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QCIF and QFAB join forces for stronger biosciences and health research impactQFAB logo

Bioinformatics expertise is available through QCIF to biosciences and health researchers across Queensland and nationally thanks to QFAB (Queensland Facility for Advanced Bioinformatics) joining forces with QCIF. 
 
The QFAB Collaboration (Griffith, QUT and UQ) formally transitions into QCIF from early April. 
 
This will create a one-stop shop, called QFAB@QCIF, for helping scientists apply advanced bioinformatics into their research and for accessing the tools and infrastructure to deliver computation and data.
 
This move is designed to make QFAB’s services more widely available. It will also direct services to meet research demand and provide a more connected set of services, including the benefits of the GVL (the Genomics Virtual Lab). 
 
QFAB and QCIF together bring solid connections into national initiatives and partners, such as Bioplatforms Australia and BRAEMBL.
 
QFAB’s staff will join the QCIF team under the leadership of Dr Dominique Gorse, the QFAB@QCIF Director. This gives QCIF an expert consulting capability that can be expanded later into other fields key to Queensland.
 
Dr Gorse welcomed the move saying QFAB would take up opportunities to grow and deliver new and improved services to an expanding user base.
 
QCIF CEO Rob Cook said, "This assembly of two service providers will make it simpler for bio research to get the informatics services it needs. At a time when life sciences and medical research is rapidly gaining importance and stature, the joined-up organisation will benefit all parties."
 
For more information about QFAB@QCIF please contact Dominique Gorse: d.gorse@qfab.org
 

Dr Collin Storlie joins QCIF as JCU's new eResearch AnalystDr Collin Storlie

Dr Collin Storlie (pictured) has joined QCIF as its new eResearch Analyst based at James Cook University’s eResearch Centre.
 
JCU researchers wanting help with eResearch technology, such as making the most of QRIScloud, can contact Collin at: collin.storlie@jcu.edu.au.
 
Collin holds a PhD in Terrestrial Ecology (JCU), a Graduate Diploma in Conservation Biology (JCU) and a Bachelor of Science in Zoology (Washington State University, U.S.).
 
His research is primarily concerned with spatial modelling of terrestrial vertebrate species distribution and abundance patterns. He has acquired extensive experience in using high performance computing clusters to create highly resolved and accurate spatial weather and climate models. This research resulted in the publication of two papers in the peer-reviewed journals Diversity & Distributions and Biology Letters
 
We welcome Collin, who has succeeded Jay van Schyndel as QCIF's JCU-based eResearch Analyst, and congratulate Jay on his appointment to the RDS (Research Data Services) project at JCU.
 

AURIN Map released for spatial data publishing

The Australian Urban Research Infrastructure Network (AURIN) has released AURIN Map, a website for researchers to publish data related to cities and urban design.
 
AURIN Map is an extension of the government’s NationalMap initiative, a website for map-based access to spatial data from Australian government agencies.
 
If you have data sets or ideas for data sets to be included in either AURIN Map or the AURIN portal, please contact AURIN directly at admin@aurin.org.au or discuss with Gavin Kennedy, QCIF Outreach and Engineering Manager: gavin.kennedy@qcif.edu.au.

QCIF is AURIN’s representative in Queensland.

AURIN Map
 

Compute Lite coming soon for lighter loads

QRIScloud has begun to implement its Compute Lite service to suit users with lighter cloud compute workloads, such as running a web service.
 
Like most public cloud services, Compute Lite improves the utilisation of QRIScompute by sharing the Compute Lite cores amongst multiple virtual machine instances. This is achieved without degrading VM performance, and complements QRIScloud’s Compute Intense service with its dedicated cores per VM.
 
Use of Compute Lite will be transparent to users and takes affect when Nectar m-flavoured instances are selected.
 
To make Compute Lite possible, QCIF has upgraded memory on the Compute Lite compute nodes. The additional memory enables support for multiple simultaneous instances to share a single compute node. 
 
QRIScloud has completed memory upgrades to 10 compute nodes and will shortly upgrade a further 17 nodes. We anticipate a short outage across 17–18 March to complete this work. The QRIScloud Help Desk will liaise with affected QRIScompute users to keep them informed of the schedule and help minimise any impact.
 
For any queries, please contact the QRIScloud Help Desk: support@qriscloud.org.au.
 

Deep learning: A QRIScloud GPU node experience

Ranju MandalQRIScloud’s special compute service has enabled a Griffith University PhD student to run document image retrieval experiments faster than before and with greater flexibility.
 
Ranju Mandal (pictured), at Griffith’s Gold Coast School of Information and Communication Technology, Is applying QRIScloud’s GPU (Graphics Processing Unit) node in his experiments. Together with a deep learning technique, his GPU algorithms can retrieve relevant documents by image queries into document repositories.
 
The goal of Mr Mandal’s research is to make querying and document retrieval based on images (e.g. a handwritten signature, seal or logo) in administrative documents a lot faster, making possible an automated process, rather than manual document scans. For example, a bank or other company could use the application to search its databases for documents featuring a particular signature. Read more
 

Beacon opens up human genomic data sets Dr Igor Makunin
 
Want to make information about the data in your human genomic data set more accessible whilst preserving the privacy of those who are sequenced?
 
Now you can thanks to the RDS Life Sciences Beacon Server Tutorial, a technically simple, open web service and tutorial powered through Nectar and developed by RCC Research Officer Dr Igor Makunin (pictured).
 
The Life Sciences (Genomics) RDS project, UQ's Research Computing Centre (RCC) and QCIF all part funded the Beacon Server.
 
As a demonstration of the technology, the Beacon Server has been populated with data from the 1000 Genomes collection. The server includes a tutorial that takes researchers through the steps required to set up a Beacon Server with their own data sets. Read more
 

NCMAS allocates first round of projects to FlashLite 

The Research Computing Centre's groundbreaking data-intensive high performance computer, FlashLite, has been allocated its first round of National Computational Merit Allocation Scheme projects. Of the nine projects in total, seven are from outside Queensland.
 
Spanning biology, chemistry, physics, agricultural and veterinary science, medical and health sciences, maths, engineering, IT and computing, these national project proposals demonstrate innovative ways of using a data-intensive machine. With its very large virtual shared memory and flash disks, FlashLite can process volumes of data like no other machine in Australia.
 
RCC and the QRIScloud Help Desk are busy working with each project’s chief investigator and their respective teams to guide them towards the most constructive use of the hardware as well as preparing accounts and establishing access to FlashLite.
 
“We look forward to seeing FlashLite being used for significant data-intensive computation and assisting in delivering results for the NCMAS project teams,” said QCIF Service Delivery Manager Stephen Bird.
 
For FlashLite queries and access, contact either the QRIScloud Help Desk (support@qriscloud.org.au) or QRIScloud eResearch Analyst Dr Marlies Hankel (m.hankel@uq.edu.au).
 

QCIF joins the SIBA Queensland branch  

SIBA logoQCIF has become a founding member of the newly formed SIBA Queensland branch.
 
SIBA is the Spatial Industries Business Association, the peak representative body for the spatial information industries in Australia and New Zealand. 
 
The SIBA Queensland branch brings together Queensland spatial industry businesses to share information on activities in the industry, and co-ordinate on state and national initiatives.
 
QCIF has joined the SIBA Queensland branch to promote research collaboration and data sharing opportunities between spatial industries and our university members as well as advancing QCIF's services and the services of its members and partners.
 
To celebrate the new Queensland branch, SIBA are holding a business breakfast on Thursday, 17 March, 7am–9am in Brisbane (more information).
 
For more information about SIBA please contact Gavin Kennedy, QCIF Outreach and Engineering Manager: gavin.kennedy@qcif.edu.au.
 

QCIF supports open data in Queensland ODI logo

QCIF has renewed its commitment to the Open Data Institute Queensland by joining its supporter program.
 
QCIF actively supports the open data movement and works with ODI Queensland to connect, equip and inspire people to innovate with data.
 
Established in December 2014, ODI Queensland’s mission is to catalyse the evolution of open data culture to create economic, environmental, and social value. 
 
The independent not-for-profit organisation is one of the pioneer nodes in the global Open Data Institute network, centred on the original ODI based in London.
 
By working with ODI Queensland, QCIF can promote data collaboration and research opportunities with government and industry on behalf of its member universities.
 
For more information please contact Gavin Kennedy, QCIF Outreach and Engineering Manager: gavin.kennedy@qcif.edu.au.
 

Sharing health data workshop comes to Brisbane Baden Appleyard 

The Australian National Data Service (ANDS), Queensland Facility for Advanced Bioinformatics (QFAB) and Health Informatics Society of Australia (HISA) are co-hosting a free workshop on sharing sensitive health data on Wednesday, 16 March at Brisbane’s Translational Research Institute.
 
Attendees will hear from researchers, data managers, local and legal experts about their experiences and advice for publishing and sharing health data.
 
Speakers include Dr Peter Croll, co-editor of Australian Guidelines for the Protection of Health Information, and barrister Baden Appleyard (pictured) of the Advisory Council on the Open Definition and AusGOAL.
 
The afternoon workshop (1:30pm–5:30pm) is free, however, places are limited and prospective attendees need to register. More information about the workshop, including the full list of speakers, is on the registration webpage.
 
QCIF is sponsoring an afternoon tea at the event. 
 

QCIF to speak at customer experience event

Nick GolovachenkoQCIF’s Nick Golovachenko (pictured) will be one of the speakers at a Sydney event on Tuesday, 15 March about managing the customer experience.
 
Through QCIF, Nick manages Nectar’s distributed help desk. He will talk about how Nectar's support teams deliver consistent, responsive support to more than 5,000 researchers and academics across the country.
  
Wilfred Brimblecombe, formerly of QCIF and now Nectar's ICT Manager, will also speak at the event, discussing how successful, customer-centric organisations are aligning to the demanding needs of today’s digital-savvy, mobile customer.
 
The event is for those leading the customer experience for their business or organisation. More information
 

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.

      
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March 2016

 



Upcoming Events


* Each Tuesday, UQ Hacky Hour, St Lucia

* 15 March, The Customer Experience: Every Moment Matters, Sydney

* 16 March, Sharing Health-y Data: Challenges and Solutions, TRI, Brisbane

* 17 March, SIBA business breakfast, Brisbane

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

 
ReDBox Lite webinar video

Featured video

ReDBox Lite webinar: In this webinar, held on 9 March 2016, you will hear all about ReDBox Lite and how it might be the solution for your institution. ReDBox is a popular data management system. Watch


Featured Article

23 February 2016—'Zika researchers release real-time data on viral infection study in monkeys', Nature

 
DNA

Featured Collection

Lambert Ancient and Modern DNA Sequence Collections and Analyses: Prof David Lambert of Griffith University, in partnership with the Beijing Genomics Institute, is investigating how animals respond to climate change by comparing the genes of ancient and modern Antarctic Adélie penguins. More
 


Milestones and Metrics

QRIScloud is now storing 197 data collections.
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