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Chaste (Cancer, heart and soft tissue environment) 3.2 released


Version 3.2 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.

Headline features of the new release include:  (see for many more details):

* (general) Ports have been made to both Windows and Mac.  The non-cardiac portions of Chaste have all been ported to Windows.  The port to Mac OS X v10.8 covers nearly all functionality.

* (general) Chaste now supports Ubuntu up to Trusty Tahr (14.04 Long-Term Support edition) and supports recent versions of PETSc (up to 3.4), VTK (up to 6.1) and Boost (up to 1.54).

* (general) We now allow access to the latest development version of the code, provide resources for external developers, and allow public registration on the Trac wiki to view and open 'tickets'.

* (cardiac) Analytic Jacobians can now be auto-generated for cardiac cell models, using Maple, and used by CVODE solvers to provide between 5-30% speed up in ODE solving.

* (cardiac) Input and output has been better tuned which speeds up cardiac output and post-processing, particularly in parallel on HPC resources.

* (cell-based)  There is a new cell-based modifier mechanism which replaces the old hierarchy where each modification involved making a new subclass of the population.  This allows for more combinations of cell-based simulation types to be run.

* (cell-based) Node-based simulations (overlapping spheres simulations) can be run in parallel.