Mr Tommy Yu
Tommy is a software engineer at the Auckland Bioengineering Institute, and has a Bachelor of Arts in Computer Science from York University, Toronto, Canada.
Research | Current
Tommy is responsible for the development of software behind the Physiome Repository (https://models.physiomeproject.org/), and the support of developer and user requirements related to this work. Other responsibilities include software development and maintenance related to Zope/Plone based infrastructures, such as the CellML website.
Selected publications and creative works (Research Outputs)
- Sarwar, D., Yu, T., Atalag, K., Carlson, B., Gennari, J., Hunter, P. J., ... Nickerson, D. P. (2018). Investigating Hypotheses through Discovery of Relevant Models of Epithelial Transport. Paper presented at Experimental Biology Meeting, San Diego, CA. 21 April - 25 April 2018. FASEB JOURNAL. (pp. 2).
Other University of Auckland co-authors: Koray Atalag, Peter Hunter, David Nickerson
- de Bono, B., Safaei, S., Grenon, P., Nickerson, D. P., Alexander, S., Helvensteijn, M., ... Yu, T. (2015). The open physiology workflow: Modeling processes over physiology circuitboards of interoperable tissue units. Frontiers in Physiology, 610.3389/fphys.2015.00024
Other University of Auckland co-authors: David Nickerson, Peter Hunter, Soroush Safaei, Bernard de Bono
- Cooling, M. T., & Yu, T. (2015). Distributed Model Construction with Virtual Parts. In M. A. Marchisio (Ed.) Computational Methods in Synthetic Biology (pp. 301-322). Springer-Verlag. 10.1007/978-1-4939-1878-2_15
- Britten, R. D., Christie, G. R., Little, C., Miller, A. K., Bradley, C., Wu, A., ... Nielsen, P. (2013). FieldML, a proposed open standard for the Physiome project for mathematical model representation. Med Biol Eng Comput, 51 (11), 1191-1207. 10.1007/s11517-013-1097-7
Other University of Auckland co-authors: Christopher Bradley, Poul Nielsen, Richard Christie, Peter Hunter
- Hunter, P., Bradley, C., Britten, R., Brooks, D., Carotenuto, L., Christie, R., ... Little, C. (2012). The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling. (pp. 205-250). 10.1007/978-88-470-1935-5_8
Other University of Auckland co-authors: Peter Hunter, Poul Nielsen, Christopher Bradley, David Nickerson, Alistair Young, Richard Christie, David Brooks, Alan Garny
- Miller, A. K., Yu, T., Britten, R., Cooling, M. T., Lawson, J., Cowan, D., ... Nickerson, D. P. (2011). Revision history aware repositories of computational models of biological systems. BMC Bioinformatics, 12.10.1186/1471-2105-12-22
Other University of Auckland co-authors: Alan Garny, Peter Hunter, David Nickerson, Poul Nielsen
- Bradley, C., Bowery, A., Britten, R., Budelmann, V., Camara, O., Christie, R., ... Heidlauf, T. (2011). OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project. Progress in Biophysics and Molecular Biology, 107 (1), 32-47. 10.1016/j.pbiomolbio.2011.06.015
Other University of Auckland co-authors: Peter Hunter, Martyn Nash, Kumar Mithraratne, Vijayaraghavan Rajagopal, Christopher Bradley, David Nickerson, Poul Nielsen, Soroush Safaei, Thiranja Babarenda Gamage
- Misirli, G., Hallinan, J. S., Yu, T., Lawson, J., Wimalaratne, S. M., Cooling, M. T., & Wipat, A. (2011). Model Annotation for Synthetic Biology: Automating Model to Nucleotide Sequence Conversion. Bioinformatics, 27 (7), 973-979. 10.1093/bioinformatics/btr048