PaperTutorials/Plos2013

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

Welcome to the Chaste wiki.

This section contains pages generated automatically from the source code accompanying "Chaste: an open source C++ library for computational physiology and biology", our paper accepted for publication in PLoS Computational Biology.

Before running these examples you will need to install Chaste's dependencies and the  source code for version 3.1. The easiest way to do this is using an Ubuntu machine (or an Ubuntu virtual machine) as discussed on InstallGuides/UbuntuPackage. Note that Chaste is only supported on Linux/Unix systems, so users of Windows or Mac OS X will need to follow the virtual machine route. For manual installation of each dependency, on any version of Linux, see DeveloperInstallGuide.

The paper is organised around four examples that are annotated and explained here. Before looking at these, you may wish to look at some of the basic user tutorials.

Click on the images below to go to the annotated code that defines the simulation for each case. The code required to run these examples can be downloaded from  the main download site. For further information on using Chaste to solve these and related problems, see our extensive guide material.


Section contents

  • CryptsAndVillus Cell-based simulation: multiple crypts and a villus
    • ElectroMechanics Cardiac electro-mechanics: a cardiac tissue wedge with varying fibre directions
      • SpheroidExperiments Cell-based simulation: tumour spheroid with oxygen diffusion and uptake
        • SpiralWave Cardiac electrophysiology: spiral wave

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