The
eResearch Australasia conference kicks off on Monday, 10 October in Melbourne and QCIF welcomes all attending to visit its exhibition booth to have a chat and pick up some useful merchandise (computer cloths, torches and tea-towels!)
QCIF will hold lightning talks during conference breaks at its booth (booth location 5 and 6), and we're happy to answer any questions you might have about QRIScloud, QCIF and its partners at any time during the event. Some of our collaborators, such as UQ's Research Computing Centre, will also have representation at the QCIF booth.
QCIF staff are involved in delivering the following sessions during the conference:
- Gavin Kennedy and Open Data Institute Queensland CEO Maree Adshead will discuss the data challenge of demonstrating quality and building trust in Open Data (Wednesday, 12 October, 11:50am–12:10pm)
- Belinda Weaver is part of a group leading a Birds of a Feather session on best practice for Research Bazaars (Wednesday, 12 October, 3:40pm–4:30pm).
QCIF will also host its popular ReDBox community meeting at the conference. The lunch-time get-together will be held on Wednesday, 12 October, 12:35pm–1:35pm, in State Room 1 and 2 at the Pullman Melbourne Albert Park hotel. For more information contact QCIF’s Gavin Kennedy:
gavin.kennedy@qcif.edu.au.
CLIMB UK adopts Australia’s Genomics Virtual Laboratory
A UK bioinformatics project has adopted Australia’s
Genomics Virtual Laboratory, delivering UK researchers a reliable turn-key bioinformatics analysis platform.
The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) has implemented a microbial version of the GVL (microGVL).
CLIMB’s ultimate goal is to help microbiologists and other researchers implement a new ‘gold standard’ in public health outbreak investigations through the use of refined analytical tools and next generation sequencing technologies.
The GVL was collaboratively developed between QCIF and the Victorian Life Sciences Computation Initiative and is supported by UQ’s Research Computing Centre. NCRIS initiatives Bioplatforms Australia and Nectar funded the tool.
VLSCI Director Assoc. Prof. Andrew Lonie said: “Such international recognition is further demonstration of Australia’s capacity to compete in these complex, technically sophisticated fields.”
Read more
October kicks off monthly Galaxy-qld meetups
A monthly Bris
bane-based Galaxy-qld meetup was launched on Wednesday, 5 October at UQ St Lucia.
The aim of the meetup is to bring Galaxy-qld users together to discuss problems, solutions and ideas, and learn about new tools and resources on the server. It is hoped the meetups will result in collaborations between researchers.
Researchers use Galaxy-qld for the analysis of genomics data. Galaxy provides bioinformatics tools and disk storage for those working with high-throughput sequencing data.
QCIF and the Victorian Life Sciences Computation Initiative co-developed the
Genomics Virtual Lab, which runs on a dedicated
Galaxy server.
Visit the
Genomics Virtual Lab blog for further information about the Galaxy-qld meetups.
New Systems Engineer in tune
with QRIScloud
Brett Milford, a trombonist and former casual performer with the Queensland Symphony Orchestra, has joined UQ’s Research Computing Centre as a QRIScloud Systems Engineer.
Brett (pictured right), who joined the team last month, has a Bachelor of Music (Hons) from the Queensland Conservatorium and is currently studying a Masters of Computing Technology extramurally with USQ.
He has worked for the last five years in UQ’s ITS division in various roles, including as a Service Desk Analyst providing remote support to researchers and as a Network Assistant where he supported changes to UQ network infrastructure.
In his new role, Brett joins the QRIScloud service delivery and infrastructure team alongside fellow QRIScloud Systems Engineers Michael Mallon and Denis Lujanski.
Brett will contribute to the upgrade in support to researchers through high-touch technical support and to maintaining committed service levels through improved QRIScloud operations development and maintenance.
Talks at UQ on why and how to cite software and the Science Gateways Community Institute
Interested in eResearch technology, based in Brisbane and unable to attend this year's eResearch Australasia conference in Melbourne? Two speakers from the conference will give similar talks at UQ St Lucia on
Friday, 14 October.
Dr Daniel S. Katz (pictured), Assistant Director for Scientific Software and Applications at the U.S. National Center for Supercomputing Applications (NCSA), will discuss why and how to cite software used in research in his talk from 10am–11am in RCC's seminar room (
more info).
Nancy Wilkins-Diehl (pictured), Co-Principal Director at the San Diego Supercomputer Centre, will precede Dr Katz in the same location with her talk, from 9am–10am, about the Science Gateways Community Institute (
more info).
No registration is necessary for these seminars and all are welcome to attend. Please email RCC for further information:
rcc-admin@uq.edu.au.
All researchers welcome to attend Gaussian workshop in Perth
The University of Western Australia in Perth is hosting a workshop on Gaussian, a software application for quantum chemistry, in early December, which researchers at all levels from academia and industry are welcome to attend.
Gaussian, Inc. is co-hosting the "Introduction to Gaussian: Theory and Practice" workshop from
Saturday to Wednesday, 3–7 December.
The workshop will provide an introduction to electronic structure theory as well as a hands-on Gaussian review for researchers active in the field, and will focus on methods for computing energies, exploring energy landscapes, studying molecular properties, and practical user considerations.
Full details including registration information are available on
Gaussian’s website. The registration fee must be received by Friday, 28 October.
More research problems to be solved in Brisbane HealthHack 2016
Brisbane HealthHack, a QCIF co-sponsored data hack weekend across 14–16 October, has a bumper crop of healthcare and medical research problems to be solved this year.
A pre-event for
Brisbane HealthHack was held on Thursday, 29 September, at River City Labs where researchers discussed and developed their ideas for problems to be hacked and solved.
QCIF/RCC/IMB eResearch Analyst Dr Nick Hamilton,
Brisbane HealthHack’s lead organiser, said numbers of “Problem Owners” were up on last year, with owners coming to present from research, public health and commercial organisations.
“One of the great features of the pre-event evening was that many of the problem owners connected with each others’ problems, and had suggestions for approaches to solutions, where to get data and useful people to talk to in a range of organisations. It was all we could do to stop them starting to solve the problems too soon!” said Dr Hamilton.
Dr Hamilton expected more research problems would come in over the fortnight between the pre-event and the HealthHack weekend.
Participation in HealthHack is free, whether as a “Problem Owner” or hacker. Hackers can be software developers, user experience (UX) designers, data analysts or visualisers.
Free childcare, food and drink will be available at the Brisbane HealthHack (
please register). Sydney, Melbourne, Canberra and Perth are also hosting HealthHack weekends simultaneously. Any queries about Brisbane HealthHack, please contact Dr Hamilton:
n.hamilton@imb.uq.edu.au.
The Brisbane HealthHack pre-event at River City Labs.
Full house at second Software Carpentry Workshop at USQ during Research Week
USQ ran a second, fully attended Software Carpentry workshop during the university’s Research Week from 26–27 September.
USQ’s QCIF eResearch Analyst, Dr Francis Gacenga, a Unix and Git expert, delivered the workshop with fellow trainer Assoc. Prof. Adam Sparks, an ‘R’ program expert, statistician and field crops pathologist. USQ helpers included: Catherine Hay, Dr David Jones, Dr Rachel King and Russell Waldron.
The workshop focused on teaching its 19 participants how to automate tasks with the Unix shell, version control with Git and reproducible analysis with R.
Dr Gacenga said there was great interest in more Software Carpentry workshops at USQ, as participants, trainers and helpers, and reproducible analysis with R is in high demand. Two people have already signed up as helpers for future workshops and three people are looking to become potential new instructors.
“The success of the USQ workshops is a credit to the continuing collaborative efforts by QCIF, USQ, and the Software Carpentry Foundation,” said Dr Gacenga.
Preparations are in gear for the next USQ Software Carpentry workshop to run in 2017.
Participants, trainers and helpers at USQ's second Software Carpentry workshop.
Griffith University's Hacky Hour helps its 100th researcher
Griffith University's Hacky Hour recently hit a milestone with its 100t
h researcher receiving help at the weekly meetup.
Hacky Hour, an informal drop-in session for those with IT-related research problems, is held each Thursday, 2pm–3pm, and alternates between the Nathan and Gold Coast campuses. Follow
@hackyhourGU on Twitter for updates.
The Griffith University
HackyHour crew (Amanda Miotto, Heidi Perrett and Kim Keogh) also host
Software Carpentry workshops, which teach researchers basic lab skills for scientific computing. Griffith has held four workshops thus far, two each on Python and the 'R' program. The next workshop will likely receive its 100th participant.
Dr Nick Hamilton gives bioinformatics talk at
WEHI
QCIF/RCC/IMB eResearch Analyst Dr Nick Hamilton (pictured) gave an invited talk on Tuesday, 13 September as part of the Walter & Eliza Hall Institute of Medical Research’s bioinformatics seminar series.
Dr Hamilton’s seminar was titled ‘
Modelling, predicting and understanding kidney development’. He discussed the kidney research he has collaborated on with teams led by Prof. Melissa Little, who heads the Kidney Research Laboratory at the Murdoch Childrens Research Institute in Melbourne and also has a co-appointment at UQ’s Institute for Molecular Bioscience (IMB), and Assoc. Prof. Ian Smyth, a Fellow in Monash University’s School of Biomedical Sciences.
NCMAS 2017 applications due this week
The National Computational Merit Allocation Scheme (NCMAS) is currently calling for applications for HPC access in 2017.
NCMAS information and application forms are available
online. Applications close 5pm AEDT (4pm AEST),
Friday, 14 October.
NCMAS is the premier competitive program for provision of high-performance computing resources for scientific research in Australia. Approximately 203 million CPU-hours are available on four national facilities in NCMAS 2017:
- Raijin (NCI)
- Magnus (Pawsey Supercomputing Centre)
- MASSIVE (Monash University)
- FlashLite (UQ/RCC).
QCIF contributed to the funding of FlashLite and has a share in time on Raijin, which researchers from QCIF’s
member organisations can apply for through the
QRIScloud portal.
If you have questions or require assistance with your NCMAS application, you can contact the NCMAS secretariat (
ncmas@nci.org.au) or the QRIScloud Help Desk:
support@qriscloud.org.au.
Join the ‘Working with Data: 101’ workshop
QCIF and the Open Data Institute Queensland (ODIQ) have partnered to develop and deliver an introductory workshop in data analytics.
'
Working with Data: 101' is designed to impart foundation level skills for those who are, or who support, decision makers and policymakers.
This practical, hands-on, full-day course starts with an introduction to the fundamental concepts and terms of data science, then moves into identifying and using best practice data structures. It teaches regular expressions for data manipulation, and the use of tools, such as
OpenRefine, for cleaning and manipulating data.
The next available ‘Working with Data:101’ workshop is on
Wednesday, 19 October 2016, at ODIQ’s office in Spring Hill. All details, costs, booking instructions and trainer information is on
ODIQ’s website. Numbers are capped, so get in early.
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'.
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.
QCIF eResearch Analyst profile: Dr Collin Storlie, JCU
Dr Collin Storlie is QCIF’s eResearch Analyst at James Cook University based within its
eResearch Centre.
Collin joined QCIF earlier this year and is available to help JCU researchers work with eResearch technologies. Although new to the QCIF team, Collin is keen and able to help JCU researchers and students apply for and obtain cloud-based storage and data computation services.
He has established a regular Hacky Hour at JCU, which is an informal meetup for researchers to get help with their research-related IT problems. JCU’s Hacky Hour is usually held weekly on Fridays, 2pm–4pm, at the eResearch Centre. Collin will confirm each week via his Twitter handle,
@JCU_QCIF_eRA, that Hacky Hour is on that particular Friday.
Through his research Collin has acquired extensive experience in using high performance computing clusters to create highly resolved and accurate spatial weather and climate models. Also, Collin enjoys using the 'R' computer language to manipulate large data sets and produce summary images and tables.
Collin holds a PhD in Terrestrial Ecology and a Graduate Diploma in Conservation Biology, both from JCU, and a Bachelor of Science in Zoology from Washington State University, U.S.A. His research has resulted in the publication of two papers in the peer-reviewed journals
Diversity & Distributions and
Biology Letters. Contact Collin at:
collin.storlie@jcu.edu.au.
QRIScloud is now storing 241 data collections, with more than 5.209 PB of data ingested.