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[Licence| Download | New Version Template] aefd_v1_0.tar.gz(41020 Kbytes)
Manuscript Title: Chaste: a test-driven approach to software development for biological modelling
Authors: Joe Pitt-Francis, Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alexander G. Fletcher, Gary R. Mirams, Philip Murray, James M. Osborne, Alex Walter, S. Jon Chapman, Alan Garny, Inge M. M. van Leeuwen, Philip K. Maini, Blanca Rodríguez, Sarah L. Waters, Jonathan P. Whiteley, Helen M. Byrne, David J. Gavaghan
Program title: Chaste
Catalogue identifier: AEFD_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 180(2009)2452
Programming language: C++.
Operating system: Unix.
Has the code been vectorised or parallelized?: Yes. Parallelized using MPI.
RAM: < 90 Megabytes for two of the scenarios described in section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation.
Keywords: Cardiac electrophysiology, intestinal crypt simulation.
PACS: 87., 87.19.Hh, 87.19.xj.
Classification: 3.

External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces.

Nature of problem:
Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac electrophysiology and intestinal crypt dynamics.

Solution method:
Coupled multi-physics with PDE, ODE and discrete mechanics simulation.

Running time:
The largest cardiac simulation described in the manuscript takes about 6 hours to run on a single 3 GHz core. See results section (6) of the manuscript for discussion on parallel scaling.