Version 3.0 of Chaste (Cancer, heart and soft tissue environment) released
Posted: 10th January 2012
Version 3.0 of Chaste has been released. Chaste (Cancer, Heart and Soft Tissue Environment) is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. The package is being developed by a team mainly based in the Computational Biology Group at Oxford University’s Department of Computer Science, and development draws on expertise from software engineering, high performance computing, mathematical modelling and scientific computing.
While Chaste is a generic extensible library, software development to date has focused on two distinct areas: continuum modelling of cardiac electrophysiology (Cardiac Chaste); and discrete modelling of cell populations (Systems Biology Chaste), with specific application to tissue homeostasis and carcinogenesis (Cancer Chaste).
Chaste 3.0 has just been released. Headline features of the new release include:
- (general) Chaste now supports Ubuntu Oneiric Ocelot (11.10), PETSc 3.1 and the latest versions of the Boost libraries.
- (general) It is relatively easy to write new solvers of coupled systems of linear PDEs, and tutorials on how to do this have been added.
- (general) We now recommend using VTK with Chaste, and the default.py hostconfig assumes it is available
- (cardiac) The mechanics (and cardiac electro-mechanics) solvers have been made significantly more flexible
- (cell-based) Lattice based cellular Potts models have been implemented
- (cell-based) There has been a major refactor of the structure of the cell-based code to make the specification of multi-cell models (such as cell-centre, over-lapping spheres, vertex-based and cellular Potts) more consistent.
- (cell-based) The handling of PDEs has been improved allowing PDEs to be coupled to node-based simulations.
Chaste 3.0 is available to download as open source or as standalone cardiac executable from http://www.cs.ox.ac.uk/chaste/download.html