Version 2.2 of Chaste (Cancer, heart and soft tissue environment) released
Posted: 28th April 2011
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 Computing Laboratory, 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 2.2 has just been released. Headline features of the new release include:
* (General) Smarter HDF5 output in parallel simulations gives better scaling.
* (General) Performance of check-pointing with large meshes has been improved.
* (General) More tutorials.
* (General) Full default test pack should now pass on more configurations.
* (Heart) Added support for the definition of multiple bath/tissue regions.
* (Heart) State variable interpolation in cardiac simulations
* (Heart) Output visualisation in parallel VTK (.pvtu) format.
* (Heart) Fixed bugs in heterogeneities
* (Heart) User may now specify a list of node indices where time traces of output variables are requested.
* (Cell) New cell population boundary condition class hierarchy.
* (Cell) Extended VTK functionality to allow for point data output from node- and mesh-based cell simulations for visualization in Paraview.
Chaste 2.2 which is now available to download as open source or as standalone cardiac executable from http://web.comlab.ox.ac.uk/chaste/download.html