Chaste - Developing software for realistic heart simulations
Lead Research Organisation:
University of Oxford
Department Name: Computer Science
Abstract
Our aim is to develop the next generation of modelling software to allow in silico modelling of the whole heart to move on to a new level of sophistication and applicability. We have chosen to focus on the heart simulation work since this is the most mature area of systems-level physiological modelling, and provides extremely challenging computational problems. The proposed research will utilise recent developments, both within our group and elsewhere, in numerical analysis, software engineering, and algorithm design to develop a new approach which will yield fully tested and robust codes that are several orders of magnitude faster than existing codes. Combined with the next generation of HPC hardware, this will open up completely novel avenues of physiological research. We will test these codes in collaboration with leading theoretical modelling and experimental research groups, by simulating a range of important research questions which cannot be addressed with the current generation of modelling software. The development and optimisation of the underlying numerical algorithms and their parallel implementation will be undertaken in collaboration with Fujitsu's European Laboratory, ensuring that the resulting code base is of production standard and can be used with confidence by the heart modelling community.
Organisations
Publications
Bernabeu M
(2013)
Chaste A case study of parallelisation of an open source finite-element solver with applications to computational cardiac electrophysiology simulation
in The International Journal of High Performance Computing Applications
Bernabeu MO
(2009)
CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Brennan T
(2009)
Multiscale modelling of drug-induced effects on cardiac electrophysiological activity.
in European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences
Pitt-Francis J
(2009)
Chaste: A test-driven approach to software development for biological modelling
in Computer Physics Communications
Pitt-Francis J
(2008)
Chaste: using agile programming techniques to develop computational biology software.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Plank G
(2009)
Generation of histo-anatomically representative models of the individual heart: tools and application.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences