Chaste: an open source C++ library for computational physiology and biology

Abstract

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.

Figure 1. 3D off-lattice simulation coupled to PDE: 3D simulation of a tumour spheroid.

A cross-section of a tumour spheroid is presented. Cell centres, nodes of a mesh, are represented by spherical shells and coloured according to the local oxygen concentration. Proliferation is dependent on oxygen, which diffuses and is taken up by cells in the spheroid, such that only cells near the outer rim divide. Cell death occurs under low oxygen conditions near the centre of the spheroid. See also Video S1.

Figure 2. 3D off-lattice simulation confined to a 2D surface: small intestinal crypts and villus.

Left: cells are labelled according to their ancestor cell; each crypt gives rise to a monoclonal population, with a multiclonal villus comprised of cells from each crypt. Right: the same simulation, here with cells labelled according to Delta levels (non-dimensionalised); Delta-Notch patterning occurs due to a signalling model inside each cell, which depends on the activity of neighbouring cells, and is thought to lead to differentiation into secretory and absorbative cell types. See also Video S2.

Figure 3. Cardiac electrophysiology: a re-entrant spiral wave.

This figure displays the membrane voltage in a 2-D monodomain simulation using the Luo-Rudy 1991 action-potential model with the modifications and protocol suggested in . See also Video S3.

Figure 4. Cardiac electromechanics in a ventricular wedge: left, fibre orientation relative to axis; middle and right, simulation of electrical propagation and deformation (middle: 1 ms after stimulus on left face (); right: 35 ms after stimulus). See also Video S4.