As the world's fourth largest exporter of wine, Australia’s wine industry is very important to the nation’s economic health. With 18 per cent of all grape plantings in Australia being Chardonnay, the variety contributes significantly to the economy and viability of the wine industry.
The Australian Wine Research Institute (AWRI) in South Australia and Canada’s BC Genome Sciences Centre at the University of British Columbia are investigating the genetic make-up of the Chardonnay grape to help the industry better understand the variety.
To crunch the numbers, the AWRI is using a QRIScloud large memory instance, which bioinformatician Dr Michael Roach described as “the workhorse for the project”. The team is also using the Nectar-funded Genomics Virtual Laboratory to test software and assemblies.
Read more
TERN, RCC and QCIF develop portal for reproducing scientific workflows and results
A Queensland-based team led by the Terrestrial Ecosystem Research Network (TERN) has developed infrastructure for reproducible science in the form of a virtual desktop called CoESRA.
CoESRA (Collaborative Environment for Ecosystem Science Research and Analysis) provides tools in the cloud and is equipped with the Kepler scientific workflow system and Nimrod software (other software can be added by users).
TERN in collaboration with RCC and QCIF developed CoESRA, with funding from TERN and the Australian National Data Service through the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS) program. QRIScloud provides CoESRA’s compute and storage infrastructure: the project is using 150 cores of QRIScompute and 5 TB of QRISdata storage.
Read more
Galaxy Queensland introduces new user policy to meet growing demand
The Queensland branch of Galaxy, a web-based platform for computational biomedical research, has a new user policy to meet increasing demand.
Galaxy-qld’s new policy was implemented on 4 August 2016 to balance the workload so all users get fair access to the processing pipeline.
Users now have a maximum number of concurrent jobs they can run: 16 jobs at a time for registered users, and one job at a time for non-registered users.
Previously, some users submitted a large number of computationally intensive or long running jobs in a very narrow timeframe, taking a significant proportion of the resources available on the server. As a result, other users’ jobs were queued for a long time.
Dr Igor Makunin of the Research Computing Centre, which administers Galaxy-qld, said the new user policy should provide better access to the server for all users. “The server went through a stress test [on 4 August] when two users submitted a couple of hundred jobs within an hour or two. In the past this would cause delays for job execution for all users, but this time most users were not affected, only jobs from the two active users were queued,” he said.
On average, about 50 new users register for Galaxy-qld each month, and the number of submitted jobs are increasing.
Galaxy-qld is a public server that anyone can register on.
Please visit the
Genomics Virtual Lab blog for more information about Galaxy-qld’s new user policy.
Have your say on the future of Australia's research infrastructure
The Australian public has until 9 September 2016 to have their say on the future direction of the federal government’s research infrastructure priorities.
Australia’s Chief Scientist, Dr Alan Finkel, opened the call for submissions on 20 July 2016 with the release of the
National Research Infrastructure Capability Issues Paper.
The issues paper is a key step in the development of the 2016 National Research Infrastructure Roadmap, which will guide future government investment. The Roadmap is due to be released by the end of the year.
NCI receives a $14 million funding boost
The National Computational Infrastructure has received a $7 million boost from the Australian Government, matched dollar-for-dollar by NCI’s collaborating partners.
The funding will ensure the ongoing delivery of NCI’s supercomputing services to more than 4,000 researchers in more than 80 per cent of Australian universities, together with government science agencies, medical research institutes, and industry, and will pave the way for the next-generation peak system.
Read more
BCCVL adds five new climate data sets 
The Biodiversity and Climate Change Virtual Laboratory (BCCVL) has integrated five new climate data sets into its existing data to extend researchers’ ability to perform advanced biodiversity and climate impact modelling.
The work is thanks to the Research Data Services’ Terrestrial Systems project, a collaboration between QCIF, James Cook University and Griffith University. Dr Collin Storlie, QCIF’s eResearch Analyst at James Cook University, prepared all the data for upload into the BCCVL.
The data sets were added as part of BCCVL’s latest release. Read more about the release and climate data sets in
BCCVL’s blog.
Join IAG's Health Geography Study Group
Queensland academics combining geography and health in their research are invited to join the Institute of Australian Geographers’ Health Geography Study Group.
The group formed two years ago and currently has almost 90 members. Through its
directory of expertise the group is keen to link like-minded researchers and grow its network. The group is active in promoting the interests of health geographers in Australia with a recent example including submissions made on behalf of the group to the Productivity Commission Data Availability and Use public inquiry.
The group meets annually prior to the IAG meeting (which is to be held in Brisbane in 2017) and produces a newsletter two to three times a year.
If you are interested in joining IAG’s Health Geography Study Group or have material that would be relevant to its newsletter, please contact Lukar Thornton:
lukar.thornton@deakin.edu.au.
S
eptember Tech Talk to focus on big data analysis tools
Date: 2 September 2016
Time: 3–4pm AEST
Brisbane venue: Room 505A, level 5, Axon Building (47), UQ St Lucia Campus (or join remotely)
Register
Next month's Tech Talk will focus on big data-related analysis tools, with speakers from CERN, Geoscience Australia and QUT.
The QUT speaker will be Dr Anthony Truskinger (pictured), Senior Research Assistant and full-stack software developer for
Ecosounds, a bioacoustics research group. The group's work featured on ABC's science TV show
Catalyst recently, more information about which can be found in
QRISnews' 'Featured Video' column.
Dr Massimo Lamanna from CERN and Dr Stuart Minchin from Geoscience Australia will fill the other speaker spots.
The monthly Tech Talk is an initative of ANDS, Nectar, QCIF, Intersect, VICNode, eRSA and Pawsey. All are welcome to join this informal discussion and networking event.
Join the free solidThinking training workshop at UQ
Join
Skyfacture and
Altair at the University of Queensland on Wednesday, 17 August for the third instalment of their Design for Modern Manufacturing workshop series.
In this free, full-day intensive software-training workshop, learn about
Inspire and
Evolve, two product-design and optimisation platforms from Altair’s
solidThinking division.
.
Inspire and Evolve are tools that work at the intersection between design and technology, enabling designers and engineers to find solutions quickly.
Please
register for this workshop. All Queensland academic staff are welcome to register, and need not have attended the previous workshops in this series.
C
ihan to join SGI as a System Support Engineer
QCIF and RCC eResearch Analyst and Geocomputing Specialist Cihan Altinay will join SGI as a System Support Engineer on 15 August 2016.
In his new Brisbane-based role, CIhan will provide technical support to research institutions across Queensland for SGI-provided high-performance computing and storage systems. He will also assist in the installation and configuration of new systems across Australia.
SGI has a long-standing partnership with QCIF and RCC to provide researchers with HPC, cloud and data storage solutions.
QCIF congratulates Cihan on his new role and looks forward to continuing to work with him.
QCIF's 'Dr Nick' co-authors mouse kidney cell paper
QCIF/RCC eResearch Analyst Dr Nick Hamilton has co-authored a paper on mouse kidney cells that was published recently in the journal
Developmental Biology.
The paper, ‘
Cap mesenchyme cell swarming during kidney development is influenced by attraction, repulsion, and adhesion to the ureteric tip’, is a collaboration between The University of Queensland’s Institute for Molecular Biology, where Dr Hamilton is based, and the University of Melbourne.
The research has resulted in a breakthrough showing that cells in kidney development are highly dynamic and not relatively static as previously thought.
Read more
September Software Carpentry workshops at Griffith and JCU
September will boast two Software Carpentry workshops for Queensland researchers, one at Griffith University about the Python software program, the other at James Cook University on the 'R' program.
The Griffith workshop will be held 15–16 September at the Nathan Campus (please
register). JCU's workshop will be held at the Townsville Campus on 27–28 September (please
register). The workshops are free.
USQ plans more Software Carpentry sessions after inaugural workshop's success
University of Southern Queensland researchers, staff and students — 29 in total — participated in the first ever Software Carpentry workshop in Toowoomba on 18–19 July 2016.
The hands-on workshop provided an essential foundation in getting the most out of research computing and data services and infrastructure provided at no cost to USQ researchers by Nectar, NCI, and RDS through QCIF. The workshop was a success and there are plans to run more at USQ in the future.
If you are at USQ and would like to learn more about Software Carpentry or are interested in attending a workshop, please contact USQ’s QCIF eResearch Analyst Francis Gacenga at:
eResearchServices@usq.edu.au.
To learn more about the USQ session and how Software Carpentry can help your research, read Francis’
blog entry about the event.
The inaugural USQ Software Carpentry class of 2016 (photo by USQ Photography).
Attended a Software Carpentry workshop? Please provide feedback for research
If you have ever attended a Software Carpentry workshop, please provide your feedback
here (it should take just 5–10 minutes).
QCIF eResearch Analyst Team Leader Belinda Weaver is surveying workshop attendees for her UQ Master of Philosophy research on 'Investigating the efficacy and usefulness of Software Carpentry training for researchers'.
QCIF's Belinda Weaver (back row, centre) ran a Software Carpentry with 'R' workshop earlier this month for the Queensland Government Department of Science, Information Technology and Innovation.
AURIN workshops prove popular in Queensland 
More than 130 registrants from Queensland universities, state and local government and community services attended the AURIN masterclasses run in South East Queensland last month.
Jack Barton and Emma Joughin from
AURIN (Australian Urban Research Infrastructure Network), with Gavin Kennedy from QCIF, ran 10 workshops across multiple Brisbane and regional locations, delivering hands-on training on the AURIN platform to researchers, analysts, policymakers and urban planners.
AURIN combines more than 1,600 geospatially-referenced data sets with a powerful statistical toolset and visualisation platform. The AURIN platform is freely available for academic and government usage, facilitated by the Australian Access Federation.
If you missed the AURIN masterclasses and would like to know more, please contact Gavin Kennedy:
gavin.kennedy@qcif.edu.au.
Jack Barton of AURIN explaining the complexities of the platform to University of Queensland researchers.
QFAB@QCIF to hold R workshops at QUT in August
QFAB@QCIF will hold four training sessions in August at QUT's Gardens Point Campus all related to the R software environment, for beginners to advanced users. The workshops include:
Click on the workshop titles above for more information and to register. All QCIF members are able to take advantage of a discount on the costs of courses. Any queries, please contact
training@qfab.org.
Nobel Prize winner to speak at eResearch Australasia 2016
Nobel Prize winner and 1997 Australian of the Year Prof. Peter Doherty (pictured) will give a keynote speech at this year's eResearch Australasia conference on Tuesday, 11 October. He will discuss the importance of evidence-based research and effective science communication.
Another keynoter, Daniel S. Katz, Assistant Director for Scientific Software and Applications at America's National Center for Supercomputing Applications, will speak about software in research and how it is under-appreciated and under-rewarded.
The
program for the conference, being held 10–14 October in Melbourne, was announced in early August. QCIF will have a booth at the conference, so be sure to visit us there and say hello.
Call for volunteers for Brisbane ResBaz 2017
If you're keen to be part of the Research Bazaar (ResBaz) at The University of Queensland, St Lucia, Brisbane, 7–9 February 2017, don't forget to volunteer. Register your interest by filling out this
form.
QFAB@QCIF profile: Michael Thang
Michael Thang is a computational biologist at
QFAB and is currently building and integrating various open source components to a multi-Omics platform on cloud infrastructure for processing high-throughput data. He has skill sets in:
- high-throughput NGS data processing and analysis
- Omics data processing
- genome assembly
- gene expressions
- Single nucleotide polymorphism identification
- miRNAs expression
- pipeline building for NGS data
- Literature mining
- Next-Generation Sequencing (NGS) library construction protocol
- enrichment analysis (e.g. pathway and GO term).
Michael’s work is mostly involved in processing and analysing different Omics data from NGS platforms. The integration of various open source tools to a platform to assist researchers managing and handling the high-throughput data has become his new interest in multi-Omics research.
As a computer science student, Michael was inspired by an introduction course on bioinformatics algorithms for the identification of DNA sequences. He then decided to pursue a higher study in genomics.
Michael received his M.S. in Bioinformatics at John Hopkins University in Baltimore, U.S., and worked as an intern at the Department of Biology at New York University. Later, he joined Taiwan’s national research institute as a research assistant in miRNAs expression using NGS technology. Contact Michael at:
m.thang@qfab.org.
QRIScloud now has 726 registered users.