Jonathan Cooper : Publications

The Cardiac Electrophysiology Web Lab

Jonathan Cooper‚ Martin Scharm and Gary Mirams

In Biophysical Journal. Vol. 110. No. 2. Pages 292−300. 2016.

Details about The Cardiac Electrophysiology Web Lab | BibTeX data for The Cardiac Electrophysiology Web Lab | DOI (10.1016/j.bpj.2015.12.012)

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.

Details about Cellular cardiac electrophysiology modelling with Chaste and CellML | BibTeX data for Cellular cardiac electrophysiology modelling with Chaste and CellML | DOI (10.3389/fphys.2014.00511) | Link to Cellular cardiac electrophysiology modelling with Chaste and CellML

Ten simple rules for effective computational research

James M Osborne‚ Miguel O Bernabeu‚ Maria Bruna‚ Ben Calderhead‚ Jonathan Cooper‚ Neil Dalchau‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Robin Freeman‚ Derek Groen and others

In PLoS Computational Biology. Vol. 10. No. 3. Pages e1003506. 2014.

Details about Ten simple rules for effective computational research | BibTeX data for Ten simple rules for effective computational research | DOI (10.1371/journal.pcbi.1003506)

Connecting models to data in multiscale multicellular tissue simulations

J.M. Cooper J Osborne

In Procedia Computer Science. Vol. 18. Pages 712−721. 2013.

Details about Connecting models to data in multiscale multicellular tissue simulations | BibTeX data for Connecting models to data in multiscale multicellular tissue simulations | DOI (10.1016/j.procs.2013.05.235)

Chaste: an open source C++ library for computational physiology and biology

Gary R Mirams‚ Christopher J Arthurs‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alberto Corrias‚ Yohan Davit‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Daniel G Harvey and others

In PLoS computational biology. Vol. 9. No. 3. Pages e1002970. 2013.

Details about Chaste: an open source C++ library for computational physiology and biology | BibTeX data for Chaste: an open source C++ library for computational physiology and biology | DOI (10.1371/journal.pcbi.1002970)

Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials

N Zemzemi‚ MO Bernabeu‚ J Saiz‚ J Cooper‚ P Pathmanathan‚ GR Mirams‚ J Pitt−Francis and B Rodriguez

In British Journal of Pharmacology. Vol. 168. No. 3. Pages 718−733. 2013.

Details about Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials | BibTeX data for Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials | DOI (10.1111/j.1476-5381.2012.02200.x)

Considerations for the use of cellular electrophysiology models within cardiac tissue simulations

D. Noble J. Cooper A. Corrias D. Gavaghan

In Prog Biophys Mol Biol. Vol. 107. No. 1. Pages 74−80. 2011.

Details about Considerations for the use of cellular electrophysiology models within cardiac tissue simulations | BibTeX data for Considerations for the use of cellular electrophysiology models within cardiac tissue simulations | DOI (10.1016/j.pbiomolbio.2011.06.002) | Download (pdf) of Considerations for the use of cellular electrophysiology models within cardiac tissue simulations

High−throughput functional curation of cellular electrophysiology models

Niederer S.A. Cooper J. Mirams G.R.

In Progress in Biophysics and Molecular Biology. Vol. 107. Pages 11 − 20. 2011.

Details about High−throughput functional curation of cellular electrophysiology models | BibTeX data for High−throughput functional curation of cellular electrophysiology models | DOI (10.1016/j.pbiomolbio.2011.06.003)

Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk

G. R. Mirams‚ Y. Cui‚ A. Sher‚ M. Fink‚ J. Cooper‚ B. M. Heath‚ N. C. McMahon‚ D. J. Gavaghan and D. Noble

In Cardiovascular Research. Vol. 91. No. 1. Pages 53–61. 2011.

Details about Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk | BibTeX data for Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk | DOI (10.1093/cvr/cvr044) | Link to Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk

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.

Details about The Virtual Physiological Human ToolKit – Evolution and Sustainability | BibTeX data for The Virtual Physiological Human ToolKit – Evolution and Sustainability | Link to The Virtual Physiological Human ToolKit – Evolution and Sustainability

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.

Details about Markup Languages for In Silico Oncology | BibTeX data for Markup Languages for In Silico Oncology | Download  (pdf) of Markup Languages for In Silico Oncology | Link to Markup Languages for In Silico Oncology

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.

Details about The Virtual Physiological Human ToolKit | BibTeX data for The Virtual Physiological Human ToolKit | DOI (10.1098/rsta.2010.0144)

A numerical guide to the solution of the bidomain equations of cardiac electrophysiology

Pras Pathmanathan‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alan Garny‚ Joe M Pitt−Francis‚ Jonathan P Whiteley and David J Gavaghan

In Progress in biophysics and molecular biology. Vol. 102. No. 2−3. Pages 136–155. 2010.

Details about A numerical guide to the solution of the bidomain equations of cardiac electrophysiology | BibTeX data for A numerical guide to the solution of the bidomain equations of cardiac electrophysiology | DOI (10.1016/j.pbiomolbio.2010.05.006)

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.

Details about Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library | BibTeX data for Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library | DOI (10.1098/rsta.2008.0309)

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 and others

In Computer Physics Communications. Vol. 180. No. 12. Pages 2452–2471. 2009.

Details about Chaste: a test−driven approach to software development for biological modelling | BibTeX data for Chaste: a test−driven approach to software development for biological modelling | DOI (10.1016/j.cpc.2009.07.019)

Toward a VPH/Physiome ToolKit

Peter J. Hunter Alan Garny Jonathan Cooper

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

Details about Toward a VPH/Physiome ToolKit | BibTeX data for Toward a VPH/Physiome ToolKit | DOI (10.1002/wsbm.63)

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.

Details about A computational study of discrete mechanical tissue models | BibTeX data for A computational study of discrete mechanical tissue models | DOI (10.1088/1478-3975/6/3/036001)

An integrative computational model for intestinal tissue renewal

Van Leeuwen‚ Ingeborg MM‚ GR Mirams‚ Alex Walter‚ A Fletcher‚ P Murray‚ J Osborne‚ S Varma‚ SJ Young‚ J Cooper‚ B Doyle and others

In Cell proliferation. Vol. 42. No. 5. Pages 617–636. 2009.

Details about An integrative computational model for intestinal tissue renewal | BibTeX data for An integrative computational model for intestinal tissue renewal | DOI (10.1111/j.1365-2184.2009.00627.x)

Automatic Validation and Optimisation of Biological Models

Jonathan Cooper

PhD Thesis 2009.

Details about Automatic Validation and Optimisation of Biological Models | BibTeX data for Automatic Validation and Optimisation of Biological Models | Link to Automatic Validation and Optimisation of Biological Models

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: Mathematical‚ Physical and Engineering Sciences. Vol. 366. No. 1878. Pages 3111–3136. 2008.

Details about Chaste: using agile programming techniques to develop computational biology software | BibTeX data for Chaste: using agile programming techniques to develop computational biology software | DOI (10.1098/rsta.2008.0096)

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.

Details about CellML and Associated Tools and Techniques | BibTeX data for CellML and Associated Tools and Techniques | DOI (10.1098/rsta.2008.0094)

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.

Details about A model−driven approach to automatic conversion of physical units | BibTeX data for A model−driven approach to automatic conversion of physical units | DOI (10.1002/spe.828)

Experience Report: A Haskell interpreter for CellML

Jonathan Cooper and Steve McKeever

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

Details about Experience Report: A Haskell interpreter for CellML | BibTeX data for Experience Report: A Haskell interpreter for CellML | DOI (10.1145/1291151.1291190)

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.

Details about On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations | BibTeX data for On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations | DOI (10.1145/1111542.1111546)