Mr Dewan Mahabub Sarwar


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Doctoral Candidate - Doctor of Philosophy


Dewan received his Bachelor of Science in Computer Science and Engineering from Khulna University of Engineering and Technology, and his Master of Science in Networks and Distributed Systems from Chalmers University of Technology. Afterwards he was a member of faculty at the American International University-Bangladesh.

In July 2015, he joined the Auckland Bioengineering Institute at the University of Auckland to pursue his doctorate.

Research | Current

Semantic Annotation and Discovery with CellML and PMR

In this project we propose to develop a knowledge management system capable of constructing multiscale renal nephron models from information extracted from the Physiome Model Repository (PMR). We specifically aim to investigate transport phenomena in the kidney at the cellular and subcellular level and the impact on nephron function. Through accurate and detailed descriptions of our computational models, encoded in CellML, we are able to capture the knowledge encapsulated by the models. Encoding the models and their description in a computable form and depositing these resources into PMR ensures this information is persistent, identifiable, and discoverable.

By using well defined vocabularies to encode knowledge deposited in this manner enables the full range of information in the repository to be explored in the quest to answer specific questions. One use of this exploration is the identification of missing knowledge, which could be addressed via more accurate description of existing resources or the addition of new knowledge to the repository. Identifying existing resources in the repository which can be integrated in order to address hypotheses put forward by users is a further use-case to be investigated in this project.

Supervisor: Dr David Nickerson

Co-supervisor: Dr Koray Atalag

Advisor: Professor Peter Hunter

Research group


Dewan is carrying out research for his doctorate under the Medical Technologies Centre of Research Excellence (MedTech CoRE).

Selected publications and creative works (Research Outputs)

  • Sarwar, D., Kalbasi, R., Gennari, J., Carlson, B., Neal, M., Bono, B. D., ... Nickerson, D. (2018). Model Annotation and Discovery with the Physiome Model Repository. 10.1101/498501
    Other University of Auckland co-authors: Koray Atalag, David Nickerson, Peter Hunter
  • de Bono, B., Helvensteijn, M., Kokash, N., Martorelli, I., Sarwar, D., Islam, S., ... Hunter, P. (2016). Requirements for the formal representation of pathophysiology mechanisms by clinicians. Interface Focus, 6 (2)10.1098/rsfs.2015.0099
    Other University of Auckland co-authors: Peter Hunter, Bernard de Bono