Dr David Phillip Nickerson

PhD (Bioengineering), ME (Engineering Science), BE

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Senior Research Fellow

Biography

David obtained his PhD in Bioengineering from the University of Auckland. Following a post-doctoral stint at the National University of Singapore, David returned to the Auckland Bioengineering Institute, where he is a Senior Research Fellow and leads the Auckland Renal Physiome project and the Physiome Model Repository, and helps lead the Physiome journal. David is a current or past elected member of the CellML and SED-ML editorial boards, as well as being the CellML delegate on the COMBINE coordination board. He also develops several software tools related to his work on model exhange as well as being involved in several ABI infrastructural software projects.

Research | Current

SPARC MAP-Core

The goal of the NIH SPARC Program is to transform our understanding of nerve-organ interactions by providing access to high-value datasets, maps, and computational studies with the intent of advancing bioelectronic medicine towards treatments that change lives. MAP-Core is one of the cores comprising the SPARC Data & Resource Center, responsible for building interactive, modular, continually updated visualizations of nerve-organ anatomy and function.

Center for Reproducible Biomedical Modeling

The center aims to enable larger and more accurate systems biology models, as well as their applications to science, bioengineering, and medicine, by enhancing their understandability, reusability, and reproducibility.

The Physiome journal

Physiome publishes reproducible and reusable mathematical models of physiological processes where the experimental details and model validation have been published or accepted for publication in a recognised 'primary' peer-reviewed journal. Physiome curators will help authors ensure that models and simulation experiments are made available using appropriate community standards prior to acceptance for publication in Physiome

Community standards for the exchange of biological models

We commonly make use of complex computational models of biological structure and function in order to help understand experimental observations. Such models often span multiple spatial and temporal scales (proteins, cells, tissue, organ, etc) and integrate various types of physical processes (chemical reactions, solute transport, fluid mechanics, mechanical contraction, etc). These models are often coded directly into computational tools in order to perform computational simulation experiments with them, making it difficult for other scientists to validate or make use of without being familiar with the exact same set of software tools. As the tools used are often proprietary, even this is not always possible.

We aim to develop and promote standards by which these models can be encoded into machine readable formats amenable to exchange independent of any particular software tool. Thus greatly improving the reuse and testing of our models, often by totally independent research groups. We also work on software tools and repositories which support these various standardization projects.

Software projects

The Auckland Bioengineering Institute maintains and develops several core software tools supporting the various projects undertaken within the institute.

libCellML aims to become an easy to use library that will be useful to developers of CellML applications.

OpenCMISS is a mathematical modeling environment that enables the application of finite element analysis techniques to a variety of complex bioengineering problems.

Committees/Professional groups/Services

  • Member of the CellML Editorial Board
  • Member of the SED-ML Editorial Board
  • COMBINE coordinator

Selected publications and creative works (Research Outputs)

As of 29 October 2020 there will be no automatic updating of 'selected publications and creative works' from Research Outputs. Please continue to keep your Research Outputs profile up to date.
  • Nickerson, D. P. (2016). Discoverable, reproducible, and reusable cardiac models. Paper presented at 16th International Conference on Biomedical Engineering, Singapore. 7 December - 10 December 2016. 10.17608/k6.auckland.4290398.v1
  • Cooling, M., Nickerson, D., Nielsen, P., & Hunter, P. (2016). Modular modelling with Physiome standards. The Journal of Physiology, 594 (23), 6817-6831. 10.1113/JP272633
    Other University of Auckland co-authors: Poul Nielsen, Peter Hunter
  • Nickerson, D., Atalag, K., de Bono, B., Geiger, J., Goble, C., Hollmann, S., ... Stanford, N. J. (2016). The human physiome: How standards, software and innovative service infrastructures are providing the building blocks to make it achievable. Interface Focus, 6 (2)10.1098/rsfs.2015.0103
    Other University of Auckland co-authors: Peter Hunter, Koray Atalag, Bernard de Bono
  • Hucka, M., Nickerson, D. P., Bader, G. D., Bergmann, F. T., Cooper, J., Demir, E., ... Schreiber, F. (2015). Promoting coordinated development of community-based information standards for modeling in biology: The COMBINE initiative. Front Bioeng Biotechnol, 310.3389/fbioe.2015.00019
    Other University of Auckland co-authors: Alan Garny
  • Nickerson, D. P., Hamilton, K. L., & Hunter, P. J. (2013). Modelling Epithelial Transport. Paper presented at The 15th International Conference on Biomedical Engineering, Singapore. 4 December - 7 December 2013. 10.6084/m9.figshare.870447
    Other University of Auckland co-authors: Peter Hunter
  • Nickerson, D. P., Hamilton, K. L., Terkildsen, J., & Hunter, P. J. (2013). Generalized Epithelial Transport Modeling: Computational Physiology. Paper presented at Joint Annual Meeting of the ASPET/BPS at Experimental Biology (EB), Boston, MA. 20 April - 24 April 2013. FASEB JOURNAL. (pp. 1).
    Other University of Auckland co-authors: Peter Hunter
  • Han, J.-C., Tran, K., Taberner, A. J., Nickerson, D. P., Kirton, R. S., Nielsen, P. M. F., ... Loiselle, D. S. (2012). Myocardial twitch duration and the dependence of oxygen consumption on pressure-volume area: experiments and modelling. J Physiol, 590 (18), 4603-4622. 10.1113/jphysiol.2012.228965
    Other University of Auckland co-authors: Denis Loiselle, Marie-Louise Ward, Poul Nielsen, Martyn Nash, Andrew Taberner, Kenneth Tran, June-Chiew Han
  • Han, J., Taberner, A. J., Tran, K., Nickerson, D. P., Nash, M. P., Nielsen, P. M. F., ... Loiselle, D. S. (2012). Relating components of pressure-volume area in Suga's formulation of cardiac energetics to components of the stress-time integral. Journal of Applied Physiology, 113 (7), 988-995. 10.1152/japplphysiol.00438.2012
    URL: http://hdl.handle.net/2292/35245
    Other University of Auckland co-authors: Andrew Taberner, Denis Loiselle, Poul Nielsen, Martyn Nash, Kenneth Tran, June-Chiew Han

Identifiers

Contact details

Primary office location

UNISERVICES HOUSE - Bldg 439
Level 6, Room 617
70 SYMONDS ST
AUCKLAND 1010
New Zealand

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