user-friendly interface to study the electrical activities of cardiac cells under various physiological and pathological conditions. Both the proposed design methods and the developed system were validated and effective by testing several typical cell models.

Highlights

  • Object-oriented design for cell modelsIn the last 50 years, a number of computational cell models had been constructed and employed to study the underlying electrophysiological mechanism of cells

  • Tusscher et al, 2004) for human ventricular cells, and the Zhang et al (Zhang) model (Zhang et al, 2000) for sinus node cells

  • In the last 50 years, a number of computational cell models had been constructed and employed to study the underlying electrophysiological mechanism of cells. These computational models mostly focused on their consistency with the experimental results, and they were usually expressed by lots of self-defined variables and many complex mathematical equations, and coded by different programming languages (Fortran, C, C++, Java, Matlab etc.)

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Summary

Object-oriented design for cell models

In the last 50 years, a number of computational cell models had been constructed and employed to study the underlying electrophysiological mechanism of cells These computational models mostly focused on their consistency with the experimental results, and they were usually expressed by lots of self-defined variables and many complex mathematical equations, and coded by different programming languages (Fortran, C, C++, Java, Matlab etc.). This made them very hard to be reused for other studies and extended to larger scale applications or to support unforeseeable functions. The users can just access general properties of cell models such as Structure, Concentration and Conductance, but they do not know the details and processes to create and compute cell model objects It is the merit of using the Abstract Factory pattern that isolates cell models from their specific applications, maintains two parts independently and -makes it flexible and direct for adding new cell models into the existing applications through a uniform interface ctreateCell()

Decorator pattern for complex applications of cell models
Bridge pattern for flexible implementations of multiple numerical solvers
The developed simulation system for computational cell models
Discussion and conclusions

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