Richard Sinnott

University of Melbourne, School of Engineering, Faculty Member

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Professor Richard O. Sinnott is the Director of eResearch at the University of Melbourne and Professor of Applied Computing Systems. In these roles he is responsible for all aspects of eResearch (research-oriented IT development) at the University. He has been lead software engineer/architect on an extensive portfolio of national and international projects, with specific focus on those research domains requiring finer-grained access control (security).

IT security (authentication, authorisation, auditing and accounting systems)
biomedical IT systems (bioinformatics, life science data management)
clinical IT systems (biobanking, clinical trials, epidemiology, disease registries)
eResearch across multiple application areas (security, HPC, data management, distributed systems)
engineering IT systems (large scale supercomputing / Grids)
public health IT systems (social, clinical, geospatial, environmental systems)
social science IT systems (social simulation, microdata)
software engineering (real time systems, formal methods, distributed systems)

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Papers by Richard Sinnott

Tools and Processes to Support the Development of a National Platform for Urban Research: Lessons (Being) Learnt from the AURIN Project

by Richard Sinnott and Luca Morandini

AbstractThe development of large-scale software systems remains a non-trivial endeavour. This is... more

The Australia urban research gateway

by Richard Sinnott, Gerson Galang, Andrew J Bromage, Luca Morandini, and martin tomko

The $20m Australian Urban Research Infrastructure Network (AURIN) project (www.aurin.org.au) bega... more The $20m Australian Urban Research Infrastructure Network (AURIN) project (www.aurin.org.au) began in July 2010. AURIN has been tasked with developing a secure, Web-based virtual environment (e-Infrastructure) offering seamless, secure access to diverse, distributed and extremely heterogeneous data sets from numerous agencies with an extensive portfolio of targeted analytical and visualization tools. This is being provisioned for Australia-wide urban and built environment researchers – itself a highly heterogeneous collection of research communities with diverse demands, through a unified urban research gateway. This paper describes these demands and how the e-Infrastructure and gateway is being designed and implemented to accommodate this diversity of requirements, both from the user/researcher perspective and from the data provider perspective. The scaling of the infrastructure is presented and the way in which it copes with the spectrum of big data challenges (volume, veracity, variability and velocity) and associated big data analytics. The utility of the e-Infrastructure is also demonstrated through a range of scenarios illustrating and reflecting the interdisciplinary urban research now possible.

SMPD1 Mutation Update: Database and Comprehensive Analysis of Published and Novel Variants

Niemann Pick Types A and B (NPA/B) diseases are autosomal recessive lysosomal storage disorders c... more Niemann Pick Types A and B (NPA/B) diseases are autosomal recessive lysosomal storage disorders caused by the deficient activity of acid sphingomyelinase (ASM) due to mutations in the SMPD1 gene. Here, we provide a comprehensive updated review of already reported and newly identified SMPD1 variants. Among them, 185 have been found in NPA/B patients. Disease-causing variants are equally distributed along the SMPD1 gene; most of them are missense (65.4%) or frameshift (19%) mutations. The most frequently reported mutation worldwide is the p.R610del, clearly associated with an attenuated NP disease type B phenotype. The available information about the impact of 52 SMPD1 variants on ASM mRNA and /or enzymatic activity has been collected and whenever possible, phenotype/genotype correlations were established. In addition, we created a locus specific database easily accessible at http://www.inpdr.org/genes that catalogs the 417 SMPD1 variants reported to date and provides data on their in silico predicted effects on ASM protein function or mRNA splicing. The information reviewed in this paper, providing new insights into the genotype/phenotype correlation, is extremely valuable to facilitate diagnosis and genetic counseling of families affected by NPA/B. This article is protected by copyright. All rights reserved.

Environmental determinants of islet autoimmunity (ENDIA): a pregnancy to early life cohort study in children at-risk of type 1 diabetes

BACKGROUND: The incidence of type 1 diabetes has increased worldwide, particularly in younger chi... more BACKGROUND: The incidence of type 1 diabetes has increased worldwide, particularly in younger children and those with lower genetic susceptibility. These observations suggest factors in the modern environment promote pancreatic islet autoimmunity and destruction of insulin-producing beta cells. The Environmental Determinants of Islet Autoimmunity (ENDIA) Study is investigating candidate environmental exposures and gene-environment interactions that may contribute to the development of islet autoimmunity and type 1 diabetes. METHODS/DESIGN: ENDIA is the only prospective pregnancy/birth cohort study in the Southern Hemisphere investigating the determinants of type 1 diabetes in at-risk children. The study will recruit 1,400 unborn infants or infants less than six months of age with a first-degree relative (i.e. mother, father or sibling) with type 1 diabetes, across five Australian states. Pregnant mothers/infants will be followed prospectively from early pregnancy through childhood to investigate relationships between genotype, the development of islet autoimmunity (and subsequently type 1 diabetes), and prenatal and postnatal environmental factors. ENDIA will evaluate the microbiome, nutrition, bodyweight/composition, metabolome-lipidome, insulin resistance, innate and adaptive immune function and viral infections. A systems biology approach will be used to integrate these data. Investigation will be by 3-monthly assessments of the mother during pregnancy, then 3-monthly assessments of the child until 24 months of age and 6-monthly thereafter. The primary outcome measure is persistent islet autoimmunity, defined as the presence of autoantibodies to one or more islet autoantigens on consecutive tests. DISCUSSION: Defining gene-environment interactions that initiate and/or promote destruction of the insulin-producing beta cells in early life will inform approaches to primary prevention of type 1 diabetes. The strength of ENDIA is the prospective, comprehensive and frequent systems-wide profiling from early pregnancy through to early childhood, to capture dynamic environmental exposures that may shape the development of islet autoimmunity. TRIAL REGISTRATION: Australia New Zealand Clinical Trials Registry ACTRN12613000794707.

Modeling coordinated multiple views of heterogeneous data cubes for urban visual analytics

by Richard Sinnott and martin tomko

With the explosion of digital data, the need for advanced visual analytics, including coordinated... more With the explosion of digital data, the need for advanced visual analytics, including coordinated multiple views (CMV), is rapidly increasing. CMV enable users to discover patterns and examine relationships across multiple visualizations of one or multiple datasets. CMV have been implemented in a web-based environment through the Australian Urban Research Infrastructure Network (AURIN) project. AURIN offers a platform providing seamless and secure access to an extensive range of distributed urban datasets across Australia. Visual exploration of these datasets is essential to support research endeavors. This paper focuses on the challenges in dealing with complexity and multidimensionality of datasets used in CMV. We rely on the concept of multidimensional data cubes as the theoretical framework for coordination across visualizations. Using the concept of data cubes and hierarchical dimensions, we present strategies to automatically build render groups. This provides an implicit coordination based on cube structures and a framework to establish links between a dataset with its aggregates in a one-to-many fashion. The CMV approach is demonstrated using aggregate-level data, which is provided through federated data services. The paper discusses the issues around our CMV implementation and concludes by reflecting on the challenges in supporting spatio-temporal urban data exploration.

TruXy: Trusted Storage Cloud for Scientific Workflows

A scalable Cloud-based system for data-intensive spatial analysis

Development of an endocrine genomics virtual research environment for Australia: building on success

by Loren R Bruns Jr, Richard Sinnott, William Hu, and Glenn Jayaputera

The $47m Australian National eResearch Collaboration Tools and Resources (NeCTAR - www.nectar.org... more The $47m Australian National eResearch Collaboration Tools and Resources (NeCTAR - www.nectar.org.au) project has recently funded an initiative to establish an Australia-wide endocrine genomics virtual laboratory (endoVL – www.endovl.org.au) covering a range of disorders including type-1, type-2 diabetes, rare diabetes-related disorders, obesity/thyroid disorders, neuroendocrine/adrenal tumours, bone disorders and disorders of sex development. This virtual laboratory will establish a range of targeted databases, clinical registries and support a range of genetically targeted clinical trials leveraging a body of international projects and experiences garnered over many years through a range of EU and MRC funded initiatives. This paper focuses on the plans for endoVL and especially, the systems it leverages in supporting large-scale clinical, collaborative environments.

The Australian Urban Intelligence Network Supporting Smart Cities

As the global population continues to grow and an increasing number of people move to cities, the... more As the global population continues to grow and an increasing number of people move to cities, there is need for ambitious approaches to provide urban information infrastructures and analytical tools to support smart urban design and planning. This chapter introduces the Australian Urban Intelligence Network, which brings together a network of researchers, planners and policy-makers from across Australia who have access to an online workbench of data and tools. The workbench comprises over 1100 datasets and 100 spatial statistical routines, and a select number of planning support systems and geodesign tools. In this chapter, we outline the urban data and analytical capability the online workbench; introduce a couple of the PSS tools and spatial statistical capabilities through a case study approach. We also discuss the user outreach and capacity building capability program which is a critical component to assist with user adoption. We conclude the chapter with some reflections on the lessons learnt and next steps in the project.

A collaborative infrastructure supporting international adrenal cancer research

A wealth of information about adrenal cancer exists in many individual specialist centres around ... more A wealth of information about adrenal cancer exists in many individual specialist centres around the world. The cancers themselves are very rare, often fatal and no common consensus on optimal treatment strategies exists, and certainly no treatments targeted to the individual genetic makeup of the tumours and individuals. In order to conduct effective and progressive research into these tumours and the surrounding conditions and treatments of individuals, it is essential to pool the expertise from specialist centres that exist in each country. The ENSAT-CANCER project is a 5-year European Union FP7-funded project tasked with this, through the development of an online environment that holds core data from a body of patients aligned with identified needs from leading specialists in the field. These data sets are also augmented with a host of tools and features that enable and support the research in this domain. This presentation will describe some of the novel features that have been developed in the project including biobank labelling and “match-making” services between centres. The presentation will also cover the hurdles involved in putting together such an enterprise – such as ethical approval for international data sharing and the establishment of canonical identification systems, and how these have been successfully overcome. The ENSAT-CANCER platform has now been used to support a portfolio of major international genetically targeted clinical trials and outcome studies. The presentation will describe the different processes involved in connecting and effectively sharing data and making best use of the ENSAT-CANCER platform.

Role of Endocrine Gland-Derived Vascular Endothelial Growth Factor (EG-VEGF) and Its Receptors in Adrenocortical Tumors.

Angiogenesis is essential for tumor growth and metastasis. Endocrine gland-derived vascular endot... more Angiogenesis is essential for tumor growth and metastasis. Endocrine gland-derived vascular endothelial growth factor (EG-VEGF) is an angiogenic factor predominantly expressed in steroidogenic organs like the adrenal gland, ovary, testes, and placenta. EG-VEGF has antiapoptotic, mitogenic, and chemoattractive properties mediated via the two G protein-coupled receptors prokineticin receptor 1 (PKR1) and prokineticin receptor 2 (PKR2). We investigated the expression of EG-VEGF and its receptors in a large number of normal adrenal glands (NAG), adrenocortical adenomas (ACA), and carcinomas (ACC) using real-time PCR (NAG, n = 12; ACA, n = 24; and ACC, n = 30) and immunohistochemistry (NAG, n = 9; ACA, n = 23; and ACC, n = 163) and evaluated its impact on patients’ survival. EG-VEGF, PKR1, and PKR2 mRNA and protein are expressed in NAG and the vast majority of ACA and ACC samples. The mean EG-VEGF mRNA expression was significantly lower in ACC (606.5 ± 77.1 copies) compared to NAG (4,043 ± 1,111) and cortisol-producing adenomas (CPA) (4,433 ± 2,378) (p < 0.01 and p < 0.05, respectively). However, cytoplasmic and nuclear EG-VEGF protein expression was either significantly higher or similar in ACC (H score 2.4 ± 0.05, p < 0.05 and 1.7 ± 0.08, n.s., respectively) compared to NAG (1.8 ± 0.14 and 1.7 ± 0.2). Nuclear protein expression of either EG-VEGF or PKR1 or both is predictive for a higher mortality compared to patients without nuclear expression (hazard ratio (HR) = 5.15; 95 % confidence interval (CI) = 1.24–21.36, n = 100, p = 0.02 independent of age, sex, and tumor stage). These findings suggest that EG-VEGF and its receptor PKR1 might play a role in the pathogenesis of adrenocortical tumors and could serve as prognostic markers for this rare malignant disease.

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Wolfram syndrome: natural history and genotype-phenotype correlation based on EURO-WABB registry show gender differences in disease severity

Endocrine Abstracts, 2015

Enabling secure, distributed collaborations for adrenal tumor research

Studies in Health Technology and Informatics, 2010

Many e-Health strategies rely on the secure integration of datasets that have previously resided ... more Many e-Health strategies rely on the secure integration of datasets that have previously resided in isolated locations, but can now in principle be accessed over the Internet. Of paramount importance in the health domain is the need for the security and privacy of data that is transmitted across these networks. One such collaboration, which spans several specialist centres across France, Germany, Italy and the UK, is ENSAT -the European Network for the Study of Adrenal Tumors. The rarity of the tumors under study means the value of accessing, aggregating and comparing data from many centres is great indeed. However this is especially challenging given that ENSAT require clinical and genomic data to be seamlessly linked, but in such a way that the information governance, ethics and privacy concerns of the patients and associated stakeholders involved are visibly satisfied. Key to this is the clear separation of clinical and genomic data sets and support for rigorous patient-identity protecting access control. This is especially challenging when such data sets exist across different organisational boundaries. In this paper we describe a prototype solution offering a security-oriented tailored portal supported by a layered encryption-driven linkage technology (VANGUARD) that offers precisely such patient-privacy protecting capabilities. We describe the architecture, implementation and use to date of this facility to support the ENSAT adrenal cancer research network.

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Towards an e-Infrastructure for Australian Urban Research

by Richard Sinnott and Gerson Galang

Towards a virtual anonymisation grid for unified access to remote clinical data

Studies in health technology and informatics

Grid technologies provide an infrastructure through which, amongst other things, data access and ... more Grid technologies provide an infrastructure through which, amongst other things, data access and integration is facilitated across highly distributed and heterogeneous resources. Different domains have their own requirements on the nature of this data access and integration. The clinical domain offers arguably the greatest challenges facing the roll-out and adoption of Grid technologies to meet the changing face of post-genomic clinical research, especially with regard to information governance, ethics and hence security solutions. This paper outlines a novel system design for secure anonymous data access and linkage that meets the needs of key stakeholders in this space including end user researchers, data providers and owners and ethical oversight bodies amongst others. We identify how existing solutions developed within the Medical Research Council funded Virtual Organisations for Trials and Epidemiological Studies (VOTES) project are being re-factored to meet the needs of these ...

Building a Spatially Enabled e-Infrastructure to Support Urban Researchers in Australia

AURIN Technical Report #1: Information Architecture – Core Technical Infrastructure Specification and Initial Implementation Report

by P. Ellingsen, Richard Sinnott, and Gerson Galang

Building an e-Infrastructure to Support Urban Research

Development of an Endocrine Genomics Virtual Research Environment for Australia: Building on Success

by Glenn Jayaputera, Richard Sinnott, and William Hu

Lecture Notes in Computer Science, 2013

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