1. Release 3.4 (changes since Release 3.3)
      1. Headline features
        1. General
        2. Cardiac
        3. Cell-based
        4. Lung
      2. New functionality & code changes
        1. General
        2. Cardiac
        3. Cell-based
      3. Future Plans

Please mention any changes to the code which will break users' code here - to be put in the release notes for the next release. Also mention any significant improvements or new features.

The real definitive release notes will be written in source:trunk/docs/ReleaseNotes.html at the time of release. To make that process easier, please structure this page in the same manner, rather than simply copying from LatestNews.

OlderReleaseNotes -- release notes for releases 1.1 to 3.3

Release 3.4 (changes since Release 3.3)

Headline features

General

  • Support for Ubuntu [up to] 15.10 added. We aim to ensure compatibility for any Ubuntu that has not reached 'end of life'.
  • Support for Boost up to 1.60 added.
  • See InstallGuides/DependencyVersions for all supported versions of dependencies.
  • The CMake builder has been extended to support compilation on Windows, Linux and Mac OS X with a range of compilers. This is part of a planned migration to a unified build system on all platforms.

Cardiac

  • A new class AbstractCvodeCellWithDataClamp allows the 'data clamp' proposed by ​Dokos & Lovell (2004) to be applied to any CellML model. Models inheriting from this class can be generated with ConvertCellModel.py --cvode-data-clamp.
  • This is the last release of Chaste for which a pre-built cardiac standalone executable can be bundled.

Cell-based

  • We have improved functionality for outputting results of cellular automaton (CA) and cellular Potts model simulations, as well as cell-based simulations on periodic domains, to VTK.
  • We have extended functionality for CA simulations, including a new location "switching" rule and division rule class hierarchies.
  • Each cell now contains a "subcellular reaction network model" as well as a cell-cycle model. This mainly affects users of the DeltaNotchCellCycleModel class, which is now implemented using the DeltaNotchSrnModel, allowing the model to be coupled with any of the cell cycle models (see UserTutorials/CreatingAndUsingANewSrnModel for details).
  • Much of the vertex model code has been refactored to improve efficiency. In addition, two new classes, MutableVertexMeshWithRosettes and CellRosetteRankWriter, have been added to implement the necessary functionality for simulating multicellular 'rosettes' (where more than three cells meet at a point).

Lung

  • A new package for investigating ventilation in the lung using reduced dimensional models has been introduced.
  • Key classes are
    1. MultiLobeAirwayGenerator allows anatomical models of the conducting airways to be created.
    2. AbstractVentilationProblem and related subclasses allow simulation of airflow on the conducting airway models using a Poiseuille flow model model with Pedley correction.
    3. DynamicVentilationProblem couples nonlinear elastic models of the acini (gas exchange area) to the ventilation model, allowing simulation of the full breathing cycle
  • Tutorials for this functionality are available on the tutorials page UserTutorials#LungChaste.

New functionality & code changes

New functionality and code changes, which may require changes to user code.

General

  • An element argument has been added to AbstractLinearParabolicPde::ComputeSourceTerm(). If you have your own PDEs inheriting from AbstractLinearParabolicPde this argument will need adding to the method (it can be ignored), see e.g. relevant change to the heat equation.

Cardiac

  • Classes inheriting from AbstractCardiacCellWithModifiers can now be archived/checkpointed.
  • We have renamed the CellML metadata leakage_current to membrane_leakage_current as there is also an SR one sometimes... This may break user projects using this metadata. There have also been other updates to the metadata which will enable more advanced features in future versions.
  • A light-weight output modifier allows the user to output specific traces during a simulation rather than at post-process time. See ChasteGuides/HowTo#Output.
  • A bug has been found in one method for partitioning of meshes in parallel code (Windows only). This method has been switched off while we investigate further.

Cell-based

  • A new tutorial (UserTutorials/CreatingAndUsingANewCellBasedSimulationModifier) shows how to create and use cell-based simulation modifiers.
  • The new class VoronoiVertexMeshGenerator uses Lloyd's Relaxation steps to generate random initial conditions for vertex model simulations.
  • The PlaneBasedBoundaryCondition class can be used in a simulation where ELEMENT_DIM != SPACE_DIM.
  • Two new force classes, DiffusionForce and DifferentialAdhesionGeneralisedLinearSpringForce, have been added.
  • The new class CellVecData enables a vector (e.g. the solution to an intracellular PDE problem) to be associated with each cell.
  • The default parameter values in NagaiHondaForce match those in the original publication.
  • Two new writer classes, CellDeltaNotchWriter and CellPopulationAdjacencyMatrixWriter, have been added.

Future Plans

  • This is the last release of Chaste that will:
    • support Ubuntu 10.04 LTS;
    • support versions of PETSc < 3.0, or boost < 1.48;
    • bundle a pre-built cardiac standalone executable (the executable is dependent on third-party libraries which are to be deprecated).
  • Work is progressing on switching the build infrastructure to use CMake and code repository to use Git.
    • The CMake build is available to test in this release; see ChasteGuides/CmakeBuildGuide for more details. (SCons will be deprecated at a later date.)
    • The switch of the code repository from Subversion to Git will happen after this release. For information on migrating please see GitMigration.