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 includes all cell-based users)

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

• Developer Install Guide
• How to specify paths to the libraries Chaste uses, etc.

Running Chaste

• Tutorials
• User build guide
• Troubleshooting -- solutions to some common, or difficult, problems are given here
• Public documentation for the latest revision and documentation for release versions including documentation for this 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 implementations -- 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

• Helpful resources for external users of development versions of Chaste
• Some best practices for developers to follow
• Developer scons build guide
• Fixing "bad" commits
• 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
• Full documentation for the latest revision (not accessible to anonymous login)

4. Advanced

• SVN access for non-developers (see also ChasteGuides/ExternalDeveloperGuide)
• HPC Install Guide
• State-variable Interpolation -- state-variable interpolation is a way of improving conduction velocity accuracy in large cardiac electro-physiology simulations
• FEM assemblers and solvers -- this page describes how the finite element solvers work internally
• Lecture notes -- lectures on a course on Numerical methods and object-oriented design, which includes various sections on Chaste architecture (especially on PDE solving)
• Solving cardiac problems -- describes the implementation of the cardiac solvers for developers (see tutorials for user guides)
• Cardiac mechanics solvers -- a bit of information on how the cardiac mechanics solvers are connected to the main mechanics solvers.

5. Chaste Administrators

• Creating a branch
• Making a release
• Configuration of chaste.cs
• How the accounts used for automated builds are set up

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Automatically generated listing of guide pages

• AutomatedBuildGuide Fixing bad commits
• BestPracticeGuide Best practices for Chaste developers
• BoostSerialization Boost Serialization
• CardiacMechanicsSolvers Mechanics solvers
• 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
• ExternalDeveloperGuide Helpful resources for users of development versions of Chaste
• FiniteElementAssemblersAndSolvers FEM assemblers and solvers
• FiniteElementImplementations FEM implementations
• HostconfigSystem The hostconfig system
• NmoodLectureNotes ChasteGuides/NmoodLectureNotes
• 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