Introduction

Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush-Larsen and Generalized Rush-Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a 'gold standard' for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior.

Publications

  1. Cellular cardiac electrophysiology modeling with Chaste and CellML.
    Cite this
    Cooper J, Spiteri RJ, Mirams GR, 2014-01-01 - Frontiers in physiology
  2. Chaste: an open source C++ library for computational physiology and biology.
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    Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, Gavaghan DJ, 2013-01-01 - PLoS computational biology
  3. On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.
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    Figueredo GP, Joshi TV, Osborne JM, Byrne HM, Owen MR, 2013-04-01 - Interface focus
  4. CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library.
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    Bernabeu MO, Bordas R, Pathmanathan P, Pitt-Francis J, Cooper J, Garny A, Gavaghan DJ, Rodriguez B, Southern JA, Whiteley JP, 2009-05-01 - Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
  5. Chaste: using agile programming techniques to develop computational biology software.
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    Pitt-Francis J, Bernabeu MO, Cooper J, Garny A, Momtahan L, Osborne J, Pathmanathan P, Rodriguez B, Whiteley JP, Gavaghan DJ, 2008-09-01 - Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Credits

  1. Jonathan Cooper
    Developer

    Computational Biology, Department of Computer Science

  2. Raymond J Spiteri
    Developer

    Numerical Simulation Research Lab, Department of Computer Science, Canada

  3. Gary R Mirams
    Investigator

    Computational Biology, Department of Computer Science

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Summary
AccessionBT003418
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByGary R Mirams