Chaste: Developing software for realistic heart simulations
Please see the Chaste main project page for a description of the software.
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.
This is an EPSRC-funded project (EP/F011628/1) under the HPC initiative.
Cellular cardiac electrophysiology modelling with Chaste and CellML
Jonathan Cooper‚ Raymond Spiteri and Gary Mirams
In Frontiers in Physiology. Vol. 5. Pages 511. January, 2015.
Chaste: A test−driven approach to software development for biological modelling
D.J.a c Pitt−Francis J.a Pathmanathan P.a Bernabeu M.O.a Bordas R.a Cooper J.a Fletcher A.G.b c Mirams G.R.d Murray P.b Osborne J.M.a c Walter A.b Chapman S.J.b Garny A.d van Leeuwen I.M.M.e Maini P.K.b c Rodríguez B.a Waters S.L.b Whiteley J.P.a b Byrne H.M.f Gavaghan
In Computer Physics Communications. Vol. 180. No. 12. Pages 2452−2471. 2009.
cited By 102
A computational study of discrete mechanical tissue models
P Pathmanathan‚ J Cooper‚ A Fletcher‚ G Mirams‚ P Murray‚ J Osborne‚ J Pitt−Francis‚ A Walter and S J Chapman
In Physical Biology. Vol. 6. No. 3. 2009.