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October national eResearch newsletter 2016

Welcome to the October2016 national eResearch newsletter!

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 CONTENTS:

AeRO Welcome
eResearch Australasia New Conference Chair
ALLCall for EOI: Astronomy Data and Computing Services
Geophysics Project Aims to Map Australia’s Underground Structure
NCI Continues to Lead Australian HPC Capabilities with Adoption of Cutting-Edge Processors
EMBL-ABR Commits to the Open-Source Investigate-Study-Assay (ISA)
RDS Omics Data Platform Released
RDS Awards $2.1m in Collaborative Project Funding
October Kicks Off Monthly Galaxy-qld Meetups

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AeRO Welcome

eResearch Australasia 2016 in Melbourne was a great success again, with a lovely buzz in the sessions and out on the exhibition floor. AeRO had two exciting announcements. Firstly, the University of Queensland Research Computing Center (UQ-RCC) is joining AeRO as our first Institutional Full Member. The other is that AeRO, in conjunction with the University of Queensland and the new chair, David Abramson (see below), will take on the management of the eResearch Australasia conference from 2017. We’re encouraging everyone to provide feedback and suggestions – what did you like, what didn’t you like, what would you like? Email markus@aero.edu.au, tweet us @AeRO_eResearch and keep an eye on our website as we start preparations for next year. Looking forward to seeing you all in Brisbane in October 2017!

Dr Markus Buchhorn, AeRO CEO

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eResearch Australasia New Conference Chair

Professor David Abramson, Director of The University of Queensland’s Research Computing Centre, was officially announced as the new Chair of the eResearch Australasia conference on Thursday, 13 October.

In a brief handover ceremony at this year’s eResearch Australasia conference, held in Melbourne 10–14 October, former co-Chairs Nick Tate and Viviani Paz gave Prof Abramson a sign to congratulate him and, jokingly, to say their phones would now be switched off.

Professor Abramson has a long involvement with the eResearch Australasia conference and was on this year’s conference Organising Committee.

Brisbane will host next year’s conference, from 16–20 October at the Brisbane Convention & Exhibition Centre, with Conference Design as the conference secretariat conference@eresearch.edu.au.

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AAL Call for EOI: Astronomy Data and Computing Services

Expressions of Interest (EOI) proposals are invited from organisations to be registered to tender to provide astronomy-focused training, support and expertise to enable astronomers to maximise the scientific return from data and computing infrastructure.

Astronomy Australia Ltd (AAL) has a budget of up to $700K for a 12-month period (Jan-Dec 2017) to subcontract to the selected tenderer(s) to provide eResearch services for the astronomy research community. Furthermore, AAL will seek to secure funding to maintain or increase its investment in eResearch-related services, beyond the initial 12-month period.

The scope of intended services are described in more detail here in the call for EOIs. The deadline for Expressions of Interest (EOI) is: 5pm (AEDT), 28 October 2016. More information is available here: http://astronomyaustralia.org.au/open-tender

A briefing session was held at 2pm (AEDT), 19 October 2016. RSVP and event info here: https://astronomyaustralia.eventbrite.com.au.

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Geophysics Project Aims to Map Australia’s Underground Structure

NCI has generated new optimisation solutions to help resolve important details emerging from magnetotelluric studies of the Australian continent. Magnetotellurics (MT) is a process by which the measurement of the variations in the Earth’s magnetic and electric fields can reveal the geological makeup of the underground. The Australian Lithospheric Architecture Magnetotelluric Project (AusLAMP), led by Geoscience Australia, will see the placement of 2800 magnetotelluric instruments across Australia allowing researchers to create a much more detailed map of the earth beneath our feet. Read more at http://nci.org.au/research/mapping-electric-underground/.

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NCI Continues to Lead Australian HPC Capabilities with Adoption of Cutting-Edge Processors

The National Computational Infrastructure in Canberra, Australia’s national advanced computing facility, is the first Australian institution to deploy the latest generation of Intel® Xeon Phi™ processors, formerly code named ‘Knights Landing’. As of last month, thirty-two Intel Xeon Phi processors are online and available to researchers at NCI, following the institution’s inclusion in Intel’s early ship program. The new processors, integrated in advanced systems from hardware vendor SGI, place NCI at the leading edge of high performance computing in Australia, and represent a significant step towards exascale computation. Read more at http://nci.org.au/2016/09/23/nci-continues-lead-australian-hpc-capabilities-adoption-cutting-edge-intel-processors/.

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EMBL-ABR Commits to the Open-Source Investigate-Study-Assay (ISA)

The open source ISA framework and tools helps to manage an increasingly diverse set of life science, environmental and biomedical experiments where one or a combination of technologies are employed.

Built around the ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) data model and serialisations (tabular, JSON and RDF), the ISA framework helps researchers provide rich descriptions of their experimental metadata (ie sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable.

In an article published in October, EMBL-ABR asked Philippe Rocca-Serra, Senior Research Lecturer at the Oxford e-Research Centre, where he co-leads the ISA-tools project for ELIXIR UK, to explain why ISA is important to life science and recommended by EMBL-ABR for adoption by Australian life scientists. Full story and associated links here: https://www.embl-abr.org.au/isa-tools/.

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RDS Omics Data Platform Released

The RDS Omics team is extremely happy to announce the first Demonstration release v0.1 of the Omics Data Platform. The RDS Omics project is an RDS-funded flagship project to provide cloud-based data services and tools for Australian Life Science Researchers to combine, analyse and interpret genomic (DNA), transcriptomic (RNA), proteomic (proteins) and metabolomic (small molecules) data.

This release represents significant development and integration work over the last 7 months by the project team across VicNode, VLSCI, EMBL-ABR, Intersect and QCIF, in partnership with the BPA Antibiotic Resistant Pathogens project (http://www.bioplatforms.com/antibiotic-resistant-pathogens/).

This release includes a connected platform made up of the following components:
7 Genomics and 2 Transcriptomics related software (https://downloads.bioplatforms.com/antibiotic_resistant_pathogens/);
All the genomics data currently available in the BPA CCG repository;
A range of pre-written analysis workflows;
Online training modules for the analysis environment.

Read more at http://www.rds.edu.au/single-post/2016/10/18/Omics-Platform-V01

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RDS Awards $2.1m in Collaborative Project Funding

RDS is pleased to announce the awarding of $2.1m in competitive grant funding for activities building on the work completed in the existing research community and flagship projects.

The purpose of this funding is to consolidate the sustainability, support, and service aspects of projects which have been resourced through the previous rounds of RDS research domain project funding.

“In this period of funding uncertainty it’s critical for our projects to be able to demonstrate a tight and enduring relationship with the communities they service as well as to develop sustainable operational models allowing them to provide benefits into the future, regardless of the structure of overall funding organisations,” said RDS Director, Ian Duncan.

Read more at http://www.rds.edu.au/single-post/2016/10/10/RDS-awards-funding.

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October Kicks Off Monthly Galaxy-qld Meetups

A monthly Brisbane-based Galaxy-qld meetup was launched on Wednesday, 5 October at The University of Queensland (UQ).

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 VLSCI co-developed the Genomics Virtual Lab (GVL), which runs on a dedicated Galaxy server. UQ’s Research Computing Centre supports the GVL with a dedicated team.

The meetups will be held on UQ’s St Lucia Campus at the Queensland Bioscience Precinct.

Visit the GVL blog for further information about the Galaxy-qld meetups: https://genomicsvirtuallab.wordpress.com/2016/09/19/galaxy-qld-meetup-in-brisbane/

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CSIRO’s Deep Learning Supercomputer

CSIRO has installed the first NVIDIA DGX-1 in the Asia Pacific region. The DGX-1 enables researchers and data scientists to harness the power of GPU-accelerated computing, applying artificial intelligence techniques to the analysis of scientific data.

The DGX-1 will be used by CSIRO scientists to expand research in areas such as medical image analysis, nano-material modelling, genome analysis, earth observation and analysis, and radio-astronomy. For radio astronomy, CSIRO researchers are hoping to re-analyse the data collected over the last 40 years by the Parkes radio telescope in the hope of detecting more pulsars.

A separate CSIRO project will use the same artificial intelligence system to process massive amounts of complex, multi-layered and dynamic data to help understand the effect of environment on disease, helping to identify protein markers and predict, prevent and treat disease.

See the CSIRO Blog for more detail, at https://blog.csiro.au/deep-learning-hpc-pie/

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Note: This Newsletter is based on contributions provided by members of the eResearch community, and also draws on the many news articles and newsletters published across our sector. The Newsletter will be published monthly, on about the 16th of each month. Please send any contributions (no more than 150 words, plus a link) or pointers to any other relevant articles or newsletters to editor@aero.edu.au. Archives of these Newsletters are held at http://aero.edu.au/newsletters/.
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