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.
• Tutorial 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

• Installation guides
• How to specify paths to the libraries Chaste uses, etc.
• Run tests to check the installation

Running Chaste

• ReleaseNotes and LatestNews on changes since the last release
• Tutorials
• Visualisation guides
• 'How to' index -- links to test code illustrating how various things can be done
• User build guide -- including how to compile optimised code
• Troubleshooting -- solutions to some common or difficult problems are given here
• Public API documentation for the latest revision and API 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
• User Projects -- for creating or checking out a personal user project, in the repository, which uses the core code
• It is also worth familiarising yourself with UsefulNotes
• Full API documentation for the latest revision (not accessible to anonymous login)
• RunningAcceptanceTests

4. Advanced

• How to run Chaste binaries directly from the command line (i.e. using scons to compile but not run).
• How to build the standalone cardiac executable
• 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 --- including how to release a tag of a user project.
• Configuration of chaste.cs
• List of build machines
• How the accounts used for automated builds are set up

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Automatically generated alphabetical listing of guide pages

• AccessCodeRepository Accessing the Chaste source code repository
• AutomatedBuildGuide Fixing bad commits
• BestPracticeGuide Best practices for Chaste developers
• BoostSerialization Implementing checkpointing for classes with Boost Serialization
• BuildingCardiacExecutable Building the cardiac executable
• CardiacMechanicsSolvers Mechanics solvers
• ChasteUnits Units used in Chaste
• 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
• HowTo Chaste HOWTO Index
• NmoodLectureNotes ChasteGuides/NmoodLectureNotes
• RunningAcceptanceTests Running Acceptance Tests
• RunningBinariesFromCommandLine ChasteGuides/RunningBinariesFromCommandLine
• RunningCellBasedVisualization Running the cell-based visualizer
• RunningFirstTests Running Chaste for the first time
• SolvingCardiacProblems Solving a cardiac problem
• StateVariableInterpolation What is State Variable Interpolation (SVI)?
• StructureOfCellBasedSimulations Structure of cell-based simulations in Chaste
• TroubleShooting Troubleshooting
• UserBuildGuide User build guide
• UsingDebugMacros Using Debug Macros
• VisualisationGuides Visualising simulation results
  • CombineConsecutiveSimulations ChasteGuides/VisualisationGuides/CombineConsecutiveSimulations
  • ParaviewForCardiac Visualising cardiac simulations with Paraview
  • UsingCmgui Visualising cardiac simulations with Cmgui
  • UsingMeshalyzer Visualising cardiac simulations with Meshalyzer