MyTARDIS at University of Newcastle

MyTARDIS is a data management system, developed by Monash University and partners, which focus was on the integration of scientific instruments and their associated facilities. It allows data from high-end imaging and other equipment to be stored and accessed in a way that is user friendly and enabling easy collaboration.

Dr Jamie Flynn from the 3D Tissue Clearing and Lightsheet Microscopy Facility, University of Newcastle Hunter Medical Research Institute, together with Dr William Palmer and Dr Antony Martin, saw the potential to gather and process the wealth of imaging and clinical data from the Hunter Cancer Biobank to set up a Virtual Biobank. Their interest in the technology behind 3D tissue clearing – a prerequisite for effective 3D imaging, was a driving force behind the project.

Why a Virtual Biobank? There are several pros. The samples last forever and can be accessed anywhere and at any time. Experiments can be repeated readily and access to a virtual biobank circumvents the months of time and piles of paperwork associated with obtaining human ethics approval to work with the original samples.

Jamie and colleagues opted to start the project with breast cancer biopsies because they comprised more than 42% of the Hunter collection of about 7,500 samples and were associated with more-or-less complete metadata.

When it came to set up the Virtual Biobank, Jamie and colleagues found that MyTARDIS, due to its requirement from the outset for high-quality data, was already geared to handle every challenging angle or require- ment they put to the test.

Another advantage of tapping into MyTARDIS has been the ability to set up a flexible licences for each dataset, based on the principles of attribution (BY), non-commerciality (NC) and share alike (SA).

MyTARDIS is part of the software stack that is deployed under the Charactersation Virtual Laboratory. Its development is coordinated by Monash University with contributions from University of Queensland, University of Western Australia and other partners.

Project website:

Image: 3D breast cancer biopsy (1.5mm diameter). Red are cell nuclei and green is background structures and fibres.