Approaching cardiac modeling challenges to computer science with CellML-based web tools

  • Authors:

  • Ricardo Silva Campos;Ronan Mendonca Amorim;Caroline Mendonça Costa;Bernardo Lino de Oliveira;Ciro de Barros Barbosa;Joakim Sundnes;Rodrigo Weber dos Santos

  • Affiliations:

  • FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil;FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil;FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil;FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil;FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil;Simula Research Laboratory, Norway;FISIOCOMP, Laboratory of Computational Physiology, Department of Computer Science, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil

  • Venue:
  • Future Generation Computer Systems
  • Year:
  • 2010

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Abstract

Cardiac modeling is being used in a variety of ways to support the tests of new drugs, the development of new medical devices and of non-invasive diagnostic techniques. Computer models have become valuable tools for the study and comprehension of the complex phenomena of cardiac electrophysiology. However, the complexity, the multi-scale and multi-physics nature of cardiac modeling still restrict its use to a few specialized research centers in the world. In addition, the issue of sharing and re-using such models has proven to be particularly problematic, with published models often lacking information that is required to accurately reproduce published results. In this work, with the aim of tackling the aforementioned issues, we present a web portal that provides support for cardiac electrophysiology modeling. This framework integrates different computer tools and allows one to bypass many complex steps during the development and use of cardiac models. The process of model development is supported by a Web-based editor for CellML, a mark-up language dedicated to the description of biological structures, processes and the associated models. The implementation of the cardiac cell models is automatically provided by a code generator that translates models described in CellML language to executable code that allows one to manipulate and solve the models numerically. The set up and use of the simulator is supported by a user-friendly graphical interface that offers the tasks of simulation configuration and execution, storage of results and basic visualization. All the tools are integrated in a Web Portal. As a result, the complex techniques and the know-how behind cardiac modeling are all taken care of by the web distributed applications.