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

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; Ingeborg M.M. van Leeuwen; Philip K. Maini; Blanca Rodríguez; Sarah L. Waters; Jonathan P. Whiteley; Helen M. Byrne; David J. Gavaghan

doi:10.1016/j.cpc.2009.07.019

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

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, Ingeborg M.M. van Leeuwen, Philip K. Maini, Blanca Rodríguez, Sarah L. Waters, Jonathan P. Whiteley, Helen M. Byrne, David J. Gavaghan

Research output: Contribution to journal › Article › peer-review

191 Scopus citations

Abstract

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 summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. 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. 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 (Section 6) of the manuscript for discussion on parallel scaling. © 2009 Elsevier B.V. All rights reserved.

Original language	English (US)
Pages (from-to)	2452-2471
Number of pages	20
Journal	Computer Physics Communications
Volume	180
Issue number	12
DOIs	https://doi.org/10.1016/j.cpc.2009.07.019
State	Published - Dec 2009
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-C1-013-04
Acknowledgements: The authorship of this paper represents contributions to the Chaste code from researchers in both cardiac and cancer modelling. We should like to thank numerous other contributors to the code-base.Chaste began thanks to the Engineering and Physical Sciences Research Council (EPSRC) of the UK under their e-Science pilot project in Integrative Biology (GR/S72023/01). Recent development work on Cardiac Chaste is supported by the EPSRC as part of a Software for High Performance Computing project (EP/F011628/1).PP is supported by the EPSRC through grant EP/D048400/1. JPW and AW are supported by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). BR is supported by an MRC Career Development Award (G0700278). SLW gratefully acknowledges funding from the EPSRC in the form of an Advanced Research Fellowship. JC is funded through the VPH NoE project (#223920) and AG through the VPH preDiCT and VPH euHeart projects (#224381 and #224495, respectively). All three VPH projects are supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies. JMO and AGF are funded through the OCISB project (BB/D020190/1) and the Life Sciences Interface and Systems Biology Doctoral Training Centres. PKM was partially supported by a Royal Society-Wolfson Merit award and NIH Grant U56CA113004 from the National Cancer Institute. PKM and HMB acknowledge support from PMI2 (British Council).Thanks to Fujitsu Laboratories of Europe for providing validation and timings necessary for Fig. 7.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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10.1016/j.cpc.2009.07.019

Cite this

Pitt-Francis, J., Pathmanathan, P., Bernabeu, M. O., Bordas, R., Cooper, J., Fletcher, A. G., Mirams, G. R., Murray, P., Osborne, J. M., Walter, A., Chapman, S. J., Garny, A., van Leeuwen, I. M. M., Maini, P. K., Rodríguez, B., Waters, S. L., Whiteley, J. P., Byrne, H. M., & Gavaghan, D. J. (2009). Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications, 180(12), 2452-2471. https://doi.org/10.1016/j.cpc.2009.07.019

@article{44f284bb9ecf4474847577e4d80a39ac,

title = "Chaste: A test-driven approach to software development for biological modelling",

abstract = "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 summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. 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. 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 (Section 6) of the manuscript for discussion on parallel scaling. {\textcopyright} 2009 Elsevier B.V. All rights reserved.",

author = "Joe Pitt-Francis and Pras Pathmanathan and Bernabeu, {Miguel O.} and Rafel Bordas and Jonathan Cooper and Fletcher, {Alexander G.} and Mirams, {Gary R.} and Philip Murray and Osborne, {James M.} and Alex Walter and Chapman, {S. Jon} and Alan Garny and {van Leeuwen}, {Ingeborg M.M.} and Maini, {Philip K.} and Blanca Rodr{\'i}guez and Waters, {Sarah L.} and Whiteley, {Jonathan P.} and Byrne, {Helen M.} and Gavaghan, {David J.}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-C1-013-04 Acknowledgements: The authorship of this paper represents contributions to the Chaste code from researchers in both cardiac and cancer modelling. We should like to thank numerous other contributors to the code-base.Chaste began thanks to the Engineering and Physical Sciences Research Council (EPSRC) of the UK under their e-Science pilot project in Integrative Biology (GR/S72023/01). Recent development work on Cardiac Chaste is supported by the EPSRC as part of a Software for High Performance Computing project (EP/F011628/1).PP is supported by the EPSRC through grant EP/D048400/1. JPW and AW are supported by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). BR is supported by an MRC Career Development Award (G0700278). SLW gratefully acknowledges funding from the EPSRC in the form of an Advanced Research Fellowship. JC is funded through the VPH NoE project (#223920) and AG through the VPH preDiCT and VPH euHeart projects (#224381 and #224495, respectively). All three VPH projects are supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies. JMO and AGF are funded through the OCISB project (BB/D020190/1) and the Life Sciences Interface and Systems Biology Doctoral Training Centres. PKM was partially supported by a Royal Society-Wolfson Merit award and NIH Grant U56CA113004 from the National Cancer Institute. PKM and HMB acknowledge support from PMI2 (British Council).Thanks to Fujitsu Laboratories of Europe for providing validation and timings necessary for Fig. 7. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

year = "2009",

month = dec,

doi = "10.1016/j.cpc.2009.07.019",

language = "English (US)",

volume = "180",

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Pitt-Francis, J, Pathmanathan, P, Bernabeu, MO, Bordas, R, Cooper, J, Fletcher, AG, Mirams, GR, Murray, P, Osborne, JM, Walter, A, Chapman, SJ, Garny, A, van Leeuwen, IMM, Maini, PK, Rodríguez, B, Waters, SL, Whiteley, JP, Byrne, HM & Gavaghan, DJ 2009, 'Chaste: A test-driven approach to software development for biological modelling', Computer Physics Communications, vol. 180, no. 12, pp. 2452-2471. https://doi.org/10.1016/j.cpc.2009.07.019

TY - JOUR

T1 - Chaste: A test-driven approach to software development for biological modelling

AU - Pitt-Francis, Joe

AU - Pathmanathan, Pras

AU - Bernabeu, Miguel O.

AU - Bordas, Rafel

AU - Cooper, Jonathan

AU - Fletcher, Alexander G.

AU - Mirams, Gary R.

AU - Murray, Philip

AU - Osborne, James M.

AU - Walter, Alex

AU - Chapman, S. Jon

AU - Garny, Alan

AU - van Leeuwen, Ingeborg M.M.

AU - Maini, Philip K.

AU - Rodríguez, Blanca

AU - Waters, Sarah L.

AU - Whiteley, Jonathan P.

AU - Byrne, Helen M.

AU - Gavaghan, David J.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-C1-013-04 Acknowledgements: The authorship of this paper represents contributions to the Chaste code from researchers in both cardiac and cancer modelling. We should like to thank numerous other contributors to the code-base.Chaste began thanks to the Engineering and Physical Sciences Research Council (EPSRC) of the UK under their e-Science pilot project in Integrative Biology (GR/S72023/01). Recent development work on Cardiac Chaste is supported by the EPSRC as part of a Software for High Performance Computing project (EP/F011628/1).PP is supported by the EPSRC through grant EP/D048400/1. JPW and AW are supported by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). BR is supported by an MRC Career Development Award (G0700278). SLW gratefully acknowledges funding from the EPSRC in the form of an Advanced Research Fellowship. JC is funded through the VPH NoE project (#223920) and AG through the VPH preDiCT and VPH euHeart projects (#224381 and #224495, respectively). All three VPH projects are supported by the European Commission, DG Information Society, through the Seventh Framework Programme of Information and Communication Technologies. JMO and AGF are funded through the OCISB project (BB/D020190/1) and the Life Sciences Interface and Systems Biology Doctoral Training Centres. PKM was partially supported by a Royal Society-Wolfson Merit award and NIH Grant U56CA113004 from the National Cancer Institute. PKM and HMB acknowledge support from PMI2 (British Council).Thanks to Fujitsu Laboratories of Europe for providing validation and timings necessary for Fig. 7. This publication acknowledges KAUST support, but has no KAUST affiliated authors.

PY - 2009/12

Y1 - 2009/12

N2 - 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 summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. 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. 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 (Section 6) of the manuscript for discussion on parallel scaling. © 2009 Elsevier B.V. All rights reserved.

AB - 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 summary: Program title: Chaste. Catalogue identifier: AEFD_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html. Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: LGPL 2.1. No. of lines in distributed program, including test data, etc.: 5 407 321. No. of bytes in distributed program, including test data, etc.: 42 004 554. Distribution format: tar.gz. 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. 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 (Section 6) of the manuscript for discussion on parallel scaling. © 2009 Elsevier B.V. All rights reserved.

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EP - 2471

JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 12

ER -

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

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