Dr David Phillip Nickerson

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

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Senior Research Fellow


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.

Software 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.

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)


Contact details

Primary office location

Level 6, Room 617
New Zealand

Social links

Web links