News

Want a better platform for your research community web portal?

A new, purpose-built QRIScloud service will provide a superior environment for running web portals supporting research communities.

The service operates on new infrastructure, designed to provide a resilient platform for hosting research portals, and will result in a higher quality of service to the portals’ users.

The new service is part of a project QCIF has been participating in to transition Nectar's National Server Program (NSP) into local services hosted at several Nectar nodes (see April’s QRISnews).

Over the coming month, QCIF will migrate Queensland’s existing NSP clients, such as TERN's Long Term Ecological Research Network (pictured), across to the new platform. Once we have completed this effort, the platform will be available for use for other widely used research portals.

If you currently host a portal for your users or research community and would like to consider migrating it to this new service, please contact the QRIScloud Help Desk: support@qriscloud.org.au.

New QRIScloud service enables easier data searching, synching and sharing

A new QRIScloud service gives users the ability to find, manipulate, share and synchronise all their files wherever they are stored through a single and simple interface.

The service, built using Nextcloud, enables easier data synching, sharing and collaboration, and is now available for pilot users to trial.

In addition to being able to access your QRISdata collections from any device, the new service enables connection to a wide range of external storage services to help researchers consolidate their data. Data can be easily synchronised with local folders, shared with others, and moved between different storage services.

QCIF is pleased to announce this new service, which is a continuation of our policy to develop innovative services that our users have requested.

If you would like to participate in the pilot trial of the Nextcloud service, please contact the QRIScloud Help Desk: support@qriscloud.org.au.

Nextcloud interface

Brisbane to host the 2017 eResearch Australasia conference

The Brisbane Convention and Exhibition Centre will house the 2017 eResearch Australasia conference from 16–20 October.

AeRO, a joint venture representing Australasian eResearch organisations, will manage and host the event. It has invited Prof. David Abramson, Director of UQ's Research Computing Centre, to be the Conference Chair in 2017, recognising his global standing as a leading computer science academic with a long track record in eResearch infrastructure and services, and a strong focus on both research and education.

Prof. Abramson said he was "delighted" to chair the 2017 event in combination with AeRO. "eResearch Australasia has evolved as an important meeting in the calendar, and provides an opportunity to bring together developers and practitioners."

The eResearch Australasia conference provides opportunities for delegates to engage, connect, and share their ideas and exemplars concerning new information-centric research capabilities, and showcase how leading-edge information and communication technologies help researchers.

Past eResearch Australasia Conference co-Chairs Nick Tate (left) and Viviani Paz (right) formally handed over the reins to RCC Director Prof. David Abramson (centre) at this year's conference in Melbourne last month.

Open call for those keen on Library Carpentry funding

The Library Carpentry suite of lessons, which QCIF’s Belinda Weaver (pictured) had a hand in developing, won the British Library Labs’s Teaching and Learning Award on 7 November.

The Library Carpentry community plan to spend the award’s £500 prize money to support a Library Carpentry workshop anywhere in the world next year, including Australia.

If your institution needs financial support to run a Library Carpentry workshop or individual librarian training, see the Library Carpentry blog for details of how to apply. The deadline for applications is 16 December 2016.

Library Carpentry is software skills training aimed at the needs and requirements of library professionals. It includes lessons on regular expressions, data structures, version control, data cleanup and more.

In June this year as part of the annual Mozilla Science Lab Global Sprint, Belinda led a team of more than 20 people in six countries to update and extend Library Carpentry's lesson material. The project is ongoing.

ReDBox version 1.9 released

QCIF is pleased to announce the release of version 1.9 of the ReDBox metadata management platform.

This release will support ORCIDs as researcher identifiers and will be compliant with the Australian National Data Service’s RIF-CS schema, version 1.6. RIF-CS (Registry Interchange Format— Collections and Services) was developed by ANDS as a data format for supporting the exchange of collection and service descriptions.

"A key feature of ReDBox is that we keep it up to date with Australian research services and codes of practice,” said Andrew Brazzatti, support lead and technical architect for the ReDBox project.

The release was introduced at the ReDBox User Group meeting in Brisbane on Wednesday, 17 November. QCIF holds these annual meetings by videoconference to keep the ReDBox community aware of new features and so its participants can help plan future releases.

If you would like to know more about ReDBox and QCIF's Engineering Services team, please contact andrew.white@qcif.edu.au.

QCIF seeks a new CEO

QCIF’s Board has accepted Rob Cook’s request to step down as CEO of QCIF after six years in the job and has initiated an executive search for a replacement. Rob (pictured) has agreed to continue to guide QCIF until the new CEO is appointed.

Since 2010, QCIF has become one of the eight nodes of the national Nectar and RDS eResearch infrastructure and enjoys the full support of its seven Queensland university members and associates. It has grown from a team of less than four full-time people to almost 30 and provides a wide range of user support and training services as well as cloud computing, data storage and high performance computing services for Queensland and national researchers.

More recently, QCIF has built a strategic plan for the future involving a concentration on informatics for health and life sciences and for terrestrial, ecological and environmental sciences, and on the big data analytics and management that these sciences require. Skills development has been recognised as a priority. The bio concentration has begun with the absorption of QFAB into QCIF enabling QCIF to deliver excellence in bioinformatics to research and to applications in the health sector.

Jo Morris joins QCIF as National eResearch Help Desk Manager

Jo Morris (pictured) of Griffith University has taken over from Nick Golovachenko as National User Support Manager on the National eResearch Help Desk.

The National eResearch Help Desk provides user support for the Nectar Research Cloud, RDS data storage, virtual laboratories and other services.

In her new role, Jo is responsible for the efficient and effective operation of the Help Desk and coordinating a geographically distributed team of user support agents from multiple organisations.

Jo has extensive experience in support and eResearch roles and was recently manager of the Development and Consultancy team within the Griffith eResearch Services group.

QCIF welcomes Jo, seconded from Griffith, and would like to thank Nick, the previous National User Support Manager, for his work. Nick was instrumental in establishing effective operations of the national distributed Help Desk and expansion of the service beyond cloud services to also include both Nectar virtual laboratories and Research Data Services.

QFAB to hire more bioinformaticians

QFAB, the bioinformatics consultancy arm of QCIF, is seeking to expand its team by hiring more bioinformaticians.

QFAB is currently advertising the following roles:

Head of Bioinformatics (Computational Biology)
Senior Bioinformatician (Computational Biologist)
Bioinformatician/Software Developer.

Click on the above links to read the full job descriptions. Applications close Sunday, 27 November 2016.

QFAB logo

UQ joins AeRO as its first institutional full member

Australasian eResearch Organisations (AeRO) is excited to announce that The University of Queensland has joined AeRO as its first institutional full member.

AeRO is a collaborative organisation of national and state-based research organisations to advance eResearch implementation and innovation in Australasia. AeRO supports partner organisations to enhance and accelerate Australasia’s lead in the global eResearch space by implementing strategic initiatives that benefit the broader eResearch community.

AeRO membership enables UQ to work closely with all AeRO members. It will be able to engage, participate in and influence the directions of projects to improve national and collective eResearch capability and infrastructure.

AeRO adds the first of many university eResearch organisations to the wide range of providers working towards a joined-up national infrastructure. Read more

QCIF’s Dr Marlies Hankel in team awarded ARC grant

QCIF eResearch Analyst Dr Marlies Hankel is a Chief Investigator on a project, recently awarded an ARC Discovery Project grant, that looks to realise low cost, long-life and safe batteries.

The grant will enable her and her collaborators Prof. Shanqing Zhang, Griffith University, Dr Delai Ye, UQ and Dr Gao Liu, Lawrence Berkeley National Lab (U.S.), to investigate sustainable natural polymers to develop green electrode technologies for manufacturing batteries with greatly reduced production and environmental costs. The project is titled ‘Functionalising sustainable natural binders for energy storage devices'.

The in-depth understandings from the combination of experiments and computation simulations will help create strategies to realise better batteries.

QCIF congratulates Marlies and her collaborators on being awarded an ARC grant.

QCIF patches systems against the Dirty COW vulnerability

QCIF is applying security patches to its various services to protect against a Unix vulnerability called Dirty COW that QRIScloud and other systems were exposed to. Over the last month, most systems were patched quickly with no reduction in service to users, while compute cluster Euramoo is currently being patched.

Rather than drain the queues and suspend services, QCIF chose to do rolling patches to Euramoo's compute nodes. This approach reduces the overall capacity of Euramoo for a short period of time, while still allowing jobs to be submitted, queued, and run. All AMD nodes have been patched, and this week, we expect to complete patching the Intel nodes.

We apologise for any inconvenience this has caused our users, however, we felt the rolling patch approach was better than the complete suspension of Euramoo. Any issues, please contact the QRIScloud Help Desk: support@qriscloud.org.au.

Events

Brisbane ResBaz 2017 is shaping up to be a big one

The preliminary schedule for next year's Brisbane Research Bazaar (ResBaz) was published last week and the event will be even bigger and better than last year's. Registrations also opened last week for the free, QCIF co-sponsored event.

ResBaz will kick off on Tuesday, 7 February 2017 at UQ St Lucia with a full festival day involving a variety of peer networking such as stalls (including bioinformatics and ecosciences themed areas), a Hacky Hour, poster session, an 'Ask a Data Scientist' booth, and the return of the popular Knowledge Bazaar. The next two days will be packed with Software Carpentry bootcamps as well as bioinformatics and ecosciences themed workshops.

USQ is planning to bus participants from several of its campuses to the event. Please contact USQ's Dr Francis Gacenga (Gacenga@usq.edu.au) to express your interest in this.

Volunteers are still being sought for ResBaz. Register your interest by filling out this form.

Join the waitlist for the Bacterial Genome Assembly and Annotation workshop

QFAB Bioinformatics' workshop on bacterial genome assembly and annotation at Griffith University’s Southbank Campus is booked out, but those interested are welcome to join the waitlist by contacting training@qfab.org by 2pm, Friday, 18 November.

The hands-on workshop on Monday, 21 November is suitable for biologists and bioinformaticians wanting to gain an insight into the processes of short-read genome assembly. The workshop will be based on the materials developed as part of the Research Data Services Omics project.

Software Carpentry Python workshop at QUT booked out

In just a matter of days, QUT's Software Carpentry workshop on Python sold out. Currently, more than 20 people are on the waitlist. Those who missed out on the 29–30 November workshop would be best placed to put their names down for the Software Carpentry workshops at the Brisbane Research Bazaar at The University of Queensland, 8–9 February 2017.

November brings city-shaping hack weekends to both Brisbane and the Sunshine Coast

Help solve city issues at CityHack16 in Brisbane or HackFest in Maroochydore this month

After a successful inaugural event last year, Sunshine Coast Council's HackFest is back and will run across the weekend of 18–20 November. Participants are expected to add to the Sunshine Coast Smart City theme by creating smart applications from open data for business and the community.

The Brisbane branch of global engineering firm AECOM is hosting CityHack16 over the 25–27 November weekend. The specific challenge will be released a week prior to the event and will be related to SE Queen HackFest

sland city-shaping.

Both hack events offer major prizes and are for people with a range of skills, not just coding. See the individual hack websites (linked above) for further information.

QCIF at eResearch Australasia 2016

Thanks to all those who visited the QCIF booth and to our partners who shared it at this year's eResearch Australasia conference, held in Melbourne from 10–14 October.

The QCIF booth had a 'Data Innovation' theme, which was represented in the booth backdrop and in the booth lightning talks by QCIF staff and our partners.

If there's anything you wish to follow up on that was discussed at the QCIF booth, e.g. ReDBox, HPC options or QRIScloud services, feel free to email Gavin Kennedy: gavin.kennedy@qcif.edu.au.

Maree Adshead, CEO of the Open Data Institute of Queensland (ODIQ), delivered a lightning talk at the QCIF booth at eResearch Australasia 2016.

Brisbane HealthHack winners join fight against superbugs

With growing fears globally about antibiotic resistance, the winners of this year’s Brisbane HealthHack have created a badly needed tool.

Team ‘Super Friends Against Super Bugs’ developed an app’ for real-time tracking of antibiotic resistant bacteria during the QCIF co-sponsored data hack weekend across 14–16 October.

During the hack, QCIF supported the Super Bugs team with the deployment of servers and software. Read more

Brisbane HealthHack 2016 winners

The winning Brisbane HealthHack 2016 team ‘Super Friends Against Super Bugs’ featuring L–R: Alan Robertson, Miranda Pitt, Jake Parker, Jasek Sokolowski and Jasek Serafinski.

Please provide your feedback on Software Carpentry

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'.

Profile

QFAB Bioinformatics: Pierre-Alain Chaumeil

Pierre is a senior software developer and data engineer. He developed several applications to make Australian data more visible to the research community. This included several tools for the creation and publication of collection descriptions on Research Data Australia, Arachnoserver and Tox-Note.

For the past two years, Pierre has been working closely with Phil Hugenholtz’s team at the Australian Centre for Ecogenomics (ACE) to develop the Genome Taxonomy DataBase (GTDB), a software platform combining data management and high throughput pipelines to work with large collections of genomic resources acquired from NCBI along with population genomes sequenced by ACE and its collaborators.

Pierre's skills span from IT to biology, including:

cloud and high performance computing
data management and integration
web-application and software development
database design and management
system administration
sequence-based analysis
phylogenetic analysis.

PIerre graduated from the University of Bordeaux (France) with a Bachelor of Science majoring in Biology of Organisms and a Masters degree in Bioinformatics. Email: p.chaumeil@qfab.org.

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.