AttendancePlan

CellBasedAttendancePlan

LungAttendancePlan

ChastePlanning

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

• UserTutorials
• TroubleShooting
• WritingEfficientCode

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

• Useful Software Books/References
• RelatedSoftware

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

• Scripts for ChangingFileSystemOrganisation
• TestCoverage
• ChasteServerChange
• UserRequirements

Other

• SpeedImprovementsSummary
• PositionPaper
• DeletedCode
• ReleaseNotes

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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

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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:

• The original crypt paper by Meineke et al (2001)
• Project Buddy Bear
• CancerUserRequirements

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