The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste

Developer wiki https://chaste.cs.ox.ac.uk/trac/wiki/GettingStarted
Chaste is only supported on Linux/Unix platforms. The recommended route for Windows and Mac users is to install Chaste on a virtual machine running Ubuntu Linux.

Example showing how to create, run and cell-based simulations in Chaste 

https://chaste.cs.ox.ac.uk/trac/wiki/UserTutorials/CellBasedDemo

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology. PLoS Comput Biol 9(3): e1002970. doi:10.1371/journal.pcbi.1002970 http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002970
 



Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt.

....

Chaste provides libraries for code which is common to many computational biology problems. Here we briefly describe the components of the code and their capabilities. We will present and discuss example simulations, and the new scientific insight Chaste has enabled, in the Results section.

• global — contains code for basic mathematics (including a random number generator), time stepping, checkpointing (saving and loading simulations) using the Boost serialization library [20], parallel vector classes, and code to handle warnings and errors.
• io (input/output) — code for reading, writing and conversion of various file formats, including modules to handle the HDF5 scientific file format [21], which enables distributed data to be collated and stored in a single file.
• mesh — code for linear or quadratic tetrahedral meshes and vertex meshes; nodes, elements, boundary properties; mesh generation; mesh distribution using METIS/parMETIS [22]; readers and writers for Triangle/TetGen [23], [24], Meshalyzer, Cmgui (http://www.cmiss.org/cmgui) and VTK (Paraview) [25] formats.
• linalg (linear algebra) — code which uses Boost uBLAS [20] and PETSc [26] for vector and matrix operations.
• ode — code for defining ODEs; solvers, basic finite difference schemes, the Sundials CVODE solver [27]; termination on root-finding capabilities.
• pde — code for defining elliptic and parabolic second-order PDEs; parallel finite element solvers of generic coupled systems of PDEs (using mesh and linalg).
• continuum mechanics — code for solving compressible and incompressible general non-linear elasticity problems.

## Jonathan Cline
## jcline@ieee.org
## Mobile: +1-805-617-0223
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