Chaste
Chaste: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library. Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (Chaste) project. Chaste is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into Chaste. Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the Chaste framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how Chaste may be developed to include new physiological functionality-such as modelling a beating heart and fluid flow in the heart-and how new algorithms aimed at increasing the efficiency of the code may be incorporated.
Keywords for this software
References in zbMATH (referenced in 23 articles , 1 standard article )
Showing results 1 to 20 of 23.
Sorted by year (- Cooper, Fergus R.; Baker, Ruth E.; Fletcher, Alexander G.: Numerical analysis of the immersed boundary method for cell-based simulation (2017)
- Emerick, Brooks; Schleiniger, Gilberto; Boman, Bruce M.: A kinetic model to study the regulation of $\beta $-catenin, APC, and axin in the human colonic crypt (2017)
- Shoffner, S.K.; Schnell, Santiago: Approaches for the estimation of timescales in nonlinear dynamical systems: timescale separation in enzyme kinetics as a case study (2017)
- Campos, J.O.; Oliveira, R.S.; dos Santos, R.W.; Rocha, B.M.: Lattice Boltzmann method for parallel simulations of cardiac electrophysiology using GPUs (2016)
- Corrado, Cesare; Lassoued, Jamila; Mahjoub, Moncef; Zemzemi, Néjib: Stability analysis of the POD reduced order method for solving the bidomain model in cardiac electrophysiology (2016)
- Figueiredo, Isabel N.; Leal, Carlos; Romanazzi, Giuseppe; Engquist, Bjorn: Homogenization model for aberrant crypt foci (2016)
- Lee, J.; Cookson, A.; Roy, I.; Kerfoot, E.; Asner, L.; Vigueras, G.; Sochi, T.; Deparis, S.; Michler, C.; Smith, N.P.; Nordsletten, D.A.: Multiphysics computational modeling in $\mathcalC\boldHeart$ (2016)
- Mirshekari, Elham; Spiteri, Raymond J.: Extending BACOLI to solve the monodomain model (2016)
- Spiteri, Raymond J.; Torabi Ziaratgahi, Saeed: Operator splitting for the bidomain model revisited (2016)
- Denisov, A.M.; Zakharov, E.V.; Kalinin, A.V.: Numerical solution of the localized inverse problem of electrocardiography (2015)
- Maclaren, Oliver J.; Byrne, Helen M.; Fletcher, Alexander G.; Maini, Philip K.: Models, measurement and inference in epithelial tissue dynamics (2015)
- Walmsley, John; Mirams, Gary R.; Pitt-Francis, Joe; Rodriguez, Blanca; Burrage, Kevin: Application of stochastic phenomenological modelling to cell-to-cell and beat-to-beat electrophysiological variability in cardiac tissue (2015)
- Arthurs, Christopher J.; Bishop, Martin J.; Kay, David: Efficient simulation of cardiac electrical propagation using high-order finite elements. II: Adaptive $p$-version (2013)
- De Matteis, Giovanni; Graudenzi, Alex; Antoniotti, Marco: A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development (2013)
- Nelson, M.R.; King, J.R.; Jensen, O.E.: Buckling of a growing tissue and the emergence of two-dimensional patterns (2013)
- Arthurs, Christopher J.; Bishop, Martin J.; Kay, David: Efficient simulation of cardiac electrical propagation using high order finite elements (2012)
- Mirams, Gary R.; Fletcher, Alexander G.; Maini, Philip K.; Byrne, Helen M.: A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt (2012)
- Pathmanathan, Pras; Mirams, Gary R.; Southern, James; Whiteley, Jonathan P.: The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations (2011)
- Osborne, J.M.; Walter, A.; Kershaw, S.K.; Mirams, G.R.; Fletcher, A.G.; Pathmanathan, P.; Gavaghan, D.; Jensen, O.E.; Maini, P.K.; Byrne, H.M.: A hybrid approach to multi-scale modelling of cancer (2010)
- Whiteley, J.P.: Computational and numerical methods for the efficient and accurate solution of the bidomain equations (2010)
Further publications can be found at: http://www.cs.ox.ac.uk/chaste/publications.html