Dr David Phillip Nickerson
PhD (Bioengineering), ME (Engineering Science), BE
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. David is an elected member of the CellML and SED-ML editorial boards, as well as being a COMBINE coordinator. 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
The Virtual Physiological Rat (NIGMS)
The Virtual Physiological Rat Project aims to simulate the integrated cardiovascular function of the rat, and to build validated computer models that account for genetic variation across rat strains and physiological response to environment (i.e., diet). In addition, new strains of genetically engineered rat will be developed with the ultimate goal of using computer models to predict the physiological characteristics of not yet realized genetic combinations, derive those combinations in the lab, and then test the predictions.
Under the VPR project, we are contributing to the development of a computational model of the kidney. In particular, we are focused on representing biophysically detailed renal solute transport processes in a multiscale model of the nephron.
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.
The Auckland Bioengineering Institute maintains and develops several core software tools supporting the various projects undertaken within the institute.
OpenCMISS is a mathematical modeling environment that enables the application of finite element analysis techniques to a variety of complex bioengineering problems.
CMISS(cm) is the original ABI finite element code base still in use for some complex bioengineering problems.
Cmgui is part of CMISS. Some of the main capabilities are field storage, 3D visualization and a mathematical field abstraction layer.
- Member of the CellML Editorial Board
- Member of the SED-ML Editorial Board
- COMBINE coordinator
Selected publications and creative works (Research Outputs)
- 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. T., Nickerson, D. P., Nielsen, P. M. F., & Hunter, P. J. (2016). Modular modelling with Physiome standards. The Journal of physiology, 594 (23), 6817-6831. 10.1113/jp272633
Other University of Auckland co-authors: Mike Cooling, 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
- 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. Frontiers in bioengineering and biotechnology, 310.3389/fbioe.2015.00019
- 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., Taberner, A. J., Tran, K., Goo, S., Nickerson, D. P., Nash, M. P., ... Loiselle, D. S. (2012). Comparison of the Gibbs and Suga formulations of cardiac energetics: the demise of "isoefficiency". Journal of Applied Physiology, 113 (7), 996-1003. 10.1152/japplphysiol.00693.2011
Other University of Auckland co-authors: Denis Loiselle, Poul Nielsen, Martyn Nash, Andrew Taberner, Kenneth Tran, June-Chiew Han
- 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: Edmund Crampin, Denis Loiselle, Marie-Louise Ward, Poul Nielsen, Martyn Nash, Andrew Taberner, Kenneth Tran, June-Chiew Han