Chaste Guides

Before reading this have a look at GettingStarted to decide whether you are a user [of releases] or a developer [contributing back to Chaste core code].

Users can download the latest release of the source code from our ​GitHub releases page to get a stable version, or check out a ​tested development branch to get the latest features.

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.

1. User Guides

Installation

• InstallGuides - How to install Chaste and its dependencies.
• ChasteGuides/CmakeFirstRun - How to configure, build, and run tests to check the installation.

Running Chaste Simulations

• 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
• Cmake first-run guide. For all available options, including compiling optimised code, see full Cmake build guide.
• 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

Writing your own code that uses Chaste

• User Projects -- for creating (or cloning an existing) personal user project which can use the core code and build/testing framework.

Miscellaneous information

• 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.
• Default parameter values​ -- read off from this file, ignore the Simulation block, which only applies to the old cardiac executable.

2. 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
• GitGuide -- how to use the git Chaste repository, in particular see the ticket workflow section.
• CmakeBuildGuide for a detailed guide of all the cmake options.
• BuildingExecutableApps - making standalone executables that don't use the CxxTest framework.
• Fixing "bad" commits
• ChasteStrategies -- see in particular the coding standards guide
• It is also worth familiarising yourself with UsefulNotes
• Full API documentation for the latest revision (not accessible to anonymous login)
• RunningAcceptanceTests
• SconsArchive - a listing of pages relating to the old scons build system, irrelevant if you are using cmake (recommended).

3. Advanced

• How to run Chaste binaries directly from the command line
• Repository access for non-core 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.
• InstallGuides/TestingMultipleVersions -- how to add new versions of libraries, for going into the testing rotation on lofty.

4. Chaste Administrators

• ChasteAdmin Root admin info page
• MakingARelease --- including how to release a tag of a user project.
• ServerSetup Configuration of chaste.cs.
• MachineNames List of build machines
• AutomatedBuilds How the accounts used for automated builds on chaste machines are set up
• ManagingUbuntuPackage - How to manage the Ubuntu debian package for Chaste dependencies.
• UpdatingTheWebsite - How to manage the Chaste web pages.
• UserPermissions - How to set user permissions for trac, the chaste git server, who can see infrastructure scripts etc.
• InfrastructureScripts - How to get the infrastructure repo.

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
• BuildBot Chaste Buildbot Setup
• BuildingCardiacExecutable Building the Cardiac Executable
• BuildingExecutableApps Building Executable Applications
• CardiacMechanicsSolvers Mechanics solvers
• ChasteUnits Units used in Chaste
• CmakeBuildGuide Cmake Build Guide
• CmakeFirstRun Cmake first-time user guide
• CodeGenerationFromCellML Using CellML electrophysiology models in Cardiac Chaste
• ConvertingAssemblersToUseNewDesign Converting assemblers to use the new FEM solver design
• DeveloperBuildGuide ChasteGuides/DeveloperBuildGuide
• DistributingCellBasedExecutables Quick Start
• ExternalDeveloperGuide Helpful resources for users of development versions of Chaste
• FindingChasteDependencies Finding Chaste Dependencies
• FiniteElementAssemblersAndSolvers FEM assemblers and solvers
• FiniteElementImplementations FEM implementations
• GitGuide Git Guide
• GitMigration Git and Cmake Migration
• HowTo Chaste HOWTO Index
• ModernCpp Modern C++
• NmoodLectureNotes ChasteGuides/NmoodLectureNotes
• Profiling Profiling (Page still very much under construction!)
• RunningAcceptanceTests Running Acceptance Tests
• RunningBinariesFromCommandLine How to run binaries directly rather than via ctest
• RunningCellBasedVisualization Running the cell-based visualizer
• RunningFirstTests ChasteGuides/RunningFirstTests
• SolvingCardiacProblems Solving a cardiac problem
• StateVariableInterpolation What is State Variable Interpolation (SVI)?
• StructureOfCellBasedSimulations Structure of cell-based simulations in Chaste
• TroubleShooting Troubleshooting
• UserProjects User Projects
  • ReleasingUserProjects Releasing User Projects
• 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