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

Handle URI:
http://hdl.handle.net/10754/597763
Title:
Chaste: A test-driven approach to software development for biological modelling
Authors:
Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M.M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.
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.
Citation:
Pitt-Francis J, Pathmanathan P, Bernabeu MO, Bordas R, Cooper J, et al. (2009) Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications 180: 2452–2471. Available: http://dx.doi.org/10.1016/j.cpc.2009.07.019.
Publisher:
Elsevier BV
Journal:
Computer Physics Communications
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
Dec-2009
DOI:
10.1016/j.cpc.2009.07.019
Type:
Article
ISSN:
0010-4655
Sponsors:
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.
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Full metadata record

DC FieldValue Language
dc.contributor.authorPitt-Francis, Joeen
dc.contributor.authorPathmanathan, Prasen
dc.contributor.authorBernabeu, Miguel O.en
dc.contributor.authorBordas, Rafelen
dc.contributor.authorCooper, Jonathanen
dc.contributor.authorFletcher, Alexander G.en
dc.contributor.authorMirams, Gary R.en
dc.contributor.authorMurray, Philipen
dc.contributor.authorOsborne, James M.en
dc.contributor.authorWalter, Alexen
dc.contributor.authorChapman, S. Jonen
dc.contributor.authorGarny, Alanen
dc.contributor.authorvan Leeuwen, Ingeborg M.M.en
dc.contributor.authorMaini, Philip K.en
dc.contributor.authorRodríguez, Blancaen
dc.contributor.authorWaters, Sarah L.en
dc.contributor.authorWhiteley, Jonathan P.en
dc.contributor.authorByrne, Helen M.en
dc.contributor.authorGavaghan, David J.en
dc.date.accessioned2016-02-25T12:56:17Zen
dc.date.available2016-02-25T12:56:17Zen
dc.date.issued2009-12en
dc.identifier.citationPitt-Francis J, Pathmanathan P, Bernabeu MO, Bordas R, Cooper J, et al. (2009) Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications 180: 2452–2471. Available: http://dx.doi.org/10.1016/j.cpc.2009.07.019.en
dc.identifier.issn0010-4655en
dc.identifier.doi10.1016/j.cpc.2009.07.019en
dc.identifier.urihttp://hdl.handle.net/10754/597763en
dc.description.abstractChaste ('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.en
dc.description.sponsorshipThe 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.en
dc.publisherElsevier BVen
dc.subjectCardiac electrophysiologyen
dc.subjectIntestinal crypt simulationen
dc.titleChaste: A test-driven approach to software development for biological modellingen
dc.typeArticleen
dc.identifier.journalComputer Physics Communicationsen
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdomen
dc.contributor.institutionOxford Centre for Integrative Systems Biology, Oxford, United Kingdomen
dc.contributor.institutionUniversity of Dundee, Dundee, United Kingdomen
dc.contributor.institutionUniversity of Nottingham, Nottingham, United Kingdomen
kaust.grant.numberKUK-C1-013-04en
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