Chaste: A test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling.Program summaryProgram title: ChasteCatalogue identifier: AEFD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: LGPL 2.1No. of lines in distributed program, including test data, etc.: 5 407 321No. of bytes in distributed program, including test data, etc.: 42 004 554Distribution format: tar.gzProgramming language: C++Operating system: UnixHas the code been vectorised or parallelized?: Yes. Parallelized using MPI.RAM:  <90 Megabytes<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.Classification: 3.External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, XercesNature 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 (Section 6) of the manuscript for discussion on parallel scaling.