All Stories

  1. A modular and reusable model of epithelial transport in the proximal convoluted tubule

    Article • PLoS ONE, November 2022, PLOS

    Dr Soroush Safaei, David P Nickerson, Leyla Noroozbabaee

  2. CellML 2.0

    Article • Journal of Integrative Bioinformatics, July 2020, De Gruyter

    David P Nickerson

  3. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

    Article • Journal of Integrative Bioinformatics, March 2018, De Gruyter

    Brett G Olivier, David P Nickerson

  4. eSolv, a CellML-based simulation front-end for online teaching

    Article • AJP Advances in Physiology Education, September 2017, American Physiological Society

    David P Nickerson

  5. SED-ML web tools: generate, modify and export standard-compliant simulation studies

    Article • Bioinformatics, January 2017, Oxford University Press (OUP)

    David P Nickerson

  6. SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

    Article • October 2016, PeerJ

    David P Nickerson

  7. SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

    Article • October 2016, PeerJ

    David P Nickerson

  8. Modular modelling with Physiome standards

    Article • The Journal of Physiology, August 2016, Wiley

    David P Nickerson

  9. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

    Article • Interface Focus, February 2016, Royal Society Publishing

    Dr Joerg Geiger, David P Nickerson

  10. The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units

    Article • Frontiers in Physiology, February 2015, Frontiers

    Dr Soroush Safaei, David P Nickerson

  11. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

    Article • BMC Bioinformatics, December 2014, Springer Science + Business Media

    Brett G Olivier, David P Nickerson

  12. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    Article • Standards in Genomic Sciences, March 2014, Springer Science + Business Media

    Brett G Olivier, David P Nickerson

  13. Standards and tools supporting collaborative development of the virtual physiological human

    Article • July 2013, Institute of Electrical & Electronics Engineers (IEEE)

    David P Nickerson

  14. Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of “isoefficiency”

    Article • Journal of Applied Physiology, October 2012, American Physiological Society

    David P Nickerson

  15. Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral

    Article • Journal of Applied Physiology, October 2012, American Physiological Society

    David P Nickerson

  16. Myocardial twitch duration and the dependence of oxygen consumption on pressure-volume area: experiments and modelling

    Article • The Journal of Physiology, June 2012, Wiley

    David P Nickerson

  17. The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling

    Article • January 2012, Springer Science + Business Media

    Professor Alistair A Young, David P Nickerson

  18. OpenCMISS: A multi-physics & multi-scale computational infrastructure for the VPH/Physiome project

    Article • Progress in Biophysics and Molecular Biology, October 2011, Elsevier

    Dr Soroush Safaei, David P Nickerson, Vijay Rajagopal, Prof Alejandro F Frangi

  19. Minimum Information About a Simulation Experiment (MIASE)

    Article • PLoS Computational Biology, April 2011, PLOS

    David P Nickerson

  20. CellML + [CMISS | OpenCMISS]

    Article • Nature Reports Climate Change, April 2011, Springer Science + Business Media

    David P Nickerson

  21. A tool for multi-scale modelling of the renal nephron

    Article • Interface Focus, March 2011, Royal Society Publishing

    David P Nickerson

  22. The Physiome Model Repository 2

    Article • Bioinformatics, January 2011, Oxford University Press (OUP)

    David P Nickerson

  23. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    David P Nickerson

  24. Revision history aware repositories of computational models of biological systems

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    David P Nickerson

  25. Workspaces, exposures, and multiscale modelling

    Article • Nature Reports Climate Change, October 2010, Springer Science + Business Media

    David P Nickerson

  26. Workspaces, exposures, and multiscale modelling

    Article • Nature Reports Climate Change, October 2010, Springer Science + Business Media

    David P Nickerson

  27. An overview of the CellML API and its implementation

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    David P Nickerson

  28. A physiome standards-based model publication paradigm

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, April 2009, Royal Society Publishing

    David P Nickerson

  29. CellML metadata standards, associated tools and repositories

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, April 2009, Royal Society Publishing

    David P Nickerson

  30. CellML and associated tools and techniques

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, September 2008, Royal Society Publishing

    David P Nickerson

  31. Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model

    Article • Progress in Biophysics and Molecular Biology, September 2008, Elsevier

    David P Nickerson

  32. Reference descriptions of cellular electrophysiology models

    Article • Bioinformatics, March 2008, Oxford University Press (OUP)

    David P Nickerson

  33. Computational multiscale modeling in the IUPS Physiome Project: Modeling cardiac electromechanics

    Article • IBM Journal of Research and Development, November 2006, IBM

    David P Nickerson

  34. Modeling Cardiac Electrical Activity at the Cell and Tissue Levels

    Article • Annals of the New York Academy of Sciences, October 2006, Wiley

    David P Nickerson

  35. A Computational Model of Cardiac Electromechanics

    Article • August 2006, Institute of Electrical & Electronics Engineers (IEEE)

    David P Nickerson

  36. Toward a Curated CellML Model Repository

    Article • August 2006, Institute of Electrical & Electronics Engineers (IEEE)

    David P Nickerson

  37. Cardiac Electromechanical Coupling

    Article • April 2006, Wiley

    David P Nickerson

  38. The Noble cardiac ventricular electrophysiology models in CellML

    Article • Progress in Biophysics and Molecular Biology, January 2006, Elsevier

    David P Nickerson

  39. Modelling the passive and nerve activated response of the rectus femoris muscle to a flexion loading: A finite element framework

    Article • Medical Engineering & Physics, December 2005, Elsevier

    David P Nickerson

  40. New developments in a strongly coupled cardiac electromechanical model

    Article • EP Europace, January 2005, European Society of Cardiology

    David P Nickerson

  41. Modeling the fluffy lens

    Article • January 2005, ACM (Association for Computing Machinery)

    David P Nickerson

  42. Mathematical modelling of the heart: cell to organ

    Article • Chaos Solitons & Fractals, June 2002, Elsevier

    David P Nickerson

  43. A model of cardiac cellular electromechanics

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, June 2001, Royal Society Publishing

    David P Nickerson

  44. A Novel Method to Describe and Share Complex Mathematical Models of Cellular Physiology

    Article • Springer Science + Business Media

    David P Nickerson