Jonathan Cooper : Publications

Journal papers

• [1]

  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)

• [2]

  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

• [3]

  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)

• [4]

  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)

• [5]

  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)

• [6]

  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)

• [7]

  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

• [8]

  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)

• [9]

  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

• [10]

  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)

• [11]

  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)

• [12]

  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)

• [13]

  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)

• [14]

  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)

• [15]

  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)

• [16]

  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)

• [17]

  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)

• [18]

  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)

• [19]

  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)

Conference papers

• [1]

  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

• [2]

  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

• [3]

  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)

• [4]

  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)

Theses

• [1]

  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