Installing Chaste, etc.
- DeveloperInstallGuide
- DisableMiddleMousePress
- BuildServerSetup - how servers such as chaste-bob.cs, scoop.cs... were set up
Useful notes for admins
- ChasteAdmin
- ServerSetup - settings on chaste.cs, adding new users, etc.
- ChasteGuides#a5.ChasteAdministrators
Useful notes for developers
Implementation notes
- ChasteUnits
- File formats
- FiniteElementImplementations
- FiniteElementAssemblersAndSolvers
- ConvertingAssemblersToUseNewDesign
- ElementLocalIndexNumberingConvention
C++ hints, tips, etc.
- AccessingMemberVariablesInTemplatedSuperclasses
- UblasPerformance
- Design Patterns
- StaticAndDynamicPolymorphism, and other notes about the use of templates, including explicit instantiation
- BoostSerialization - how to checkpoint/save/load simulations and write archiving code in Chaste
- WritingPortableCode
- C++ reference website
How-tos
- Running MemoryLeakDetection
- MatlabVisualisationCode
- RunningCellBasedVisualization
- PlottingCellTypeDataInGnuPlot
- MakeEclipseBuildTheTestThatIsOpen
- CreateChasteCopyrightTemplateInEclipse
- Applying a Patch
- Using Debug Macros
- FindingBrokenWikiLinks
- RunningAcceptanceTests
- DebuggingParallelCode
References
Chaste practicals, presentations and animations
- Cell-based Chaste practical, John Innes Centre (2017)
- Cell-based Chaste practical for Oxford Computational Biology course (2016)
- Cell-based Chaste workshop, Oxford (2016)
- Cell-based Chaste workshop, Dundee (2016)
- Cell-based Chaste tutorial for Lake Como Summer School (2014)
- Cell-based Chaste workshop, Oxford (2012)
- Chaste logos
- PresentationsFiles
- SimulationAnimations
- DemoAgenda
Historical interest
Other
Useful cardiac Chaste notes
Iteration review history
- IterationSixReviewMeeting
- IterationSevenPlanningMeeting
- IterationEightReviewMeeting
- IterationNineAttendancePlan
- IterationElevenReviewMeeting
- IterationFourteenRetrospective
- IterationFifteenRetrospective
- IterationNineteenRetrospective
- IterationTwentyFourRetrospective
Workshops
- Chaste cardiac users' workshop 23-25 March 2009
- List of participants for the above workshop
- Feedback during/from this workshop
Useful cancer/cell-based Chaste notes
Planning pages and retrospectives
- Planning pages for cancer/cell-based iterations
- Cancer/cell-based iteration review history
- Work done between cancer/cell-based iterations
Workshops and practicals
- Details of Chaste cell-based modelling workshop (January 2012)
- Planning page for Chaste cell-based modelling workshop (January 2012)
- Cancer Chaste practical (used for the DTC computational biology course)
- Details of cancer programming week (2006)
Meetings and grant proposals
- Cell-based Chaste progress meetings
- Notes from cancer Chaste meeting with Helen Byrne (11 March 2010)
- Notes from meeting with Helen Byrne on 26th March 2009
- Long-term ideas for cancer Chaste
- Notes for cancer Chaste HPC grant
- Notes from meeting on 20th June 2007
Miscellaneous
Notes on implementing large refactors and new functionality:
- Generalizing cell mutation states to abstract cell properties
- Refactoring cell cycle and signalling pathway models
- Lattice-based models
- Visualization
- TissueConfig Refactor
- Cellular Potts Models
- Cell vertex models
- Crypt projection model
- Simple (non-mesh based) tissues
- Large refactor of tissue mechanics classes
- Large refactor of cell cycle model classes
- Solving nutrient PDE on a coarse mesh
- Work on cell adhesion
- Work on a proper crypt geometry
- Work on spheroid simulations
- Work on Wnt gradient
- Files to go in the first cancer release
Previous "easy wins" and ideas for papers:
- Ill-fated Wnt cell cycle paper
- Work on cell labelling experiments
- Work on mutant cell experiments
- "Easy win" notes on extending the crypt model to include contact inhibition of cell division
- "Easy win" notes on extending the crypt model to include APC mutations
Other:
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