CSIRO is responsible for managing National Research Infrastructure on behalf of the broader scientific community to help with the delivery of research.

CSIRO research scientist and beetle curator Dr Adam Slipinski holds a weevil fossilised in amber at the Australian National Insect Collection.

There are two types of National Research Infrastructure: National Research Facilities and National Biological Collections.

As the national provider of a range of specialised laboratories, scientific and testing equipment and other research facilities, CSIRO provides science-ready facilities for use by Australian and international researchers through application and user-funded arrangements related to the facility.

The National Research Facilities include the:

  • Australian Animal Health Laboratory (AAHL), Geelong
  • Australia Telescope National Facility (ATNF) comprising:
    • Parkes Radio Telescope, NSW
    • Australia Telescope Compact Array near Narrabri, NSW
    • Australian Square Kilometre Array Pathfinder (ASKAP) and the Murchison Radio-astronomy Observatory (MRO), WA
    • Mopra Telescope at Coonabarabran, NSW
  • Marine National Facility (MNF), Hobart
  • Pawsey Supercomputing Centre, Perth
  • Atlas of Living Australia (ALA).

The National Research Collections Australia (NRCA) comprise:

  • Australian National Fish Collection (ANFC) of marine fish
  • Australian National Herbarium (ANH) of native plants and weeds
  • Australian National Insect Collection (ANIC) of terrestrial invertebrates
  • Australian National Wildlife Collection (ANWC) of terrestrial vertebrates
  • Australian National Algae Culture Collection (ANACC) of living microalgae cultures
  • Australian Tree Seed Centre (ATSC) supplying tree seed to both domestic and overseas customers.
Table 3.10: Summary of our Performance for Activity 3
KPI and metric Target Result

Maintenance and operation of the research infrastructure to appropriate standards

Compliance with Australian legislation and regulations and ISO accreditations

G

Our research infrastructure achieved compliance with relevant Australian and international standards.

AAHL continues to maintain or exceed the regulatory requirements certified by the Department of Agriculture and Water Resources, the Office of the Gene Technology Regulator and the Department of Health’s Security Sensitive Biological Agents legislation, and all relevant ISO accreditation.

Utilisation of the facilities and collections as measured through: successful observations, time lost during observations, core hours used, outward loans and successful research days delivered

Minimum of 70% successful astronomy observations

G

The ATNF achieved 74.7% successful astronomy observations and lost 3.3% of time to unscheduled outages.

Maximum 5% time lost during scheduled observation

90% core hours on Magnus supercomputer

G

92% core hours on Magnus wereachieved.

70% outward loans (over 5 years) – combined utilisation of national research collections

G

The NRCA achieved 70% outward loans. We also increased the proportion of the national biological collections that are digitised. The Australian National Algae Culture Collection maintained 100% digitisation.

Minimum of 90% successful research days delivered on Marine National Facility

G

The MNF achieved 100% successful research days with no time lost during scheduled operations.

Maximum of 10% time lost during scheduled Marine National Facility operations

Utilisation of SIEF funded research infrastructure as measured through timeallocations

>60% operational time used, 20% usage in collaborative projects

G

60% utilisation of operational time achieved for Research Infrastructure equipment that has been fully commissioned. Usage in collaborative projects is limited at this stage, but will increase as equipment is progressively installed and commissioned (please see the SIEF report on pages 147 and 149 for details).

Green shading indicates positive progress for the year and the target has been achieved.

Australian Animal Health Laboratory

Our national biocontainment laboratory

The Australian Animal Health Laboratory (AAHL) provides Australia’s highest level of biocontainment within a purpose-built biosecurity infrastructure. AAHL is recognised nationally and internationally as a centre of excellence in disease diagnosis, research and policy advice in animal health and human diseases of animal origin. AAHL helps protect Australia’s billion-dollar livestock and aquaculture industries, and the community, from exotic and emerging infectious diseases assisting to maintain Australia’s economy, environment, and the health and social wellbeing of our nation. It is built and operated to safely store and enable work on the most dangerous pathogens and our experience developed in biosecurity and biosafety is sought by governments and customers around the world.

AAHL’s infrastructure and scientific expertise enables it to deliver a vital service to the Department of Agriculture and Water Resources (DAWR) as Australia’s Reference Laboratory for emerging animal diseases and high-consequence pathogens of animal origin. Over the past 30 years there has been a marked increase in the public health threat of emerging infectious diseases of animal origin, known as zoonoses, which has resulted in increased global demand for biocontainment laboratory space at PC3 and PC4.

AAHL is funded primarily by CSIRO appropriation. DAWR provides funding for an ongoing diagnostic service and the National Collaborative Research Infrastructure Strategy has provided funds to enable national and international researchers to access the facility. AAHL also delivers diagnostic and research services to Australian and state governments as well as to industry and international bodies. AAHL is recognised as a crucial part of Australia’s biosecurity infrastructure.

AAHL’s customer base has expanded through initiatives that deliver to local and international customers, while remaining true to the DAWR contract to provide a diagnostic, surveillance and response service to underpin Australia’s licence to trade in animal products.

Services offered in 2017–18 included:

  • access to high-containment laboratories and animal facilities for research
  • collaborations with CSIRO Business Units to develop vaccines and therapeutics against dangerous pathogens
  • research on vector-borne diseases such as Dengue and Zika viruses
  • quarantine testing for horses, birds, aquatic species and companion animals
  • training courses for vets in the diagnosis of animal diseases and biosafety training for scientists
  • services that enhance regional biosecurity and food security across Asia.

Maintenance and operations

Maintaining and updating the microbiological and physical security of AAHL is an ongoing priority. Significant effort has been directed to upgrade the software used to plan, monitor and record maintenance activities at AAHL. Ongoing minor infrastructure works to replace end-of-life plant have included completion of stand-by boiler replacement, replacement of access control hardware, and design and tendering of pure water system and fire protection, and alarming systems for upgrade in 2018–19. Installation of dunk tanks to PC4 animal spaces was completed to satisfy regulatory requirements for transfer of material.

Planning is underway for a broader capital upgrade program as part of a third-of-life re-fit to ensure the facility continues to meet regulatory requirements of both the Commonwealth and State of Victoria. The business case for this was submitted in December and approved in the 2018 Federal Budget.

Each year, AAHL analyses samples from around 3,500 cases for diagnostic testing, including over 700 for rapid response emergency disease exclusion, covering 73 diseases. Other samples are received from around the world for a range of purposes, including to enable global movements of healthy animals, facilitate import of biological materials, exclude exotic diseases in Australian livestock or characterise viruses detected in our region. AAHL also plays a significant role in public health, testing for important zoonotic diseases. AAHL recently became the first animal health lab in Australia to gain accreditation under the Therapeutic Goods Administration’s In-vitro diagnostic registration scheme, which regulates human testing.

To fulfil its role in emergency response, AAHL maintains and updates an Emergency Laboratory Response Plan. The template scenario for the plan is an outbreak of foot-and-mouth disease – a terrestrial animal disease.

3,500 cases tested, covering 73 diseases

Internationally, during 2017–18 AAHL staff contributed to policy advice and guideline setting through a range of World Organisation for Animal Health (OIE) and World Health Organization ad hoc groups, including those with a focus on bio-banking, aquatic and terrestrial disease diagnosis, response framework for zoonotic diseases and investigation of intentional use of biological agents. This latter area has also led to engagement with Departments of Defence and Foreign Affairs, and the United Nations. Support for laboratory capability development within the region has also expanded, with both the Food and Agricultural Organisation and OIE now supporting this program of work, which includes 22 laboratories across 16 countries.

Since 2014, AAHL has run an annual ‘Recent Advances in Emergency Animal Diseases’ symposium for veterinarians. In 2017, 104 vets attended this training event, which brought the total annual number of vets trained to 393. Other training activities included hands-on training in sampling and post mortem techniques, state-based training and internships. At the undergraduate level, AAHL has reached out to over 500 veterinary students every year since 2015 through a university engagement project.

Helping New Zealand manage a Mycoplasma bovis outbreak

The Australian Animal Health Laboratory plays an integral role in investigating exotic and emergency disease incidents in Australia and globally, with a strong commitment in the Asia-Pacific region.

Our staff are members and active participants in many significant international and national networks, including the International Animal Health Emergency Reserve (IAHER) arrangement. This arrangement permits signatory countries to share personnel in the event of an emergency animal disease outbreak to supplement their domestic emergency response capabilities.

In July 2017, the bacterial infection Mycoplasma bovis was found in cattle in the Oamaru area of New Zealand’s South Island. Since then, the New Zealand Ministry for Primary Industries has been working hard to control the spread of the disease and, if possible, eradicate it from the country with support from local farmers, industry bodies and communities.

Mycoplasma bovis can cause a range of serious conditions in cattle including mastitis that doesn’t respond to treatment, pneumonia, arthritis and late-term abortions, posing a risk to animal welfare and productivity. Fortunately, it does not infect humans and presents no food safety risk.

Although Mycoplasma bovis is widespread internationally and occurs in Australia, this is the first time it has been found in New Zealand. It is listed as an ‘Unwanted Organism’ under New Zealand’s Biosecurity Act 1993, so when the organism was confirmed the New Zealand Government declared a biosecurity response. To eradicate the disease, it has approved $85 million for operational and compensation costs, while several industry bodies have committed an extra $11.2 million.

In August 2017, New Zealand activated the IAHER arrangement requesting assistance at its National Laboratory to manage the surge in testing as a result of the outbreak. The IAHER involves Australia, Canada, Ireland, New Zealand, the United Kingdom and the United States, but on this occasion, New Zealand decided to activate it with Australia only. This is the first time the arrangement has been ‘activated’ under the current agreement.

After an outbreak of Mycoplasma bovis in New Zealand, AAHL staff provided support with the surge in testing.

AAHL provided nine staff, including serologists and molecular biologists, for two weeks each between August and October 2017. Their assistance enabled New Zealand to cope with the surge in testing after the disease was initially detected as well as quickly identify infected properties, which has helped to rapidly manage and control the disease outbreak.

In a letter to Australia’s Chief Veterinary Officer regarding Australia’s support, New Zealand was very grateful for AAHL’s prompt and professional response to its request for skilled resources to help with this emergency animal biosecurity issue. This outbreak has allowed for the IAHER arrangement and processes to undergo a real-world test for a medium-scale response.

AAHL’s work in supporting other countries to control and eradicate infectious animal diseases reduces disease risk to these countries, but also helps to maintain Australia’s biosecurity through better threat assessment and preparedness.

Australia Telescope National Facility

Australia’s premier astronomy infrastructure

The Australia Telescope National Facility (ATNF) comprises world-class radio-astronomy facilities operated by CSIRO and associated instrumentation and research programs. ATNF observatories are located near the towns of Parkes, Narrabri and Coonabarabran in eastern NSW and in the mid-west region of Western Australia. In 2017–18, Australian Government funding supported merit-based access to the Australian Square Kilometre Array Pathfinder (ASKAP), the Australia Telescope Compact Array (ATCA) and the Parkes Radio Telescope.

Approximately 20 per cent of observing time on the Parkes Radio Telescope and all observing time on the Mopra telescope, near Coonabarabran in NSW, was funded by external partners. ATNF observatories also contain other instruments: the Murchison Radio-astronomy Observatory, home to ASKAP, also hosts the low-frequency Murchison Widefield Array (MWA) and is where an instrument of the international Square Kilometre Array will be built.

ATNF telescopes support galactic, extragalactic and cosmological research in fields as diverse as the interstellar medium, the formation and evolution of stars and galaxies, cosmic magnetism and understanding the extreme physics of pulsars and black holes.

ATNF comprises the major part of CSIRO Astronomy and Space Science, which also operates the Canberra Deep Space Communication Complex (CDSCC) on behalf of the US National Aeronautics and Space Administration (NASA). CDSCC is responsible for meeting the government’s obligations under the US–Australia agreements for deep space tracking and communications in Australia. CSIRO, through the CDSCC, provides critical front-line mission control support to NASA for its deep space missions. CDSCC currently supports around 40 missions representing 27 nations worldwide that operate deep space telescopes and probes. CSIRO also manages Australian astronomers’ access to these antennas, which are often used in conjunction with ATNF telescopes as part of the Long Baseline Array (LBA), an array linking radio telescopes in Australia and overseas.

CDSCC supports around 40 missions representing 27 nations worldwide

Utilisation of the ATNF

Observing time on ATNF telescopes is awarded on the basis of scientific merit. New users of the Parkes telescope and the ATCA typically first observe from the Science Operations Centre at ATNF headquarters in Sydney, where they are provided with training and support. Once qualified, astronomers can operate these telescopes from their home institutions.

The full 36-antenna array of ASKAP was completed in November when the last of CSIRO’s multi-award-winning phased array feed (PAF) receivers was installed. Commissioning of the receivers continued during the year with 24 currently online, available in two science sub-arrays.

Five Survey Science teams have been using ASKAP’s Early Science imaging array of 12 antennas with over 1,000 hours of observations carried out to date. Several petabytes of data have been stored and are now being investigated. In parallel, a different subset of ASKAP antennas has been used in a highly successful search for fast radio bursts (FRBs). FRBs are a hot topic in astronomy – they are bright spikes of radio waves lasting a few milliseconds, but their cause is a mystery. The first FRB was discovered using the Parkes Radio Telescope in 2007 and only two dozen had been found since, until astronomers started finding them with ASKAP. It is hoped that ASKAP will be one of the first telescopes to pinpoint an FRB on the sky, which may lead to an understanding of their origins.

In 2017–18, research teams of 830 astronomers from 34 countries submitted proposals to use ATCA, Parkes and the LBA. For ASKAP, 10 major survey science projects, representing 363 investigators from 131 institutions, were selected to be allocated most observing time in the first five years of full operation. The Mopra telescope is no longer offered for merit-based access: observing time on Mopra is allocated to a consortium of universities that fund its operation.

Observers on ATNF telescopes other than ASKAP have 18 months after the observation during which they have sole access to their data. After this, the data are made publicly available to astronomers worldwide through CSIRO’s public data archives. ASKAP data have no proprietary period and are released into the archive as soon as they have passed quality assurance checks.

Figures for 2017–18 include the merit-based allocation for ATCA and the Parkes Radio Telescope. Time allocated to observations rose slightly this year as less time was spent testing new receivers at the Parkes Radio Telescope.

Table 3.11: utilisation of the ATNF, in %
Target 2015–16 2016–17 2017–18

Successful astronomy observations (%)1

70 (min)

77.5

72.0

74.7

Time lost during scheduled observations (%)2

5 (max)

3.0

2.0

3.3

Radio-quiet zone lets us see ‘cosmic’ dawn

The extreme ‘radio quietness’ of a CSIRO observatory has made possible a landmark discovery: a signal showing when the first stars burst into life.

A radio telescope can detect a radio signal a million billion times smaller than the ones a mobile phone can. That’s because, just as starlight is fainter than streetlights, cosmic radio signals are far fainter when they reach us than the radio waves from our technology. Mobile phones, radio stations and television transmitters use part of the radio spectrum and their signals can hide or overwhelm natural radio emission from the cosmos. Radio astronomers call these human-made radio waves ‘interference’.

CSIRO gave its new Australian SKA Pathfinder telescope (ASKAP) a head start in beating radio-frequency interference by establishing its home far from big cities. The Murchison Radio-astronomy Observatory (MRO) in Western Australia is 315 km from Geraldton. It lies in Murchison Shire, which is 49,500 square kilometres in size but home to just 100 people, so there are very few radio-emitting devices around. Strict on-site standards and procedures also help keep interference down and radio interference is further curbed by a legislated ‘radio-quiet zone’ around the observatory.

The value of these steps became clear in 2015 when early observations with ASKAP revealed a tiny signal from a galaxy five billion light-years away – a signal that started travelling before Earth formed. At many other sites such a signal would have been missed, blotted out by stronger human-made ones.

Now another radio telescope on the site has found a far tinier signal. In March, the Experiment to Detect the Global Epoch of Reionization Signature (EDGES) team, led by Dr Judd Bowman from Arizona State University, announced a stunning coup: they’d found evidence of the first stars in the universe lighting up, just 180 million years after the Big Bang. EDGES has been running for nine years at MRO, which Bowman and his team decided was the best place on the planet to do their work.

This is the first time astronomers have observed a signal from this early in the evolution of the universe.

The sign at the entrance to the Murchison Radio-astronomy Observatory, reminding visitors of the need to keep human-made radio waves, known as ‘interference’, to an absolute minimum.

Studying these signals is the key to understanding how the cosmos evolved. These primordial stars not only shaped the matter around them but, in particular, their explosive deaths created the soup of heavier elements, such as carbon and oxygen, from which later stars formed.

Other researchers are now seeking to repeat the detection. They will also seek to go beyond just a detection, eventually mapping where and when the first stars formed.

Doing this will need an extremely sensitive low-frequency array. The MRO will soon host such an instrument, SKA-LOW, the low-frequency telescope of the international Square Kilometre Array. SKA-LOW is due to start construction in the next few years.

Marine National Facility

Australia’s world-class marine research capability

The Marine National Facility (MNF) is a key element of Australia’s research infrastructure. MNF operates the research vessel Investigator to provide a world-class, blue-water research capability for Australian researchers and their international collaborators for work in Australia’s vast and largely unexplored marine areas.

MNF includes the world-class research vessel Investigator, a suite of scientific equipment, staff to support delivery of research vessels and more than 30 years of marine data that are freely available.

Investigator is a multi disciplinary research vessel capable of servicing the Australian marine science community for 300 days per year, for up to 60 days per voyage without re-supply. Each voyage is able to accommodate 40 scientists, technical staff and other participants and cover 10,000 nautical miles, with operational range from the Antarctic ice edge to the tropics. Onboard scientific facilities include multibeam seafloor mapping capability to 11,500 metres, deployment of oceanographic equipment to 7,000 metres and trawling to depths of 5,000 metres. In addition to onboard capabilities, Investigator has an extensive suite of scientific equipment, which can be added to voyages as required.

Each Investigator voyage can cover 10,000 nautical miles

Access to the vessel is offered through two streams: MNF Granted Voyages (GV) and MNF User Funded Voyages (UFV). GV – the primary means of accessing ship time – are offered through a competitive, independent, peer-reviewed application process focused on scientific and technical excellence, the potential to contribute to Australia’s national benefit and the ability of the research team. Sea time for GV is funded by the Australian Government with successful proponents responsible for meeting all other project costs. The UFV stream provides a mechanism for any unallocated sea time to be made available to research organisations and their collaborators under a charter arrangement.

MNF enables excellent scientific research in the national interest, providing key information to the broader scientific community, government, industry, policy makers and the Australian public. Research data support evidence-based decision-making on challenges affecting regional and global climate, fisheries management, geological resources, coastal and offshore developments, and marine operations.

Utilisation of the MNF

Several voyages undertaken this year highlighted both public interest and enhanced capability of Investigator and the science operations conducted on board:

  • We launched the Floating Classrooms program as part of 2017 National Science Week. This program addresses one of MNF’s five strategic pillars, student training, and aims to promote the use of the Facility. During selected port periods, Investigator makes on board laboratories accessible to secondary, tertiary and TAFE students for STEM studies.
  • While transiting from Sydney to Broome, Investigator located the final resting place of the SS Macumba in the Arafura Sea off the coast of Arnhem Land. Macumba was a steel steamer sunk by the Japanese during World War II with the loss of three lives. Data collected by Investigator will help inform a detailed wreck inspection report and future management as a protected historic shipwreck.
  • MNF initiated an Educator on Board program in September 2017, following a successful trial in January. It provides primary and secondary STEM teachers with an opportunity to help scientists with marine research; enhance their STEM content knowledge; run outreach activities, including live video broadcasts; and develop curriculum-linked resources to be trialled in their own classroom and shared with other teachers. The program aims to inspire STEM students and develop future generations of marine scientists. To date, nine teachers from across Australia have participated in this program.
  • A voyage led by CSIRO during October and November studied the long-term impact of trawling on fish and seafloor species on the North West Shelf off Western Australia. This area was subjected to heavy trawling in the 1970s and 1980s by Australian fishers. The outcomes of this work will aim to inform fisheries policy and management for industry and government both within Australia and internationally. Significantly, this voyage was the first time Investigator had transited along the Western Australian coast, which completed the ship’s circumnavigation of Australia.
  • During January and February, CSIRO and the Bureau of Meteorology led a 42-day voyage to the Southern Ocean and Antarctic ice-edge to study the ocean and atmospheric conditions in the Southern Ocean and the impact these have on our climate. Eleven robotic Argo floats were deployed to continuously measure changes over the next 5 to 6 years 5,000 m below the ocean surface (measurements were previously only available to 2,000 m). The atmospheric component of this voyage included a combination of aircraft, ship-based and satellite observations to collect data on clouds and the interaction between incoming radiation, aerosol production and rainfall. The data collected during this voyage fill a significant gap in current data and will enable more accurate future climate projections.
Table 3.12: utilisation of THE MNF, IN %

Target 2017–18

Successful research days delivered (%)3

90 (min)

100

Time lost during scheduled operations (%)4

10 (max)

0

Enabling globally significant research in our marine environment: North West Shelf trawling study

CSIRO delivers the Marine National Facility program for Australia. As part of this program, we own and operate the marine research vessel Investigator. The vessel houses a suite of multi disciplinary and cutting-edge scientific equipment, which enables us to collect high-quality, high-volume data to inform decision-making by government, industry and community.

Thanks to its technological capability, Investigator has made it feasible and affordable to address key challenges that face Australia’s marine environment policy makers and resource managers. These challenges include the effects of trawling on the marine environment, particularly the seabed, which are a major issue for fisheries management globally due to a widespread lack of baseline and monitoring data. Such information gaps mean government is less able to set evidence-based policy and industry faces significant challenges in adopting effective practices to safeguard the sustainable management of fisheries.

In October and November 2017, CSIRO’s Oceans and Atmosphere Business Unit led a 26-day research voyage on Investigator to study the long-term recovery of trawled marine communities on the North West Shelf off Western Australia. Forty researchers collaborated on the voyage from eight research institutions including Australia’s WA Fisheries, University of Tasmania, Macquarie University and Museums Victoria, and China’s Ningbo University and Chinese Academy of Sciences. This demonstrates the value of the Marine National Facility as an international collaboration hub for knowledge exchange between scientists and, importantly, between scientists and the public through the communication activities delivered during the voyage.

The Investigator’s significant capability and capacity allowed researchers to set and complete an ambitious program of deployments that delivered a record number of operations carried out on a single voyage. We deployed a wide range of equipment in 584 operations during the 26 days including demersal fish trawl net, epibenthic sled, deep-tow camera, Conductivity, Temperature, and Depth (CTD) sensors, sediment grab and plankton nets.

The voyage included four supplementary projects, which offered a significant additional benefit by delivering multidisciplinary science outcomes. These included detailed seafloor mapping of Ningaloo Commonwealth Marine Reserve, which has provided Parks Australia with data to better manage and conserve this high profile and globally significant marine environment.

Scientists standing on the deck of the RV Investigator with marine biodiversity samples.

RV Investigator enables vital surveys of our marine biodiversity.

In total, 100 individual stations were sampled during the voyage. The flexible platform offered by Investigator, combined with expertise of the Marine National Facility and ASP Ship Management technical support staff, enabled reliable data to be collected from nearly all stations. This demonstrates the value of the Facility in delivering highly efficient operations that enable significant volumes of data and samples to be collected, which can be accessed for future analysis and benefit of all.

The data obtained – approximately 4 terabytes – and samples collected will enable us to evaluate the recovery of benthic habitats and demersal fish assemblages 30 years after very significant reductions in trawl effort. The data will also help us to make comparisons with areas that have been trawled continuously over the same period. The ability to do this with access to comparative data collected during the 1980s is unprecedented – made possible as a result of this voyage.

This voyage will significantly improve our understanding of the long-term recovery of trawled marine habitats and the effectiveness of management responses to protect and enable recovery of impacted ecosystems. The results will be significant in an international context and relevant to the management of trawl fisheries in Australia and overseas.

Pawsey Supercomputing Centre

A world-class high-performance supercomputing facility

The Pawsey Supercomputing Centre is one of only two high-performance computing facilities in Australia that enables researchers to tackle large-scale data problems and simulations. The Centre provides researchers in government, academia and industry access to world-class expertise and infrastructure in supercomputing, data and visualisation services, including access to one of the most powerful supercomputers in the Southern Hemisphere.

Pawsey currently serves over 80 organisations and is achieving unprecedented results in science domains including radio astronomy, geosciences, resources engineering, bioinformatics and health sciences. It also supports the Square Kilometre Array (SKA) Pathfinder research.

Pawsey is an unincorporated joint venture between CSIRO, Curtin University, Edith Cowan University, Murdoch University and the University of Western Australia. Its operations are governed by a Members’ Agreement, with effective governance provided by a Board comprised of core member representatives, independent members and an independent chair.

CSIRO owns and operates the Centre’s building, which is located at our Kensington site and offers a range of supercomputing and large-scale data facilities including Magnus (a petascale system) and data-storage capabilities in excess of 100 petabytes. It also houses Galaxy, a Cray XC30 dedicated to the operational requirements of the Australian precursor projects to the Square Kilometre Array (SKA): the Australian Square Kilometre Array Pathfinder (ASKAP), operated by a CSIRO facility, and the Murchison Widefield Array (MWA), run by Curtin University.

The Centre supports over 1,500 researchers across Australia

Pawsey is primarily funded by the Australian Government, the West Australian Government and Pawsey members. Pawsey previously employed staff from all five member organisations, however, since 1 July 2017 all staff have been employed through CSIRO. Pawsey currently has 43 staff members whose expertise enables Australian researchers to take advantage of the Centre’s wide range of services.

Utilisation of Pawsey

Pawsey provides access to its supercomputing resources through several national and stakeholder merit allocation schemes. Schemes operating in 2017–18 were the:

  • National Computational Merit Allocation Scheme – 25 per cent of resources allocated. The call for proposals was made in September/October, with 12-month allocations, budgeted quarterly
  • Energy and Resources Merit Allocation Scheme – 15 per cent of resources allocated, with 12-month allocations, budgeted quarterly
  • Pawsey Partner Merit Allocation Scheme – 30 per cent of resources allocated, with 12-month allocations, budgeted quarterly
  • Pawsey Director’s Allocation Scheme – 5 per cent of resources allocated. Responsive-mode grant assessment process, available most of the year and most resources were small (<0.1 per cent of available resource time), 3-month allocations
  • Radio-astronomy Scheme – 25 per cent of Pawsey resources allocated (i.e. Galaxy).

The Centre supports over 1,500 researchers across Australia, a number which has increased by 30 per cent in the last two years. Demand has already exceeded availability: last year, the three major allocation schemes recorded an average of 47 per cent success rate (time allocated vs time requested). More than 550 million core hours were requested when only 270 million core hours were available.

TABLE 3.13: Allocation of the Magnus Supercomputer, in %

Target 2017–18

Core hours used on the Cray XC-40 supercomputer Magnus (%)

90

92

Pawsey helps protect Perth’s water supplies

In Western Australia’s capital city of Perth, where around 80 per cent of the state’s 2.6 million people live, dams and rivers are all but redundant. Years of below-average rainfall have caused water supplies to dwindle, creating increasingly drier catchments. Consequently, the groundwater system is vital to meeting Perth’s public and private water needs. Each year, the state government manages 400 gigalitres of groundwater from aquifers, making up 46 per cent of the total supply. With a growing population and climate change impacting on aquifer recharge, it is an increasing challenge to sustain these precious water resources.

With the help of Pawsey’s flagship system, the Magnus Cray XC40 supercomputer, Professor Brett Harris and his team from Curtin University Department of Exploration Geophysics created detailed 3-D models of Perth’s groundwater aquifers from the surface to more than 2 km below.

To map Perth’s complex multi-level aquifer system, they collected data spanning thousands of square kilometres by sending airborne electromagnetic survey measurements directly to the powerful supercomputer for near-real-time data processing. With the sheer volume of data being sent back and forth, using Magnus was vital – turning a job estimated to take several years on a single computer processing unit into one that could be completed in a matter of hours.

The speed and power of Magnus allowed the team to spot errors on-the-go, test new ideas and build the 3-D maps as quickly as possible. The system also provided the capacity for the team to integrate data from multiple sources and accurately model the geology of the aquifers. Two hundred simulations had to be run on each survey reading to ensure accurate conversion to information about rock type and groundwater chemistry.

These maps are critical to support the government’s plans for Water Corporation to add new extraction and replenishment wells on the Gnangara system, the largest groundwater source in Western Australia.

By increasing the understanding of how the different parts of the groundwater system are connected, and where and how water moves through the systems – especially from the superficial aquifer into the deeper aquifers – the government can identify locations and rates for taking groundwater that have less impact on the environment and other water users.

The research has already informed the Department of Water and Environmental Regulation to recommend replenishment and abstraction sites based on their ability to deliver goals of both maximum redraw and optimum environmental benefits, supporting groundwater levels near lakes, wetlands and areas of seawater intrusion risk.

Detailed 3-D models of Perth’s groundwater aquifers, created using Pawsey’s powerful supercomputer, are helping the Western Australian Government to protect and maintain the city’s water supplies.

Magnus will continue to supply the processing power required as the team writes code to automate the processing and integration of data from many sources, enabling electromagnetic readings to be instantly inverted to inform groundwater models. Ensuring an accurate framework from the beginning is crucial to support long-term forecasting over the next 50 to 100 years.

Groundwater replenishment is the ‘dam building’ of the 21st century. It is accepted in areas like Perth as a better storage option for harvested and recycled water and helps offset water losses from climate change, evaporation and water use.

National Research Collections of Australia

Biodiversity science research infrastructure

Australia is home to more than half a million species of plants and animals. Three-quarters of these are found nowhere else on Earth. This unique biodiversity is a national treasure and is a crucial environmental asset, providing ecosystem services and economically valuable resources.

CSIRO is the custodian of several collections of animal and plant specimens that contribute to national and international biological knowledge. The National Research Collections of Australia (NRCA) are a vital resource for conservation, science and industry innovation. They provide a history of Australian fauna and flora. NRCA’s six biological collections contain more than 15 million specimens, representing a 240-year time series of data on the occurrence and distribution of native and introduced plants, terrestrial vertebrates, insects, fish and algae.

These collections are Australia’s most reliable set of nationally representative biological collections. They underpin research in agriculture, biosecurity, biodiversity and climate change and are used by researchers all over the world. The collections allow us to identify, quantify and explore Australia’s biodiversity over time and also inform public policy decisions, support biosecurity and contribute to environmental management.

NRCA’s role is to protect and explore the rich biological information in its collections to conserve and exploit unique biodiversity for the benefit of our environment, the community and industry. The Environomics Future Science Platform (FSP) is a research-intensive enterprise developing new ways to reveal and make use of genomic resources in nature. These novel technology ‘platforms’ will meet our customers’ needs to gather more accurate environmental information at greater speed and accuracy than currently possible and support new business for CSIRO Business Units. The Environomics FSP is hosted by the National Research Collections and partnered with Oceans and Atmosphere, Land and Water, and Data61, as well as four universities and three National Collaborative Research Infrastructure Strategy (NCRIS) facilities.

The NCRIS-supported Atlas of Living Australia (ALA) is a world-leading informatics, visualisation and analytics platform that integrates Australian biological and environmental data from a wide variety of sources and makes them available to users online for education, research and policy development. The use of open source occurrence data to inform biological research, environmental management and conservation planning, education and community engagement is now widely accepted. In 2017–18, the ALA explored the addition of environmental DNA, or eDNA, data to its infrastructure, and helped to establish global standards and common practices for the management of DNA-derived data and the delivery of trait data.

Utilisation of the collections

This year, the Australian National Herbarium (ANH) contributed to national and global research through loans and exchanges with more than 41 herbaria in 18 countries. In addition, ANH developed a new classification system for Australian grasses based on awn morphology and is determining the origins of key agricultural weeds.

ANH was deeply involved in the Environomics FSP, where it used novel genomics approaches to quantify pollination services in alpine plant communities and developed a deeper understanding of plant biology, which will inform how it creates portable devices to study plants in the field.

More than 80 per cent of specimen records are digitised and available through Australia’s Virtual Herbarium and the ALA. Imaging of newly accessioned ANH type specimens is continuing, with images now publicly available through the Global Plants Initiative hosted by the digital library JSTOR. In addition, a further 60,500 images of specimens from ANH’s general collection have been captured. These images will be publicly available when the new Collections Management System is deployed.

In 2017–18, the Australian National Insect Collection (ANIC) hosted over 100 national and international researchers and provided 24 tours of the collection. Research by staff and affiliates on ANIC specimens resulted in the descriptions of 20 new genera and over 200 new species of insects. In addition, more than 7,000 specimens were loaned to 16 Australian institutions and 20 institutions overseas to support national and global taxonomic research.

Over 72,000 ANIC specimens were either primarily databased (from label data) or imaged and sent for transcription in DigiVol by the National Collections and Marine Infrastructure digitisation team. ANIC staff continued to act as trusted advisors in biosecurity for the Federal Government and will deliver a training course in insect preservation and identification for Northern Australian Quarantine Staff in early 2019. Two Department of Agriculture and Water Resources staff work as part of ANIC to identify hundreds of insects intercepted at Australia’s borders each year.

The Australian National Wildlife Collection (ANWC), especially its cryo-frozen tissue collection, is a major research resource for the international community, with 553 samples sent for DNA sequence-based research during 2017–18. ANWC digitised 1,255 specimens and 2,055 genetic samples. New material primarily involved bird specimens collected from south-eastern Western Australia.

The Australian National Algae Culture Collection (ANACC), through the Australian National Algae Supply Service (ANASS), provides microalgae strains as starter cultures to industry, research organisations and educational institutions in more than 70 countries, with a particularly strong customer base in Oceania, Africa and Asia. During 2017–18, ANASS managed 173 orders representing a total of 351 living microalgae cultures to 83 customers (66 per cent Australian and 34 per cent international). ANACC is working towards licencing a subset of strains for commercial exploitation. Core culture and accession information is digitised for all ANACC specimens, and most of these are publicly available through an online database. Additional imaging, geo-referencing, genomic and phenotypic characterisation have been digitised to different levels. Overall digitisation rates have remained the same as 2016–17.

The Australian Tree Seed Centre (ATSC) supplies wild and genetically improved native tree seeds to Australian and international customers. During 2017–18, ATSC filled 99 seed orders (47 per cent Australian and 53 per cent international) to 78 customers. This year, ATSC focused on updating germination testing of older seedlots of long-lived species, including desert acacias and collection of eucalypt species native to the ACT and southern NSW.

The Australian National Fish Collection (ANFC) is one of CSIRO’s most accessible collections due to the high proportion of digitised specimens that are publicly available through the ALA. These records include 151,000 fish specimens, 65,000 images of fishes, 11,000 x-rays, and 16,000 tissues for genetic analyses, representing marine species from Australia, the Antarctic and the Indo-Pacific region. In 2017–18, work focused on innovative methods for extracting high-quality genomic information from preserved specimens that represent snapshots of past levels of genetic diversity. This allows estimations of historical ecological parameters for important Australian fisheries.

The ALA is now established as biodiversity data delivery and integration infrastructure in seven countries around the world. Another 10 countries are currently investigating its use and including development funds in proposals. It is also the primary mechanism through which NRCA’s digitised biological collection data is made freely available.

The ALA holds close to 75 million records

A major refresh of the user interface has delivered new initiatives and data streams, e.g. trait and genomic data. The Atlas holds close to 75 million records provided by partnering with museums, state and local governments, non-government organisations, universities and CSIRO. As of 2017–18, approximately 15 billion records in total have been downloaded for uses in education, research and management.

TABLE 3.14: COMBINED UTILISATION OF NATIONAL RESEARCH COLLECTIONS, IN %5

Target

2017–18

Outward loans
(% over 5years)

70%

70%

A daisy weed seed key to protect Australia’s biosecurity and support trade

CSIRO is working to protect Australia’s biosecurity by developing new tools for faster, more efficient border diagnostic services.

Each year, between 20 and 40 percent of crops are lost to plant pests and weeds globally. Weed infestations have a devastating impact on primary production and the natural environment and are estimated to cost Australia billions of dollars each year.

Many of the world’s 25,000 species of daisies are aggressive weeds. Around 1,000 daisy species are native to Australia, but many others occur here as invasive weeds, including dandelions, cudweeds, thistles, bitou bush and fireweed. Daisies are especially effective weeds and the seeds of many species spread very easily on the wind.

Daisy seeds can accidentally enter Australia at our air and sea ports on cargo such as containers, cut flowers, machinery and cars. When daisy weed seeds are intercepted at our borders they need to be identified quickly and accurately. Are the seeds a new weed risk, a native species or a weed that is already established here? Does the shipment need to be put through an expensive and time-consuming cleaning process?

Herbarium specimen of <em>Chrysanthemoides monilifera</em> subsp. <em>rotundata</em>.

Herbarium specimen of Chrysanthemoides monilifera subsp. rotundata, which is included in the daisy weed seed key.

The seeds of weedy daisies can be difficult to identify. Around 40 per cent of seeds that are found during quarantine inspections belong to daisies. Before our weed seed key, around one in five of these seeds couldn’t be accurately identified. Daisies can cost businesses money when their seeds delay shipments from entering the country.

The Australian National Herbarium in Canberra has a collection of expertly identified daisies, native species and weeds. Stored pressed on archival paper sheets, many of these specimens were collected during or after fruiting and contain seeds within the flower head. Using the Herbarium’s collection, supplemented by loans from other institutions and visits to overseas herbaria, we created an interactive, visual key that enables the seeds of weedy daisies to be easily identified. After a recent update, the key includes 98 species of biosecurity importance.

Unlike traditional single-entry identification keys, our weed seed key6 presents all relevant seed characteristics to the user, illustrated with diagrams and photos. This allows biosecurity officers to use whatever seed features they have found, even if part of the seed is missing.

The development of the key was an initiative of the ON program, Australia’s sci-tech innovation accelerator. It was co-funded by CSIRO and the Department of Agriculture and Water Resources (DAWR). DAWR uses the seed key when quarantine inspectors at Australia’s borders send daisy seed samples to be identified by DAWR’s scientific support staff. The key helps stop new weeds becoming established in Australia and prevents existing weeds being strengthened by new genetic diversity.

  1. Success measures that observations were able to be completed. Encompasses all time allocated to astronomy observations, and allows for planned and unplanned non-availability e.g. maintenance, upgrades, weather events, etc.    
  2. Includes time lost through malfunction on fully operational facilities, but not commissioning time for new equipment or facilities.
  3. Successful research days from a possible 180 days (appropriation funded component), where success means the science was able to be completed consistent with the voyage objectives and allows for planned and unplanned non-availability e.g. maintenance, upgrades, weather events, etc.
  4. Includes time lost through malfunction on fully operational facilities, but not commissioning time for new equipment or facilities.
  5. 5 Excludes ATSC and ANACC because the function of these collections is a supply service, not coverage.
  6. The key is available online at http://keys.lucidcentral.org/keys/v3/daisy_fruit/

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