1. For users of the Cardiac Chaste executable
This section is for users of the cardiac chaste standalone executable, which can be downloaded from the downloads section of the public Chaste website. The executable does not require any installation of supporting software, takes in XML input files, and outputs the results of simulations in Meshalyzer, Cmgui and Paraview-readable formats.
- Start by reading the README file that is supplied with the executable, which explains how to run the executable
- The file ChasteParametersFullFormat.xml, also supplied with the executable, can be used as a reference when altering the XML parameters file; or, when read through, describes the full functionality of the executable.
- Examples of simulations using the executable
- Default parameters values -- read off from this file
- File format information is given in the file docs/FileFormats.html, supplied with the executable (files such as, for example, input files referred to in the XML parameters file and read in by the executable).
2. For users of the Chaste code
This section is for users of the Chaste source code. The latest release of the source code can be downloaded from the downloads section of the public Chaste website (do not download the release if you are a new developer (including users based in Compbio/CMB with full wiki and svn access); instead see below). If you have downloaded the latest release you can either follow the installation instructions supplied with the code (see the README file), or use the installation guide below.
New developers should, rather than downloading the release, follow the installation instructions below, including the part on checking-out the latest version of the code.
Installation
Running Chaste
- Tutorials
- User build guide
- Troubleshooting -- solutions to some common, or difficult, problems are given here
- The working code documentation -- not available to anonymous login, please check documentation for the current release
Miscellaneous information
- Default parameters values -- read off from this file, ignore the Simulation block, which only applies to the executable.
- File format information is given in the file docs/FileFormats.html, supplied with the release. (The latest version of this file may also be viewed here - click on the 'download in original format' link at the bottom of the page).
- Units of parameters used in Chaste
- Equations and finite element methods -- the pdf file attached to this page describes the exact PDEs being solved in various parts of Chaste and the finite element methods used to solve them.
3. Further information for developers
New developers (including users based in Compbio/CMB with full wiki and svn access) should read the 'users of the source code' section above, and also see
- Developer scons build guide
- ChasteStrategies -- see in particular the coding standards guide
- Creating and checking out User Projects -- for creating a personal user project, in the repository, which uses the core code
- it is also worth familiarising yourself with UsefulNotes
4. Advanced
- State-variable Interpolation -- state-variable interpolation is a way of improving conduction velocity accuracy in large cardiac electro-physiology simulations
- HPC Install Guide
- SVN access for non-developers
- FEM assemblers and solvers -- this page describes how the finite element solvers work internally
- Solving cardiac problems -- describes the implementation of the cardiac solvers for developers (see tutorials for user guides)
5. Chaste Administrators
Automatically generated listing of guide pages
- BoostSerialization Boost Serialization
- ChasteUnits Units
- CodeGenerationFromCellML Using CellML models of cardiac cells in Chaste
- ConvertingAssemblersToUseNewDesign Converting assemblers to use the new FEM solver design
- DeveloperBuildGuide Developer Build Guide
- FiniteElementAssemblersAndSolvers FEM assemblers and solvers
- FiniteElementImplementations FEM implementations
- HostconfigSystem The hostconfig system
- RunningCellBasedVisualization Running the cell-based visualizer
- SolvingCardiacProblems Solving a cardiac problem
- StateVariableInterpolation What is State Variable Interpolation (SVI)?
- SvnAccessForNonDevelopers Accessing the Chaste source code repository
- TroubleShooting Troubleshooting
- UserBuildGuide User build guide
- UsingDebugMacros Using Debug Macros