Christopher Bayliss

The Australia urban research gateway

The

A data-driven urban research environment for Australia

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. Copyright

Understanding Soil Acidification Process Using Animation and Text: An Empirical User Evaluation With Eye Tracking

The Australian Urban Research Infrastructure Network (AURIN) project (www.aurin.org.au) is tasked with developing an e-Infrastructure to support urban and built environment research across Australia. As identified in [1], this e-Infrastructure must provide seamless access to highly distributed and heterogeneous data sets from multiple organisations with accompanying analytical and visualization capabilities. The project is tasked with delivering a secure, web-based unifying environment offering a one-stop-shop for Australia-wide urban and built environment research. This paper describes the architectural design and implementation of the AURIN data-driven e-Infrastructure, where data is not just a passive entity that is accessed and used as a consequence of research demand, but is instead, directly shaping the computational access, processing and intelligent utilization possibilities. This is demonstrated in a situational context.

Security Attribute Aggregation Models for E-research Collaborations

This chapter presents a user study in which the participant performance is comparatively measured using two ways of presenting information: animation and text. The stimuli contain equivalent information, but use fundamentally different ways of communicating this information. We designed a workplace to simulate the process as it may occur in the real world. First, a representative task from an actual website was selected (i.e., understanding the soil acidification process). 50 participants first took part in a short ‘study session’, where they were told to remember as much as possible. Then they took a multiple choice test using either the animation or the text in an “open book” setting. The tested media have been assessed through the classical measures of effectiveness (error rate), and efficiency (time to complete the multiple choice test). Text users achieved a slightly higher score in the multiple choice test and required less time compared to animation users. In contrast, more of the animation users considered the questions “easy”. Thus, against all intuition (yet in agreement with some of the previous findings in literature) animation does not appear to perform better for the tasks in this experiment. To further strengthen the experiment, an eye tracking study was also conducted with the animated displays for a more in-depth effort to explore user strategies when asked to ‘remember as much as possible’.

High Throughput Method for Analysis of Repeat Number for 28 Phase Variable Loci of Campylobacter jejuni Strain NCTC11168

Supporting distributed, research collaborations is a fundamental demand of e-Research infrastructures (e-Infrastructures). To be successful, e-Infrastructures must address the needs of all parties involved including end user researchers and associated stakeholders, e.g. organizations that make resources available. These needs often translate into ensuring the security and integrity of systems and data sets used for research purposes. Whilst a cornerstone of e-Research has been to support single sign-on, i.e. where users are not required to provide multiple username/passwords, the reality is that most single sign-on solutions have been based around authentication-oriented only models based on public key infrastructures. For many researchers and organizations, finer-grained access control (authorization) is essential. Such authorization solutions typically depend on delivery of security attributes that determine the privileges of individuals that can subsequently be used to determine their access requests to organizational resources. In this paper we identify attribute delivery patterns that support different authorization-oriented collaborative models. These patterns are currently being explored within the context of the Australian Urban Research Infrastructure Network (AURIN -- www.aurin.org.au).

Elastic Scaling of e-Infrastructures to Support Data-Intensive Research Collaborations

Mutations in simple sequence repeat tracts are a major mechanism of phase variation in several bacterial species including Campylobacter jejuni. Changes in repeat number of tracts located within the reading frame can produce a high frequency of reversible switches in gene expression between ON and OFF states. The genome of C. jejuni strain NCTC11168 contains 29 loci with polyG/polyC tracts of seven or more repeats. This protocol outlines a method—the 28-locus-CJ11168 PV-analysis assay—for rapidly determining ON/OFF states of 28 of these phase-variable loci in a large number of individual colonies from C. jejuni strain NCTC11168. The method combines a series of multiplex PCR assays with a fragment analysis assay and automated extraction of fragment length, repeat number and expression state. This high throughput, multiplex assay has utility for detecting shifts in phase variation states within and between populations over time and for exploring the effects of phase variation on adaptation to differing selective pressures. Application of this method to analysis of the 28 polyG/polyC tracts in 90 C. jejuni colonies detected a 2.5-fold increase in slippage products as tracts lengthened from G8 to G11 but no difference between tracts of similar length indicating that flanking sequence does not influence slippage rates. Comparison of this observed slippage to previously measured mutation rates for G8 and G11 tracts in C. jejuni indicates that PCR amplification of a DNA sample will over-estimate phase variation frequencies by 20-35-fold. An important output of the 28-locus-CJ11168 PV-analysis assay is combinatorial expression states that cannot be determined by other methods. This method can be adapted to analysis of phase variation in other C. jejuni strains and in a diverse range of bacterial species.

Integrating Security Solutions to Support nanoCMOS Electronics Research

For many research endeavours, e-Infrastructures need to provide predictable, on-demand access to large-scale computational resources with high data availability. These need to scale with the research communities requirements and use. One example of such an e-Infrastructure is the Australian Urban Research Infrastructure Network (AURIN -- www.aurin.org.au) project, which supports Australia-wide research in and across the urban and built environment. This paper describes the architecture of the AURIN infrastructure and its support for access to distributed (federated) and highly heterogeneous data sets from a wide range of providers. We present how this architecture solution leverages the intersection of high throughput computing (HTC), infrastructure as a service (IaaS) Cloud services and big data technologies including use of NoSQL resources. The driving concept in this architecture and the focus of this paper is the ability for scaling up or down depending on resource demands at any given time. This is done automatically and on demand avoiding either under-or over-utilization of resources. This resource-optimization-driven infrastructure has been designed to ensure that peak loads can be predicted and successfully coped with, as well as avoid wasting resources during non-peak times. This overall management strategy has resulted in an e-Infrastructure that provides a flexible, evolving research environment that scales with research needs, rather than providing a rigid (static) end product.

Privacy Preserving Geo-Linkage in the Big Urban Data Era

The UK Engineering and Physical Sciences Research Council (EPSRC) funded project ¿Meeting the Design Challenges of nanoCMOS Electronics¿ (nanoCMOS) is developing a research infrastructure for collaborative electronics research across multiple institutions in the UK with especially strong industrial and commercial involvement. Unlike other domains, the electronics industry is driven by the necessity of protecting the intellectual property of the data, designs and software associated with next generation electronics devices and therefore requires fine-grained security. Similarly, the project also demands seamless access to large scale high performance compute resources for atomic scale device simulations and the capability to manage the hundreds of thousands of files and the metadata associated with these simulations. Within this context, the project has explored a wide range of authentication and authorization infrastructures facilitating compute resource access and providing fine-grained security over numerous distributed file stores and files. We conclude that no single security solution meets the needs of the project. This paper describes the experiences of applying X.509-based certificates and public key infrastructures, VOMS, PERMIS, Kerberos and the Internet2 Shibboleth technologies for nanoCMOS security. We outline how we are integrating these solutions to provide a complete end-to-end security framework meeting the demands of the nanoCMOS electronics domain.

Erratum for Aidley et al., "Nonselective Bottlenecks Control the Divergence and Diversification of Phase-Variable Bacterial Populations".

Big data technologies and a range of Government open data initiatives provide the basis for discovering new insights into cities; how they are planned, how they managed and the day-to-day challenges they face in health, transport and changing population profiles. The Australian Urban Research Infrastructure Network (AURIN – www.aurin.org.au) project is one example of such a big data initiative that is currently running across Australia. AURIN provides a single gateway providing online (live) programmatic access to over 2000 data sets from over 70 major and typically definitive data-driven organizations across federal and State government, across industry and across academia. However whilst open (public) data is useful to bring data-driven intelligence to cities, more often than not, it is the data that is not-publicly accessible that is essential to understand city challenges and needs. Such sensitive (unit-level) data has unique requirements on access and usage to meet the privacy and confidentiality demands of the associated organizations. In this paper we highlight a novel geo-privacy supporting solution implemented as part of the AURIN project that provides seamless and secure access to individual (unit-level) data from the Department of Health in Victoria. We illustrate this solution across a range of typical city challenges in localized contexts around Melbourne. We show how unit level data can be combined with other data in a privacy-protecting manner. Unlike other secure data access and usage solutions that have been developed/deployed, the AURIN solution allows any researcher to access and use the data in a manner that meets all of the associated privacy and confidentiality concerns, without obliging them to obtain ethical approval or any other hurdles that are normally put in place on access to and use of sensitive data. This provides a paradigm shift in secure access to sensitive data with geospatial content.

A lightweight authorization mechanism for spatially enabled health data services

Volume 8, no. 2, e02311-16, 2017, https://doi.org/10.1128/mBio.02311-16. The byline and affiliation line of our article should appear as shown above. The following should also be added to the end of Acknowledgments: “M.A.J. was supported by the BBSRC (grant BBI02542).” Published 8 August 2017 Citation Aidley J, Rajopadhye S, Akinyemi NM, Lango-Scholey L, Jones MA, Bayliss CD. 2017. Erratum for Aidley et al., “Nonselective bottlenecks control the divergence and diversification of phase-variable bacterial populations.” mBio 8:e00878-17. https://doi .org/10.1128/mBio.00878-17. Copyright