Australian Imaging Service (AIS): Building a national federation

Dr Ryan Sullivan1, Australian Imaging Service1,2,3,4,5,6,7,8,9,10,11,12, A/Prof David Abbott2,9, Michael Cartwright10, Dr Oren Civier2,8, Dr Thomas Close1,2, Mr Alasair Ferguson4, Dr Andrew Mehnert2,12, Dr Aswin Narayanan2,11, Mr Dean Taylor11, Mr Chris Williams6, Mr Craig Windell6, Mr Fang Xu1

1The University of Sydney
2National Imaging Facility
3Australian Research Data Commons
4Macquarie University
5Queensland Cyber Infrastructure Foundation
6Queensland University of Technology
7SAHMRI
8Swinburne University
9The Florey Institute of Neuroscience and Mental Health
10University of New South Wales
11University of Queensland
12University of Western Australia

Universities and clinical sites across Australia share common challenges in managing large volumes of imaging data, balancing patient privacy, and the value earned through secondary-use by trusted research communities. The Australian Imaging Service (AIS) will transform the imaging sector by leveraging institutional investments and providing enhanced data management and analysis. The distributed federation will consist of multiple institutional Trusted Data Repository (TDR) deployments linked with a federated search layer, common community practice, support for expanded data types, and a Trusted Tool Repository (TTR) ensuring ongoing ownership and accountability of data.

The 2020 project consists of 4 streams:

Building on independent but convergent initiatives, we are deploying standardized AIS nodes at USYD, Monash, MQ, QUT, UNSW, UQ, and UWA across commercial cloud, NECTAR, Pawsey, and on-premise infrastructure, built around XNAT. We aim to reach IRAP (Protected), HIPAA, and GDPR compliance to allow better integration with clinical systems.

Expansion of containerized pipelines will create larger toolsets for image analysis and QC, including a TTR, vetted by the National Imaging Facility.

Expansion of supported imaging modalities and open data formats to cover a wider research base.

Integration with key related platforms including CLARA for machine learning and REDCap.

We will present on our strategy and approaches, covering technologies, standards, clinical practices, containerization, and sustainability in order to facilitate discussion. We welcome new entrants into the federation along with input from potential user groups wishing to shape this national platform through the creating working groups around standard analysis, QC/QA, ethics, and ML.

https://australian-imaging-service.github.io/


Biography:

Dr Ryan Sullivan is the Product Manager overseeing digital platforms for Characterization research at the University of Sydney. He sits across the Research Technology Group in ICT and the Operations team of the Core Research Facilities.

Ryan leads the Australian Imaging Service platform and works to bridge the research-clinical gap across all facets of characterization.

eResearch in action: what isn’t in scope?

Prof. Matthew Bellgard1

1Queensland University of Technology, Brisbane, Australia

eResearch is the term given to the role of digital transformation in disciplinary, multi-, inter- and trans- disciplinary research where every research question can be framed in the context of eResearch touch points at different stages: digital platforms; data management, open data, curation, governance, contracts, access, and privacy; Internet of Things; artificial intelligence; decision support; bioinformatics; security; visualisation; algorithms, advanced analytics; network latency challenges; high performance computing and cloud computing.

Critical to the quantifiable success of eResearch is ongoing close engagement with end-users to deliver solutions, continual improvements in work practices and tools leveraging expertise, and obtaining efficiencies through automation. It would seem logical to draw on these successes for broader benefit and impact.

This presentation showcases a confluence of successful eResearch interrelated exemplars: i) enabling and driving research across multiple disciplines; ii) optimised advanced computing within a heterogenous computing environment; iii) delivery of scalable and reusable eResearch solutions to support diverse institutional research infrastructure including imaging, HASS and biotechnology; iv) deployment of advanced data and analytics platforms for real-world challenges for external partners; v) a revised research data management policy and associated functional guidance material to support internal institutional processes; and vi) developing eResearch standard operating procedures for continual improvement across the eResearch team for rapid response and promote feedback for end-users be they, researchers, students, faculties, schools, Centres and Divisional key stakeholders [1, 2]. Measures of eResearch success are defined and presented by which it becomes possible to share and exchange best of breed eResearch approaches across institutions and organisations.

References

  1. Bellgard, M.I. ERDMAS: An exemplar-driven institutional research data management and analysis strategy, International Journal of Information Management, Vol 50, 2020, Pages 337-340, ISSN 0268-4012, https://doi.org/10.1016/j.ijinfomgt.2019.08.009.
  2. Bellgard, M.I., Snelling, T. & McGree, J.M. RD-RAP: beyond rare disease patient registries, devising a comprehensive data and analytic framework. Orphanet J Rare Dis 14, 176 (2019). https://doi.org/10.1186/s13023-019-1139-9.

Biography:

Professor Matt Bellgard is the inaugural eResearch Director at Queensland University of Technology. He has personally attracted over $45m in research funding, is co-inventor of 5 full/20 provisional patents, co-designed and commissioned a world’s top 100 supercomputer, co-authored over 152 peer reviewed articles in areas including human/animal/plant genomics, bioinformatics, health informatics, AI, biosecurity, eResearch, HASS, remote sensing and radio astronomy. He has led the design and development of digital health solutions for government, industry and academia and is Chair of the APEC Rare Disease Network.

Preservation of Legacy Geoscience Collections – the McNaughton Collection as a Template for Preserving High Value Collections for Future Research

Dr Eleanore Blereau1,2, Ms Amanda Bellenger1, Prof Brent McInnes1,2

1Curtin University, Bentley, Australia
2John de Laeter Centre, Curtin University, Bentley, Australia

Introduction

The project set out to secure, digitise, and make publicly available the physical specimens and associated records in the collection of Professor Neal McNaughton, one of the founding investigators of the Curtin University SHRIMP (Sensitive High Resolution Ion MicroProbe) Facility. The collection comprises over a thousand sample mounts used by a range of researchers covering 25 years of SHRIMP operations.

Methods

The collection has a significant lifespan beyond that of the initial research therefore facilitating re-use of the collection was a primary objective. A secondary objective was to develop a case study that would provide a template for other institutions who seek to preserve and facilitate re-use of high value physical samples in their own research collections.

Results

A team in the John de Laeter Centre compiled metadata on the samples using contextual details in the associated materials, research outputs, and information provided directly by Prof McNaughton. Associated materials containing imaging and log files were digitised for public access. The Library worked on the project to facilitate the minting of identifiers (IGSNs and DOIs) and the contribution of records to Research Data Australia, the Geological Survey of WA’s GeoVIEW portal and AuScope’s AusGeochem platform.

Conclusion

The McNaughton collection provides a useful template for institutions to facilitate re-use of high value collections, including suggestions for future researchers on how to store, manage, and retain records of their samples. The project preserved over 1000 physically irreplaceable samples and resulted in over 4000 globally located sample records from all over the world.


Biography:

Dr Eleanore Blereau (ORCID:0000-0001-8850-397X) is a geoscience researcher at Curtin University and the Geological Survey of Western Australia. In addition to conducting multidisciplinary research to understand the evolution of the Earth and assisting in analytical facilities, she was the project manager for the AuScope funded ‘Preservation of Legacy Collections’ project which was responsible for creating a template for preserving high value research sample collections and was a key creator of the McNaughton Legacy collection.

Amanda Bellenger (ORCID: 0000-0002-0996-6827) is the Manager of the Research and Copyright team at Curtin University Library. She has worked in a range of library positions since 2000, with roles relating to acquisitions, licensing, copyright compliance, archives, the institutional repository, and researcher support services. She led the library team on the ‘Preservation of Legacy Collections’ project, who were responsible for general project support, guidance on metadata, minting of identifiers, and support to publish the research dataset to Research Data Australia.

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