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RCC News: August 2015

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Join the FlashLite info session

Prof Michael NormanWant to learn how the new data intensive high performance computer FlashLite can help your research?
Join RCC’s information session on Friday, 7 August, 10:30am–4:30pm in RCC’s videoconferencing facility on UQ’s St Lucia Campus (please RSVP to
The session will start with Prof Michael Norman (pictured), Director of the San Diego Supercomputer Centre, discussing the experience of the NSF funded Gordon supercomputer (which inspired FlashLite’s design), and how this has supported a range of data intensive applications.
From 1pm–3:30pm, RCC’s David Green will conduct a hands-on FlashLite workshop (please bring your laptop).
If you have not used a HPC service or might be a bit rusty, RCC will hold a hands-on workshop on Friday, 31 July at 1pm. Please RSVP to
More FlashLite info

Be an early adopter

If you are keen to be a FlashLite and/or Euramoo (RCC's new Cluster in the Cloud service) early adopter, please contact:

New computing seminar schedule announced

Pete BeckmanSpeakers from some of the best computing institutions feature in the RCC led QURPA/MURPA* seminar schedule, which had its second-half-of-the-year lineup announced recently. 

This Friday, 31 July, Dr Pete Beckman (pictured), Director of the Exascale Technology and Computing Institute (ETCi) at Chicago's Argonne National Laboratory, will speak remotely about Waggle, a platform for distributed smart wireless sensors and in-situ parallel computation.

For those at UQ, the seminar will be held at 9–10am in RCC's videoconferencing facility, room 505, level 5, Axon Building (47), St Lucia Campus, UQ. 

See the full list of 2015 seminars

*QURPA/MURPA is the UQ/Monash Undergraduate Research Projects Abroad program. However, all those interested in these free seminars are welcome to attend, including postgraduates and staff. 

Barrine's reconfiguration a success

High performance computer Barrine was successfully reconfigured in July, ensuring its continued operability. 

Users should consult the Barrine Reconfiguration User Guide before logging in as some changes have occurred. 

Any issues with Barrine, please contact the RCC Support team:

Read the Barrine webpage for further information about the reconfiguration process. 

New tools and resources on Galaxy-qld

Galaxy-qld is a public server developed by the Genomics Virtual Laboratory and maintained by RCC on the QRIScloud node of the NeCTAR computer cloud.
Dozens of UQ researchers and scientists from other Australian institutions use Galaxy-qld for genomics research and analysis of next-generation sequencing data. RCC provides both IT and bioinformatics support for the server.
With more than 500 registered users and growing, Galaxy-qld is steadily broadening its capability with new software and reference datasets in response to user requests. The server now offers the ultra-fast STAR gapped aligner for RNA-sequencing data, with precomputed indices for the mouse and human genome assemblies.
A new release of the popular BEDtools package was installed, as well as Find and Replace tools for text manipulation. The GATK2 package was updated, and the GATK bundle is now available as a data library. GTF files with annotations of human genes are also available as a data library.
The Galaxy-qld support team liaise with UQ researchers and assist in data analysis, workflow development and Galaxy training. For any Galaxy-qld inquiries please contact RCC’s Igor Makunin:

RCC Director wins ARC grant

David AbramsonRCC Director Prof David Abramson (pictured) and colleagues were awarded an ARC Linkage grant of $430,000 in July.
The grant supports an ongoing collaboration with global supercomputer company Cray Inc. to explore energy efficiency in high performance computing, a critical challenge in building supercomputers. More info 

Lien Le joins RCC

Lien LeLien Le (pictured) has joined RCC as Bioinformatics Team Leader.
She forms part of the Queensland BRAEMBL node in conjunction with the hub at the University of Melbourne to gather bioinformatics expertise. She is tasked with providing technical and strategic direction for BRAEMBL's Data Integration team. 
Lien has previously instigated and led the successful setup of an Australian-based data repository and will continue to provide assistance to researchers in chaperoning their data to public visibility. 
Lien’s past appointments have been with the Australian Genome Research Facility and the Queensland Institute of Medical Research.

Paper accepted for 2015 IEEE SupercomputingSC15 logo

A paper discussing high performance debugging techniques by researchers from RCC and Cray Inc. has been accepted by SC15, the world’s leading international supercomputing conference. The conference will be held in Austin, Texas, 15–20 November.
SC15 received 358 submissions this year, and only accepted 79 papers. SC15 is expected to attract about 5,000 people to participate in its technical program, and about 11,000 people overall.

Kepler workshop opens collaboration

The RCC Kepler workshop on 14 July opened up potential research collaborations as attendees discussed their research focus and needs.
The scientific workflow system workshop attracted more than 15 UQ scientists and researchers from varied disciplines.
They were exposed to Kepler applications through a range of use cases from different disciplines, including wild fire control and prediction; vegetation and animal conservation planning; and computational fluid dynamics optimisation problems.
The highlight of the workshop was the hands-on session supported by the CoESRA virtual desktop system. Participants learned to build Kepler workflows and parallelise the computation using the Nimrod suite.
Dr Ilkay Altitas, from the San Diego Supercomputer Center and Kepler’s co-founder, launched the workshop via videoconference with an excellent talk about workflow-based science and using the Kepler system in automating complex scientific process. 

Kepler workshop
RCC's Dr Minh Dinh speaking at the Kepler workshop.

Largest turnout yet for bioinformatics Winter School 

The largest bioinformatics training event in Australia, the 12th Annual Winter School in Mathematical & Computational Biology, was held 6–10 July at UQ.

Attendee numbers were up this year with more than 240 participants from some 60 institutions from as far afield as Italy, Mexico, Poland and Canada.
Dr Nick Hamilton of RCC/IMB chaired this year's event, which both RCC and QCIF sponsored.
Some 40 presentations were given across the week from a range of international and national leaders in the field of bioinformatics.  A new feature was the Faculty of 1000 Speaker Prizes, which were awarded by popular vote to Prof John Quackenbush (Harvard) Ken McGrath (AGRF) and Seán O’Donoghue (CSIRO).
Winter School in Mathematical & Computational Biology  
AGRF's Ken McGrath explaining Game of Thrones in terms of sequencing machines.

Full house for software carpentry bootcamp

software carpentry bootcamp
There were no spare seats at the Brisbane Software Carpentry bootcamp at UQ, 2–3 July.
RCC’s Belinda Weaver, who organised the bootcamp, said it was great to see that almost half of the 40 attendees were women.
The bootcamp, for which RCC and QCIF jointly sponsored a morning tea, introduced attendees to the Unix shell, Git, Python and SQL. Read more.
A second UQ Software Carpentry bootcamp is scheduled for 28–29 September: More info
people and technology

What's On

Waggle seminar, 31 July, 9–10am, UQ St Lucia. More info
Hands-on HPC workshop, 31 July, 1pm, UQ St Lucia. RSVP to
Open Data and Instrumenting Cities, 7 August, 9–10am, UQ St Lucia. More info
FlashLite info session, 7 August, 10:30am–4:30pm, UQ St Lucia. RSVP to
Experiences with the First Flash-based Supercomputer, 7 August, 10:30–11:30am, UQ St Lucia. More info
A Large Hadron Collider Case Study, 14 August, 9–10am, UQ St Lucia. More info
HPC and Industrial Innovation, 21 August, 9–10am, UQ St Lucia. More info
Adaptive, Large-Scale Computing Systems, 28 August, 9–10am, UQ St Lucia. More info
Software Carpentry Bootcamp, 28–29 Sept, UQ St Lucia. More info
Dr Nick's Image Clinic, most Monday mornings, for IMB researchers and held, by Dr Nick Hamilton, at IMB.
SC15, The International Conference for HPC, Networking, Storage & Analysis, 15–20 Nov, Austin, Texas. More info
people and technology


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