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Jonathan Cooper : Publications

Personal orderingBibtex


The Virtual Physiological Human ToolKit

Jonathan Cooper‚ Frederic Cervenansky‚ Gianni De Fabritiis‚ John Fenner‚ Denis Friboulet‚ Toni Giorgino‚ Steven Manos‚ Yves Martelli‚ Jordi Villa−Freixa‚ Stefan Zasada‚ Sharon Lloyd‚ Keith McCormack and Peter V. Coveney

In Phil Trans R Soc A. Vol. 368. No. 1925. Pages 3925−3936. August, 2010.


Markup Languages for In Silico Oncology

David Johnson‚ Jonathan Cooper and Steve McKeever

In Georgios Stamatakos and Dimitra Dionysiou, editors, Proceedings of the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (4th IARWISOCI) – The ContraCancrum Workshop. Pages 108–110. September, 2010.


The Virtual Physiological Human ToolKit – Evolution and Sustainability

Jonathan Cooper‚ John Fenner‚ Keith McCormack‚ David Gavaghan and Peter Coveney

In Abstract booklet for VPH2010. Pages 39−41. September, 2010.


Toward a VPH/Physiome ToolKit

Peter J. Hunter Alan Garny Jonathan Cooper

In Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009.


Automatic Validation and Optimisation of Biological Models

Jonathan Cooper

PhD Thesis 2009.


Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library

M.O. Bernabeu‚ R. Bordas‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Cooper‚ A. Garny‚ D.J. Gavaghan‚ B. Rodriguez‚ J.A. Southern and J.P. Whiteley

In Phil Trans Roy Soc (A). Vol. 367. No. 1895. Pages 1907−1930. May, 2009.


CellML and Associated Tools and Techniques

Alan Garny‚ David Nickerson‚ Jonathan Cooper‚ Rodrigo Weber dos Santos‚ Steve McKeever‚ Poul Nielsen and Peter Hunter

In Phil Trans Roy Soc A. Vol. 366. No. 1878. Pages 3017–3043. 2008.


Chaste: Using Agile Programming Techniques to Develop Computational Biology Software

Joe Pitt−Francis‚ Miguel O. Bernabeu‚ Jonathan Cooper‚ Alan Garny‚ Lee Momtahan‚ James Osborne‚ Pras Pathmanathan‚ Blanca Rodriguez‚ Jonathan P. Whiteley and David J. Gavaghan

In Philosophical Transactions of the Royal Society A. Vol. 366. No. 1878. Pages 3111−3136. 2008.


A model−driven approach to automatic conversion of physical units

Jonathan Cooper and Steve McKeever

In Softw. Pract. Exper.. Vol. 38. No. 4. Pages 337−359. 2008.


Experience Report: A Haskell interpreter for CellML

Jonathan Cooper and Steve McKeever

Pages 247–250. New York‚ NY‚ USA. October, 2007. ACM Press.


An integrative computational model for intestinal tissue renewal

HM Byrne IMM van Leeuwen GR Mirams A Walter A Fletcher P Murray J Osborne S Varma SJ Young J Cooper B Doyle J Pitt−Francis L Momtahan P Pathmanathan JP Whiteley SJ Chapman DJ Gavaghan OE Jensen JR King PK Maini SL Waters

In Cell Proliferation. Vol. 42. Pages 617−636. 2009.


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.


On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations

Jonathan Cooper‚ Steve McKeever and Alan Garny

In PEPM '06: Proceedings of the 2006 ACM SIGPLAN Symposium on Partial Evaluation and Semantics−Based Program Manipulation. Pages 12–20. New York‚ NY‚ USA. 2006. ACM Press.