Fighting Superbugs: Omics Data Services Platform
Queensland will play a major role in a new NCRIS RDS Food and Health Flagship Project
to build and operate a data platform supporting bacterial pathogen, infectious diseases and antibiotic resistance research.
Many areas of Health and Life Science research are being revolutionised by combining genomic, transcriptomic, proteomic and metabolomic techniques (referred to as omics) to characterise biological samples. Combining data from these complementary platforms greatly enhances understanding of how complex biological systems work, leading to new drug targets.
The RDS Flagship project will provide Health and Life Science researchers around the country with an open multiomics data platform and with training in the use of this platform and associated technologies. The platform will support the storage, integration, analysis, annotation, visualisation, sharing and publication of data generated from combined genomic, transcriptomic, proteomic and metabolomic techniques.
The platform development will complement a new Bioplatforms Australia (BPA) project on Antibiotic Resistant Pathogens
(known as SEPSIS). This symbiotic development of a major science program with a matching parallel data platform is new and will provide interesting learnings for future projects.
The RDS Flagship is being led by VicNode with QCIF and Intersect as project partners.
QRIScloud services and support over the holiday period
QRIScloud’s QRIScompute and QRISdata services remain available throughout the Christmas and New Year period.
QRIScloud’s Help Desk will operate with limited staffing from 17- 24 December
. From 25 December to 3 January, support from the Help Desk will be unavailable. Normal support services will resume on Monday, 4 January 2016.
NeCTAR's Core Services Team and Distributed Help Desk will be unavailable from 25 December to 3 January.
QRIScloud enhances Collection access and management
QRIScloud has improved its data collection service in a couple of important ways based on user feedback:
Existing collections will need to be enabled to use the new access facilities. From January 2016, the QRIScloud team will begin to work with collection owners to enable these capabilities. For more information please contact the QRIScloud Help Desk (email@example.com
) or your local QRIScloud eResearch Analyst
QUT to host Queensland's first ResBaz
ResBaz, a free-of-charge event, is targetted at RHD students and early career researchers helping them to grow essential digital skills and network with like-minded researchers.
QUT’s Gardens Point campus will host the inaugural Brisbane Research Bazaar from 1-3 February, 2016. All Queensland researchers are welcome to attend.
The event will feature Software and Library Carpentry workshops, a Software Credit seminar, and other research-related activities. There will be a Knowledge Bazaar, an extended Hacky Hour, poster sessions, stalls and icebreaker social events.
QCIF staff are helping to organise and run the event, and QCIF will sponsor an as-yet-to-be-announced prize.
Want to help out? Suggest an idea? Sponsor an activity? Run a stall? Volunteer here
The ResBaz Brisbane website
will be updated as more activities are added.
The ResBaz concept was first developed at the University of Melbourne and has since spread across Australasia. Melbourne, Brisbane, Sydney, Perth, Dunedin and Auckland will all run a ResBaz next year.
QRIScompute upgrades to benefit research collaboration
Through September and October QRIScloud’s compute platforms have been upgraded enabling the future development and deployment of new user services. This has been accomplished in the background and without disruption to user services.
The upgrades have included the:
Kilo brings a raft of minor improvements as well as the ability to run Neutron. Neutron enables QCIF to build additional networking services such as Load Balancing and Virtual Private Networks, which can be used by the Virtual Laboratories and other PaaS/SaaS services to enhance their services to researchers. We expect to make Neutron-based services available to users during the first half of 2016.
If you might be an early adopter or have any questions about these or other QRIScloud services please contact the QRIScloud Help Desk at firstname.lastname@example.org
QRIScloud: Helping to power the 'one stop modelling shop'
The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is enabling researchers to tackle data modelling without needing technical skills.
According to Professor Brendan Mackey, Director of Griffith University’s Climate Change Response Program, who helped shape BCCVL
, it is a “one stop modelling shop to simplify the process of modelling species responses to climate change and enable more efficient investigation of related problems in the fields of conservation biology, ecology, and vector-borne diseases."
What researchers won’t see is QRIScloud, the NeCTAR research cloud, and National Computational Infrastructure (NCI) all working away behind the scenes, providing cloud compute and data storage for the virtual lab. Read more
Terrestrial Sciences Data workshop results in new collaborations
QCIF and the Queensland Government’s Department of Science Information Technology and Innovation hosted the inaugural Terrestrial Sciences Data Collaboration workshop in October.
The workshop aimed to stimulate collaboration and data sharing amongst Queensland’s terrestrial sciences community by bringing data custodians, data users, service providers and infrastructure managers from universities and government together.
Researchers from UQ, QUT and Griffith University, and scientists from Queensland Government departments the Department of Science, Information Technology and Innovation, Department of Agriculture and Fisheries and Department of Natural Resources and Mines, attended the workshop, held at the Queensland Government’s Ecosciences Precinct in Dutton Park, Brisbane.
QCIF’s Outreach Manager, Gavin Kennedy, and Queensland Government’s Director of Science Information Services, Steve Jones, are planning further events to build on this great start.
Access the 2015 workshop's presentations here
ELIXIR Director gives UQ talk on Europe's life sciences data
The Director of ELIXIR
, the European life science infrastructure for biological information, delivered a QCIF co-sponsored seminar on Tuesday, 1st of December at UQ.
Dr Niklas Blomberg (pictured standing below), gave a talk on life sciences data across public and private sectors and how ELIXIR is constructing a distributed e‐infrastructure of bioinformatics services—a data nodes network—built around established European centres of excellence. He also talked about ELIXIR’s approaches to handling, analysing and archiving large and highly diverse data sets.
was supported by QCIF, UQ's Research Computing Centre
and EMBL Australia
QCIF eResearch Analyst profile:
Marlies Hankel, UQ
Marlies Hankel is a QCIF eResearch Analyst, Research Fellow at UQ’s Australian Institute for Bioengineering and Nanotechnology (AIBN
), and a nano-materials and HPC computing specialist for UQ's Research Computing Centre
Marlies manages the AIBN specialised parallel HPC computer cluster. She has been managing and installing clusters since 2004 and is an expert in their maintenance and installation, as well as maintenance of software for HPC systems and providing user support.
Marlies is currently:
Marlies holds a master’s degree in Mathematics from the University of Darmstadt (Germany) and a PhD in Theoretical and Computational Chemistry from the University of Bristol (UK). Her research, in collaboration with other AIBN researchers has resulted in two papers, in The Journal of Physical Chemistry C
, and Advanced Functional Materials