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/CellBasedDemoChaste: 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
##
jcl...@ieee.org## Mobile:
+1-805-617-0223########################