QRIScloud's large memory node helps QBI gain advantage
The use of one of QRIScloud’s large memory nodes has given the
Queensland Brain Institute a competitive edge in the prototyping of new research domain specific information technology facilities.
Jake Carroll (pictured), QBI’s Senior Information Technology Manager (Research), said QBI used the node as a deconvolution pipeline prototype for its high throughput microscopy facilities.
Deconvolution is a computationally-intensive image processing technique that is being increasingly used to improve the contrast and resolution of digital images captured via high-end microscopy facilities.
Mr Carroll said QBI was appreciative of the consolidated compute power in the large memory node and the support that QCIF, Nectar and UQ’s Research Computing Centre provided, saying the large memory node “has given us a significant advantage in the production of publishable outputs as we work towards a mature deconvolution pipeline.”
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Marcus Fitzpatrick joins QCIF as Griffith's new eResearch Analyst
Marcus Fitzpatrick has joined QCIF as its new Griffith University-based eResearch Analyst. He represents QCIF in conjunction with his continuing role as Senior Analyst within the University’s eResearch Services Division based at the Nathan Campus.
Marcus provides IT consultancy services to researchers for grant funding, project management and process management. He has a Master’s degree in Project Management from the University of Sydney and specialises in process improvement.
At Griffith he assists with the
BCCVL (Biodiversity and Climate Change Virtual Laboratory) and other research groups such as Griffith’s Eskitis Institute and Queensland Health’s Logan Beaudesert Health Coalition. He works with researchers to align their research needs to services to fulfil their goals.
If you are based at Griffith and wanting to further your research and would like assistance with services provided by the University’s eResearch Service Division or QCIF, including
QRIScloud,
AURIN, BCCVL, and other virtual labs, please contact Marcus at:
m.fitzpatrick@griffith.edu.au.
JCU and Griffith adopt QRIScloud as a trusted service provider 
QRIScloud has become an accepted, trusted and integrated part of the portfolio of information infrastructure services offered by James Cook University and Griffith University to their research teams.
Researchers at JCU and Griffith can take advantage of the leading edge QRIScloud research methods, compute cloud and data collection storage and access with confidence. QCIF looks forward to significant increases in their usage and uptake as a result.
USQ and CQU endorsed QRIScloud earlier this year. Other Queensland universities are part way through an agreed endorsement procedure that acknowledges the service quality, reliability, security and privacy demonstrated by QRIScloud. This involves a formal process of evaluation and acceptance.
QCIF to repeat Parallel Computing with MATLAB seminar
Due to a number of requests, QCIF will repeat the Parallel Computing with MATLAB seminar it held on 15 April at UQ.
QCIF is working with MathWorks,
MATLAB developer and deliverer of the training, to schedule a new session, likely to be in the second half of this year. Contact QCIF's Stephen Bird to register your interest in this MATLAB seminar:
stephen.bird@qcif.edu.au.
MATLAB is a multi-paradigm numerical computing program used in engineering, science and economics. UQ has access to MATLAB on computer cluster
Euramoo. Giving other QCIF members access is a work in progress and at various stages of implementation.
QRISnews will announce in future issues which members have gained access to MATLAB.
A MathWorks trainer delivered the MATLAB seminar at UQ on Friday, 15 April. (
Photo by Dr Nick Hamilton.)
QCIF's eResearch Analysts upskill in three-day workshop
QCIF’s eResearch Analyst team got together last month in Brisbane for three days of training and planning on how they can better support researchers in QCIF’s member universities.
Two days were spent in an upskilling and development workshop, which aimed to sketch out a new, ‘high touch’ model of engagement with researchers. Participants suggested updating the eResearch Analyst role description to cover promotion of QCIF services, researcher skills development, and to provide expert informatics advice to researchers.
One day was spent in a ‘Train the Nectar Trainer’ workshop, run by Martin Paulo and Jared Winton from The University of Melbourne. QCIF plans to run some short workshops soon for Queensland researchers and support staff on accessing and using the Nectar cloud.
A happy by-product of the training was that new members of the QCIF eResearch Analyst team — Dr Collin Storlie from JCU and Marcus Fitzpatrick from Griffith — met their colleagues face-to-face for the first time.
QCIF eResearch Services Manager Nigel Ward said QCIF would continue to ensure its staff received the best training in order to deliver the best service to its members. “QCIF’s eResearch Analysts are critical to supporting our mission of accelerating Queensland research through data-intensive services and infrastructure. Data-intensive infrastructure can be daunting to most researchers. QCIF’s eResearch Analysts play an important ‘bridging’ role by matchmaking researcher needs to our service offerings.”
Workshop attendees L–R: Stephen Crawley (QCIF), Hoylen Sue (QCIF), Dr Collin Storlie (JCU), Marcus Fitzpatrick (Griffith), Dr Francis Gacenga (USQ), Martin Paulo (Nectar trainer), Dr Minh Dinh (UQ), Jared Winton (Nectar trainer), Belinda Weaver (UQ), Cihan Altinay (UQ) and Jason Bell (CQU). (Missing from this picture are QCIF eRAs Dr David Green and Dr Marlies Hankel (UQ).
Photo by Dr Nick Hamilton (UQ).
BCCVL introduces Multi-Species Distribution Modelling 
QCIF partner the Biodiversity and Climate Change Virtual Laboratory has a new feature that allows users to run not just one Species Distribution Model, but potentially thousands in one hit.
BCCVL users can upload a standard .csv file featuring multiple species and the Multi-Species Distribution Modelling (MSDM) experiment then splits these data and runs an SDM for each species. Users can then easily grab the MSDM result and feed it into BCCVL’s
Biodiverse Experiment to get measures of species richness, endemism and rarity in a given place or region. This analysis helps to drive conservation efforts by identifying hotspots of biodiversity now, and into the future.
Contact BCCVL for further information.
RCC selects a new UQ high performance computing system
A new high performance computing system for broad use across UQ called
Tinaroo began operation last month.
UQ’s Research Computing Centre (RCC) selected Tinaroo, an SGI Rackable HPC system.
Tinaroo features an 80 per cent increase in number of processor cores, four-fold increase in average memory and eight-fold peak performance increase over previous HPC system Barrine, which was decommissioned earlier this year.
Tinaroo is the third component in a Barrine replacement strategy which also includes data-intensive HPC
FlashLite and computer cluster
Euramoo. Whilst Tinaroo is for UQ use only, FlashLite and Euramoo are available to all QCIF members.
Tinaroo has been co-located with
QRIScloud and uses QRIScloud's identity management system to ensure interoperability with storage infrastructure and FlashLite and Euramoo. Tinaroo has access to QRIScloud data collections. This means researchers can process data they have previously stored using Tinaroo, FlashLite and QRIScloud.
RCC Director Prof. David Abramson (pictured) said, “Tinaroo offers a significant increase in the computing power at UQ. The ability to move data transparently between systems will enhance the ease of use.”
June's Tech Talk to focus on minting DOIs for data
Date: Friday, 10 June
Time: 3–4pm AEST
Brisbane venue: Room 505A, level 5, Axon Building (47), UQ St Lucia Campus
More info
Following the success of the inaugural Monthly Tech Talk on 6 May, the June session will focus on minting Digital Object Identifiers (DOIs) for data.
Yet-to-be-announced presenters will discuss how insitutions mint DOIs, and how to leverage Nectar virtual laboratories to mint DOIs. Gerry Ryder of the Australian National Data Service will talk about ANDS' perspective on DOIs.
The Monthly Tech Talk is an initiative of ANDS, Nectar, QCIF, Intersect, VicNode, eRSA and Pawsey. Attendees meet in capital city hubs and connect nationwide via videoconferencing networks. The event is for anyone who wants to know more about NCRIS facilities and the technical aspects of research data.
Slides from the 6 May Tech Talk featuring three 'Cloud Power Users' are available below:
The Brisbane node of the Monthly Tech Talk on 6 May was connected virtually to about 50 other attendees in Sydney, Melbourne, Adelaide and Perth. (
Photo by Dr Nick Hamilton.)
QFAB@QCIF workshops open to QCIF members
QFAB@QCIF is currently offering the following two workshops in the remainder of May at UQ:
- Data Interpretation and Reporting with R (11 May)
- Differential Gene Expression Analysis with R (microarray and NGS) (25 May).
All QCIF members are able to take advantage of a discount on the costs of courses. Visit the
QFAB training webpage for further information.
eResearch Australasia 2016 call for participation
Researchers, educators and practitioners from diverse disciplines are invited to participate in this year's eResearch Australasia conference, which will be held 10–14 October in Melbourne.
You can participate by submitting an abstract for a presentation, point/counterpoint debate, birds of a feather session (BoF), poster, or workshop. This year's conference theme is "eResearch — the next steps." Check the
conference website for further information.
Seminar: Research Data Alliance US Chair to speak at UQ on data-driven research
Professor Francine Berman (pictured), the US lead of the global
Research Data Alliance, will speak at UQ on Friday, 27 May, 11am–12pm, on building a sustainable ecosystem for data-driven research.
For her accomplishments, leadership, and vision, Prof. Berman was recognised by the U.S. Library of Congress as a "Digital Preservation Pioneer", as one of the top women in technology by
BusinessWeek and
Newsweek, and as one of the top technologists by IEEE Spectrum.
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 profile: Dr Dominique Gorse
Dr Dominique Gorse is the Director of
QFAB@QCIF, the consulting branch of QCIF providing customised analytics solutions to life science and clinical researchers. He provides technical, operational and management leadership to ensure successful outcomes for all stakeholders.
Dominique is at heart a data scientist with more than 20 years of experience in software development, information management, data mining and data modelling across life science, drug discovery and health, with skill sets in:
- gene expression, pathway and network analysis
- molecular similarity/diversity (cheminformatics)
- interactive visualisation
- statistics and machine learning
- experimental design
- data management, integration and mining
- laboratory information management systems.
Dominique holds a MPhil in physical science and informatics (1989) and a PhD in computational science from the University of Bordeaux-France (1993). He received his MBA from UQ in 2012 and is a Certified Professional of the Australian Computer Society.
d.gorse@qfab.org
QRIScloud is now storing 218 data collections.