QRISnews banner — storing national medical data

Queensland medical and health researchers, especially those in medical research institutes, now have greater engagement with national research data storage thanks to QCIF’s involvement in an RDS national project.
QCIF is one of three RDS nodes (with VicNode and Intersect) involved in the project. is an RDS-funded facility providing petabyte-scale research data storage and related high-speed networked computational services to Australian medical and health research organisations, including a large storage facility in Queensland.

RDS has recently funded QCIF to help medical researchers transfer their data onto QRIScloud and manage their data.
As one of its services, has produced an in-depth analysis of the legislative and IT security requirements of hosting clinical health and medical data on the cloud. These data sets usually contain de-identified personal information that still need to be handled sensitively.
Ultimately, will produce a ‘How To’ guide outlining the roles and responsibilities of data custodians, researchers and node operators in sensitive data storage, and the tools and services available via to enable clinical data to be used and re-used by researchers according to best practice.
Dr Xin-Yi Chua ( and Kathy Dallest ( of QFAB, which officially merged with QCIF on 3 April, are the main contacts for Queensland medical and health researchers and support staff seeking further information about (Dr Chua is the domain specialist profiled below). 

Trialling high-speed data storage fabricRCC's Prof David Abramson promoting MeDiCI

QCIF is participating in the trial of an experimental data storage fabric at UQ. The goal is to ensure the fabric can be extended to all QCIF members through QRIScloud.

UQ’s Research Computing Centre is building MeDiCI, Metropolitan Data Caching Infrastructure, an on-campus cache to speed up off-site data access. (RCC Director Prof David Abramson is pictured promoting MeDiCI.)

MeDiCI will connect on-campus computing hardware via a high-speed network to the significant storage and processing capabilities of Springfield’s Polaris Data Centre, where QRIScloud is sited. This will allow researchers on campus to access local, high-speed storage, whilst leveraging QRIScloud.

RCC expects to introduce a prototype service to UQ during 2016. QCIF will monitor the trial and liaise with its members to determine how best to extend MeDiCI to their campuses. (Read more: ITnews and RCC News.) 

QRIScloud users to gain access to MATLAB MATLAB logo

QCIF has struck a deal to allow users of its compute clusters, such as Euramoo, to access MATLAB, a multi-paradigm numerical computing program used in engineering, science and economics.
Users will be able to run MATLAB jobs either by accessing their university’s license or by using their own personal license.
This is due to QCIF recently signing a Hosting Provider Agreement with MATLAB developer MathWorks.
Once QCIF has the MATLAB software in place in a few weeks’ time, its team can work with members to enable access to their respective license servers so that users correctly access MATLAB features and components they are entitled to run.
If you have any questions on using MATLAB on QRIScloud, please contact the QRIScloud Help Desk:

Seminar: Parallel Computing with MATLAB 

Date: Friday, 15 April 2016
Time: 10:00am–11:30am
Venue: Room 505A, Axon Building 47, The University of Queensland, St Lucia Campus
For researchers who deal with large data and run algorithms that are computationally expensive, distributing computations to available parallel hardware resources is one approach to speed-up the response time of algorithms.
MATLAB, developed by MathWorks, is a multi-paradigm numerical computing program used in engineering, science and economics.
In this free seminar, attendees will:
  • gain an overview of the various MathWorks solutions to perform distributed computing
  • participate in a demonstration of the numerous ways users can distribute their computations on local and remote resources
  • discuss scaling-up applications to compute on the cloud
  • discuss how to perform computations with MathWorks Hosting Providers, such as QCIF, in Australia.
Please email QCIF Service Delivery Manager Stephen Bird ( to register to attend this seminar, or if you have any queries. 

QRISdata storage: Meeting researchers' changing needs 

QCIF is reviewing the QRIScloud storage and network architectures to ensure ongoing planning and investment matches current and emerging researcher requirements and member business needs for the coming years.
The QCIF team has already met with a number of researcher support teams and member and partner representatives, and the following requirements have emerged:
  • Simpler access to QRIScloud research data from member computing hardware and scientific instruments, QRIScompute and shared HPC facilities, including options for storage of derived data;
  • Ability to upload large amounts of experimental data from scientific instruments to QRIScloud for computational analysis;
  • Enhanced research data publishing and sharing options and performance;
  • Use of QRIScloud to mirror and provide access to national and international reference data sets;
  • Low-touch file synchronisation and share services including integration with services such as AARNet CloudStor and DropBox;
  • More object storage and capacity to support enhanced sharing of, and access to, QRIScloud research data between researchers and across platform applications; and
  • Non-functional requirements including research data privacy and security assurance.
QCIF will present the outcomes of the review along with a transition plan to QCIF member representatives in early May 2016. Please contact QCIF Service Delivery Manager Stephen Bird ( to provide input on your requirements.

The Nectar National Server Program National Server Program 

Since 2010, Nectar has been operating its successful National Server Program (NSP) to provide a means of delivering production cloud services to researchers.  Now that the underlying hardware is near its end-of-life, Nectar has decided to transition services that use NSP to the research cloud or to commercial services — choices unavailable in 2010.
As a result, QCIF and four other Nectar nodes will be upgraded and will make similar production levels of service to the NSP available to virtual labs and national capabilities.
Over the next 12 months, QCIF, alongside the four other nodes, will be establishing new, local services to support national research, and transitioning existing NSP clients to the new services.
The existing NSP service will continue during this period to allow time for a smooth transition.
QCIF will implement an additional component of QRIScloud to host and support long-lived national services.

QFAB banner logoBioinformatics workshops extended to QCIF members 

Due to its merger with QFAB, which became official on 3 April, QCIF is now able to offer QFAB bioinformatics training. All QCIF members are able to take advantage of a discount on the costs of courses.

QFAB@QCIF is currently offering the following three workshops in April and May at The University of Queensland:
  • Design of experiments and surveys.
  • Data Interpretation and Reporting with R.
  • Differential Gene Expression Analysis with R (microarray and NGS).
Visit the QFAB training webpage for further information.
QCIF is conducting its annual customer survey survey
Following the exceptional feedback received last year, QCIF is currently conducting its 2016 customer survey.
This year’s survey has a greatly expanded audience, with almost 700 QRIScloud users invited to participate.
The survey gives our users the opportunity to provide valuable feedback on how we have been performing, the services we offer, and how we can improve. 
QCIF uses the feedback to help tailor our services to better meet the needs of our users and improve the experiences for researchers and research communities.
Thank you to everyone who has responded so far, and for those who are yet to respond, we kindly ask that you consider taking a few moments to complete our short survey.
If you did not receive the survey but wish to participate, please contact Stephen Bird, QCIF Service Delivery Manager:

Hardware issue causes QRIScloud compute node outage technical issues

An unfortunate and unexpected QRIScloud compute node outage lasted from mid-March to early April due to hardware issues that became apparent during routine memory upgrades.
To introduce QRIScloud’s new Compute Lite service, QCIF has been adding memory to many of the QRIScloud compute nodes. During this process on 17–18 March, hardware faults prevented three compute nodes from being returned to service. While most users were able to transition their workloads to other compute nodes, the few who were not, were unable to continue their work until the faults were corrected.
Over a three-week period, QCIF worked with the vendor to correct these hardware faults, ultimately requiring replacement parts to be supplied and installed.
As of 6 April, the hardware issues were resolved and the compute nodes were returned to service without compromising users’ work in progress.
QCIF sincerely apologises for any inconvenience caused to QRIScloud users. 

ANDS kicks off Monthly Tech Talk virtual meetings 

Rowland MosbergenOn Friday, 6 May, the Australian National Data Service (ANDS) will start its Monthly Tech Talk virtual meetings on topics of interest to those working with the technical aspects of research data.
The aim is to provide a forum for Australian research institution-based developers, data technologists, data scientists, data librarians and researchers building data tools, and enable them to engage with NCRIS facilities, such as ANDS, Nectar, RDS and QCIF, about their requirements.
The NCRIS facilities will jointly propose the initial topics, with future topics driven by those attending.
The series will initially feature speakers from Nectar’s Power Users group, such as those working on Stemformatics (such as Rowland Mosbergen, pictured), Ecosounds, the BCCVL and the GVL. They will discuss the issues they face running services on the cloud.
Each month, a meeting room will be booked in Australian capital cities for attendees, with the rooms linked via videoconferencing software. Brisbane's meeting room will be room 505a, Axon Building (#47), The University  of Queensland, St Lucia Campus. 

More information, or contact QCIF's Belinda Weaver:

QCIF's Belinda Weaver elected to global committee

Belinda WeaverQCIF eResearch Analyst Team Leader Belinda Weaver (pictured) was recently elected to the global Software Carpentry Steering Committee as its sole southern hemisphere representative.
The committee of seven (plus four non-voting attendees) is directly elected by Software Carpentry instructors and meets virtually each fortnight to decide issues such as new partnerships and affiliations, instructor training schedules, and financial matters. It also oversees the work of a number of task forces and sub-committees such as mentoring and communications.
Other 2016 Steering Committee members hail from the UK, Canada, Norway, and the US.
Belinda will serve a 12-month term and is keen to raise the profile of Software Carpentry both in Australia and around the world. She will attend an in-person two-day Steering Committee meet-up in New York early next month.

QCIF extends Software Carpentry to DSITI staff

QCIF eResearch Analyst Team Leader Belinda Weaver is extending her Software Carpentry mission to include the Queensland Government Department of Science, Information Technology and Innovation this week.
Belinda and fellow instructors Amanda Miotto and Kim Keogh (both from Griffith University), and helpers Anup Shah and Paula Andrea Martinez (both from The University of Queensland), are running a two-day workshop for DSITI staff, particularly researchers, across 11–12 April.
The workshop is focusing on R, a programming language for data exploration, visualisation, and statistical analysis. More info

DSITI Software Carpentry workshop
Getting stuck into R at the DSITI Software Carpentry workshop on Monday, 11 April.

Seminar: Prof Fran Berman to speak at UQ on data-driven research

Professor Francine BermanProfessor Francine Berman (pictured), the U.S. lead of the global Research Data Alliance, will speak at The University of Queensland on Friday, 27 May, 11am–12pm, on building a sustainable ecosystem for data-driven research.
She will discuss sustainability, infrastructure and data, and explore the opportunities and challenges of creating a viable ecosystem for the data on which current and future research and innovation increasingly depend.
Prof Berman’s career has involved many accomplishments and she is regarded as a leader in digital data preservation and cyber-infrastructure.
As well as being the US Chair of RDA, a community-driven international organisation created to accelerate research data sharing worldwide, she is the Edward P. Hamilton Distinguished Professor in Computer Science at Rensselaer Polytechnic Institute.
UQ’s Research Computing Centre is hosting Prof Berman, and the seminar will take place on UQ’s St Lucia Campus. All are welcome to attend this free seminar, and registering is not required. More info

QFAB@QCIF domain specialist profile: Dr Xin-Yi Chua

Dr Xin-Yi ChuaDr Xin-Yi Chua is Head of Informatics at QFAB and is currently leading a team with more than 100 years of collective bioinformatics, biostatistics and IT experience across multiple domains, with skill sets in:
  • NGS analysis
  • biostatistics analysis (integrative–omics analysis, time-course analysis)
  • cloud and high performance computing
  • data management, integration and mining
  • web-application development
  • data analysis using machine learning approaches, and
  • visualisation. 
Dr Chua has worked on a range of diverse projects: from computational biology, such as biomarker discovery, classification modelling and workflow development; to eResearch-based projects, such as web-application development and implementing clinical ePathway applications.
She is motivated by the need to bridge the now apparent gap between data generation and data analysis in life science. The ability to automate repeatable discovery processes and quickly highlight regions of interest for further verification will improve and maximise researchers’ efforts.
Dr Chua received her doctorate from QUT for her work in applying machine learning approaches to enhance performance in inferring transcriptional regulatory interactions in bacteria using comparative genomics. From this work, she developed a keen interest in visual analytics, investigating methods to capture information from large-scale genomic data to facilitate intuitive and rapid comprehension.

QRIScloud is funded by the Australian Government, the Queensland State Government and the QCIF member universities. The Australian Government directs funds through the National eResearch Collaboration Tools and Resources (NeCTAR) Project (led by The University of Melbourne), and the Research Data Storage Infrastructure Project, completed in 2015, and the Research Data Services (RDS) Project (both data projects led by The University of Queensland) using the National Collaborative Research Infrastructure Strategy (NCRIS) and Education Investment Fund (EIF). The Queensland Government directs funds through the Department of Science, Information Technology and Innovation (DSITI) and its Co-investment Fund.

       USQ logo


      RDS logo
April 2016


Upcoming Events

* Each Tuesday, UQ Hacky Hour, St Lucia

* 15 April, MATLAB seminar, UQ, Brisbane

* 21 April, QFAB@QCIF workshop: Design of experiments and surveys, UQ, Brisbane

* 6 May, ANDS Monthly Tech Talk, UQ, Brisbane

* 11 May, QFAB@QCIF workshop: Data Interpretation and Reporting with R, UQ, Brisbane

* 25 May, QFAB@QCIF workshop: Differential Gene Expression Analysis with R (microarray and NGS), UQ, Brisbane

* 27 May, RCC seminar: Building a sustainable ecosystem for data-driven research, UQ, Brisbane

* 4–8 July, 2016 Winter School in Mathematical & Computational Biology, UQ, Brisbane


Featured video

BCCVL's MOOC series: BCCVL (The Biodiversity and Climate Change Virtual Laboratory) has a 10-part course on species distribution modelling. Watch

Featured Article

3 April 2016—'Susan Ley to unveil new Medical Research Future Fund advisory board', Australian Financial Review

Queensland Speaks

Featured Collection

Centre for the Government of Queensland Datasets: QRIScloud is storing Government of Queensland data sets that have been used to generate the following five websites: More

Milestones and Metrics

QRIScloud is now storing 207 data collections, with 3.87 PB ingested.
Copyright © 2016 QRIScloud, All rights reserved.
Email Marketing Powered by Mailchimp