CSIRO hosts National Research Infrastructure on behalf of the broader scientific community to assist with the delivery of research. 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
  • The Australia Telescope National Facility (ATNF) comprising:
  • The Parkes telescope, NSW
  • The Compact Array telescope, Narrabri
  • The Australian Square Kilometre Array Pathfinder (ASKAP), Murchison
  • The Mopra telescope at Coonabarabran
  • The Murchison Radio Observatory
  • The Marine National Facility (MNF), Hobart
  • Pawsey Super Computing Centre in Perth.

The National Research Collections Australia, including the Atlas of Living Australia, 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.

This year our national facilities and collections program continued to perform well. Table 2.11 provides an overview of the results against each performance criterion as published in the PBS, followed by a more detailed analysis and evidence for each of the facilities and collections.

Table 2.11: PERFORMANCE SUMMARY FOR PROGRAM 1.2

PERFORMANCE CRITERION

RESULT

National research infrastructure maintained and operated to appropriate standard

We achieved compliance with relevant Australian and internationalstandards.

New users of the ATNF telescopes are required to observe from the Science Operations Centre at the ATNF’s headquarters in Sydney, where they are provided with training and support. Once qualified, astronomers can also operate Parkes or the Compact Array from their home institutions.

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

Maintain or increase the proportion of collections available to researchers and the public, including digitised and non-digitised collections

The national biological collections continued to increase in size and representation and overall the proportion of the collections that are digitised also increased particularly in ATSC and ANIC. The ANACC maintained 100% digitisation.

Analysis of our performance

The national research infrastructure CSIRO hosts is of global significance, and is used by the international and Australian research communities. Increasingly, major facilities and instruments are beyond the capacity of a single entity to run. This gives rise to multinational, interdisciplinary and applied research institutions collaborating and co-investing in resources. These arrangements present opportunities of efficiency, effectiveness and sustainability, but can also present challenges regarding their use.

Additionally, science is experiencing rapid growth in the application of digital technologies and data digitisation in international natural history collections. CSIRO will continue to manage the national collections employing digital and genomic technologies to provide rapid access to comprehensive and reliable data.

In 2016, CSIRO engaged with the 2016 National Research Infrastructure Roadmap process under the leadership of the Chief Scientist. In 2017, CSIRO will continue to advocate for the ongoing development and upgrade of key facilities in the national interest.

The following sections give an overview of the activities at CSIRO’s National Facilities and Collections and additional details for each criterion where relevant.

Australian Animal Health 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 public, from exotic and emerging infectious diseases. 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 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 emergency 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.

The AAHL is funded primarily by CSIRO appropriation. DAWR provide funding for an ongoing diagnostic service, and the National Collaborative Research Infrastructure Strategy (NCRIS) has provided funds to enable universities 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.

The AAHL 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. From July 2017, AAHL will formally be able to service a wider customer base that delivers benefits not only to the agriculture sector, but also in the health and defence sectors.

Examples of services offered include:

  • 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 works to upgrade and reinforce many of its existing external security access systems occurred following a security review in 2014–15. Ongoing minor infrastructure works to replace end-of-life plant have included completion of clean steam generator upgrades, replacement of water softener systems and replacement of SCADA (System Control and Data Acquisition) network switches. 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.

In May 2017, the World Organization for Animal Health (OIE) General Session in Paris confirmed the designation of AAHL, the University of Melbourne and Massey University, New Zealand, as OIE Collaborating Centres for Diagnostic Test Validation Science in the Asia Pacific region.

Each year, AAHL analyses samples from around 3,000 cases for diagnostic testing. 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.

An example of the preventative or ‘insurance’ work of AAHL is foot-and-mouth disease (FMD). Every month AAHL receives samples to confirm the exclusion of FMD, collected by field veterinarians in Australia – a critical service to our livestock industries. This is because FMD is a highly contagious animal disease and an outbreak in Australia would cause major production losses. A FMD outbreak would seriously interrupt Australia’s international livestock trade and cost the economy tens of billions of dollars. If FMD were diagnosed, the government’s National Response to a Foot and Mouth Disease Outbreak would be enacted and AAHL, which was built to cope with an FMD outbreak, would lead the national laboratory response.

Emergency response to white spot disease

The diagnostic skills and knowledge of AAHL scientists, including specialists in the diagnosis of disease in aquatic animals, is an important component of Australia’s ability to deal with an emergency animal disease outbreak.

In late November 2016, white spot disease was identified in a commercial prawn farm in Queensland. Until that time, Australia was one of the few countries in the world with a prawn farming industry that had remained free of the highly contagious viral infection that affects crustaceans. With the Australian prawn industry having a gross value of prawn production worth $413 million in 2015–16, and employing 5,000 people, it is of national significance to control disease outbreaks.

AAHL received the first sample of suspected white spot disease from Queensland Biosecurity on 30 November 2016 and confirmed the disease within 24 hours. AAHL confirmed a second property as being infected on 6 December, with a third property, along with six samples from the Logan River being confirmed positive on 8 December. A fourth property was confirmed infected on 14 December and a fifth on 29 December 2016. Two more properties were confirmed as infected on 3 and 13 February 2017.

During December 2016, AAHL received an all-time monthly high of over 1,000 submissions and 21,000 samples for testing. The AAHL team responded quickly and effectively to the surge in testing demand not only for this outbreak but all the other diagnostic submissions received in the same period.

The Queensland Department of Agriculture and Fisheries has completed its work to drain and decontaminate all seven prawn farms hit by white spot disease on the Logan River. They now carry out ongoing surveillance and biosecurity management within the Queensland Movement Control Area.

The national Aquatic Consultative Committee on Emergency Animal Diseases, of which CSIRO is a member, continues to meet regularly in response to this outbreak. Based on current information and good progress, the committee maintains the view that the disease can be eradicated. Since the start of the outbreak, AAHL has conducted over 58,400 tests for white spot disease on 22,500 samples.

AAHL’s ability to rapidly diagnose disease and confirm suspected outbreaks is an important capability supporting Australia’s biosecurity system. Our work protects the health of Australia’s aquaculture species, wildlife and livestock to ensure the competitiveness of Australia’s agriculture and trade.

Prawn with white spot disease.  ©Biosecurity Queensland

Australia Telescope National Facility

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 2016–17, 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 Parkes and all observing time on the Mopra telescope was funded by external partners. ATNF observatories also contain other instruments: the Murchison Radio-astronomy Observatory, home to ASKAP, also hosts the Murchison Widefield Array 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.

The 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 antennae, 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.

Maintenance and operations

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.

Early science with the ASKAP in Western Australia commenced in October with 12 antennae fitted with the enhanced second generation of CSIRO’s multi-award-winning phased-array feed (PAF) receivers. Observing with ASKAP is currently performed by CSIRO staff. Thirty ASKAP antennae are fitted with PAFs and commissioning of these continued during the year. We continue to manufacture and install the remaining receivers to complete the full 36-antenna array.

Several times each year, ATNF telescopes are linked with other telescopes in Australia and overseas, and sometimes CDSCC antennae, as part of the LBA. This enables improvement – by a factor of several thousand – in the detail in resulting images.

In 2016–17, research teams of more than 540 astronomers from more than 25 countries submitted proposals to use ATCA, Parkes and the LBA. For ASKAP, 10 major survey science projects, representing 363 investigators from 131 institutions, were awarded 75 per cent of observing time in the first five years of full operation. Most of the observing time on Mopra is allocated to a consortium of universities that fund its operation.

Observers on ATNF telescopes other than ASKAP have an 18-month period after the observation during which they have sole access to their data. After this, the data are made publicly available to astronomers worldwide. Data from ATCA, Mopra, Parkes and LBA are archived on the Australia Telescope Online Archive and most Parkes data from pulsar observing is archived on the CSIRO Data Access Portal. ASKAP data has no proprietary period and is released into the Science Data Archive as soon as it has passed quality assurance checks.

Metrics for time allocation are calculated by dividing the time awarded to an observing project by the number of members in that observing team. Figures for 2016–17 include the merit-based allocation for ATCA and Parkes. Time allocated to observations dropped slightly this year as an increased amount of time at Parkes was used for testing new receivers and upgrades to the telescope.

Table 2.12: Utilisation of the ATNF, in %

2012–13

2013–14

2014–15

2015–16

2016–17

Time allocated to observations

76.7

76.8

76.3

77.5

72.3

Time lost to equipment failure

2.7

3.3

2.2

3.0

2.0

Time allocated to CSIRO staff

22.0

19.0

22.5

21.5

24.0

Time allocated to other Australian researchers

28.0

30.3

28.4

33.6

30.3

Time allocated to international researchers

50.0

50.7

49.1

44.9

45.7

Tech leaps prime telescopes for discovery

The ASKAP telescope finished the first chapter of its story this year with the completion of the basic construction, and embarked on the next phase, which will dominate its work for many years – collecting data for big survey projects.

ASKAP commenced observations in October 2016, for the Widefield ASKAP L-Band Legacy All-sky Blind survey (WALLABY), a giant census of galaxies. By the end of the year, researchers had gathered more than 400 hours of data. WALLABY detects atomic hydrogen gas, which galaxies draw on to form stars. This gas can show how galaxies interact, for plumes of it are stripped off as they wrestle and collide.

To understand the WALLABY galaxies’ star formation rate, total mass and dark matter content, the team will use complementary data from other southern hemisphere telescopes, such as CSIRO’s Compact Array and the optical telescopes of the European Southern Observatory. In future, ASKAP will also work with SKA-mid antennae of the Square Kilometre Array based in South Africa.

WALLABY is a big project. It will detect more than half a million galaxies, 20 times more than the total found by similar surveys to date. A survey this size is possible with ASKAP because of the telescope’s PAFs, a kind of ‘radio camera’ that gives the telescope a field of view 60 times the size of the full moon.

In the 1990s, CSIRO’s Parkes telescope carried out another survey of atomic hydrogen in galaxies, smaller than WALLABY, but ground-breaking for its day. It too was made possible by unique CSIRO technology, the Parkes multi-beam receiver. The multi-beam system proved so successful that CSIRO has now built variants for other telescopes around the world, including FAST, China’s new 500-hundred-meter Aperture Spherical radio Telescope. The FAST multi-beam receiver was completed and handed over to China this year.

In 2007, a scientist using the Parkes multi-beam data made an extraordinary discovery: a super-strong burst of cosmic radio waves lasting just a few milliseconds. Two dozen of these fast radio bursts (FRBs) have now been found. They appear to come from far across the Universe and signpost extremely powerful, still unknown phenomena. So far only one FRB has been located precisely enough to link it to a specific galaxy.

Due to its excellent instrumentation, Parkes has discovered most of the known fast radio bursts, but it will soon cede its crown to ASKAP, which recently found its first fast radio burst after less than four days of searching, followed by an additional two detections. This rapid rate of discovery is made possible by the telescope’s large field of view, setting ASKAP up to become a world leader at detecting fast radio bursts. By working with the Compact Array and the European Southern Observatory’s large optical telescopes, it will also be able to pinpoint their locations, and thus answer the decades-old question about where fast radio bursts originate.

CSIRO’s Australian Square Kilometre Array Pathfinder radio telescopes in fly’s eye mode. Usually dishes all point at one part of the sky, but they can be made to point in different directions, like the segments of a fly’s eye, when searching for fast radio bursts. Image: Kim Steele

We acknowledge the Wajarri Yamatji people as the Traditional Owners of the Murchison Radio-astronomy Observatory site.

Marine National Facility

The Marine National Facility (MNF) is a key element of Australia’s research infrastructure. The 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.

Access to the vessel is offered through two streams: MNF Granted Voyages (GV) and MNF User Funded Voyages (UFV). GV 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, within the primary schedule, to be made available to research organisations and their collaborators under a charter arrangement. UFV recipients pay for sea time, with the cost established via an assessment of the national benefit and the risk posed by the proposal.

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

Maintenance and operations

The new model of interdisciplinary science voyages spanning atmospheric, oceanographic, biological and geoscience research has brought with it new challenges for the MNF with regard to health, safety and the environment. To meet these challenges, the MNF completed a detailed review of its health and safety systems in 2016–17 to ensure that new and existing risks were identified and adequately mitigated. As a result of the review, the MNF introduced a range of new processes and controls to ensure that the work conducted on board causes no harm to people or the environment.

This year saw the successful introduction of a new expert panel to assist with the assessment of applications for GV. The National Benefit Assessment Panel is tasked with assessing applications and the contribution to the national benefit in parallel with the Science Advisory Committee’s assessment of science excellence and the science team’s ability. The expertise brought to bear by the panel builds on the MNF’s robust framework of governance designed to ensure sea time is awarded meritoriously.

Several voyages undertaken this period have highlighted the public interest in Investigator and the science operations conducted on board. Significant national media coverage was achieved during the:

  • Reef2Rainforest research voyage to the Great Barrier Reef, led by Professor Zoran Ristovski, Queensland University of Technology
  • 51-day Totten Glacier research voyage, led by Associate Professor Leanne Armand, Macquarie University
  • Sampling the Abyss voyage led by Dr Tim O’Hara, Deputy Head of Marine Sciences, Museums Victoria.

Investigator provides a platform for the next generation of Australian marine researchers, not only through student participation in the majority of voyages, but through the pilot program – Collaborative Australian Postgraduate Sea Training Alliance Network (CAPSTAN) led by Macquarie University. The MNF Steering Committee has awarded one voyage per year over the next three years for the pilot. A high-level voyage planning process commenced in late 2016, soon followed by a call for trainers and students in early 2017. The program gives 25 Australian postgraduate marine research students a unique opportunity to obtain blue-water research experience. The program aims to establish a national syllabus incorporating marine industry safety and survival training certification. The inaugural CAPSTAN voyage will commence on Investigator in November 2017.

The MNF was successful in securing two UFV to fill remaining days available outside of those funded by the Australian Government for GV in 2016–17. The first of these, delivered by CSIRO Energy in a collaboration with Chevron, conducted research in the Great Australian Bight. The second, with the Australian Hydrographic Survey (AHS), was delivered during May 2017 to conduct bathymetry in an area of Bass Strait. The relationship with AHS is a key strategic relationship for the MNF, with further opportunities possible for 2017–18.

Table 2.13: Utilisation of the MNF

2014–15

2015–16

2016–17

Research days scheduled

44

248

234

Research days delivered

44

248

234

Scientist days possible

1,300

9,110

9,600

Scientist days delivered

947

8,549

7,707

Time allocated to CSIRO researchers (%)

61

63

26

Time allocated to other Australian researchers (%)

39

37

74

Delivering a world-first biodiversity survey of the abyss

The marine life at abyssal depths (>4000m) along Australia’s eastern coastline is little understood. The lack of baseline data about species and their distribution makes it difficult to set policy and measure change. A core mission of Investigator is to collect high-quality data to reliably inform decision-making by community, industry and government, in particular those shaping environmental research and policy.

In May and June 2017, Museums Victoria led a 31-day voyage on Investigator to conduct the first dedicated survey of marine life and the geophysical features of the abyss from Tasmania to Queensland. The voyage involved 38 scientists and support staff from seven countries and 14 institutions, including CSIRO, Museums Victoria, Australian Museum and the UK’s Natural History Museum.

A broad range of research was undertaken during the voyage using a wide suite of the MNF scientific equipment, including deep water biodiversity sampling using nets, sleds and underwater cameras as well as processing, sampling and analysing specimens recovered using the ship’s on-board laboratory facilities.

Almost 5,000 specimens were collected with over one third of the invertebrates thought to be new species. New vertebrate species will require description and be housed at museums and institutions across Australia, providing future material for research and study.

Highly detailed sea floor bathymetry surveys were also completed in seven marine reserves for the managing authority, Parks Australia. Better understanding of these habitats will assist Parks Australia to manage these important but little understood parts of our national marine assets.

Weird and wonderful deep sea species, such as this spiny crab, were discovered during RV Investigator’s Sampling the Abyss voyage.  ©Asher Flatt

The bathymetry voyage also surveyed marine debris and micro-plastics encountered in surface waters and from abyssal depths. This research is only possible due to the space and flexibility that Investigator offers. The information gathered from this project will contribute to better understandings of the impact of human activity on natural environments far removed from cities and homes.

Investigator demonstrates the value of the MNF as an international collaboration hub for knowledge exchange between scientists and, importantly, between scientists and the public. The significant public interest this voyage generated means that the data collected are already having an impact. Using the ship’s communication and broadcast capabilities, the science and discoveries were shared in the media during the voyage and reached a combined global audience in the millions. This increases awareness of life in our deepest oceans and how human activity can impact on it.

Pawsey Supercomputing Centre

CSIRO owns and operates the Pawsey Supercomputing Centre (Pawsey), one of two Australian high-performance computing facilities enabling Australia’s commitment to the solution of ‘Big Science’ problems. The Centre provides access to one of the most powerful supercomputers in the Southern Hemisphere for researchers in government, academia and industry. Pawsey is currently serving over 80 organisations and achieving unprecedented results in science domains including radio astronomy, geosciences, resources engineering, bioinformatics and health sciences.

The Centre is located at CSIRO’s Kensington site and offers advanced data-storage capabilities and tools critical to processing, storing and analysing the data, including from CSIRO’s ASKAP facility and the Murchison Widefield Array, run by Curtin University. Pawsey also partners with the International Centre for Radio Astronomy Research to curate and publish the data for the international research community.

Pawsey is a collaboration hub involving an unincorporated joint venture between the Australian Government represented by CSIRO, the Western Australian Government and university partners (Curtin University, Edith Cowan University, Murdoch University and the University of Western Australia) in a consortium. Rather than a single-service agency, Pawsey is focused on providing integrated research solutions by giving users access to world-class expertise and infrastructure in supercomputing, data and visualisation services.

Pawsey is governed by a Board comprised of core member representatives and several independent members, including the chairman. Its primary funding partners are the Australian Government Department of Education and Training, the Minister for Science (WA Government) and the Pawsey members. To 30 June 2017, Pawsey hosted seconded staff from all five member organisations.

Maintenance and operations

Pawsey provides access to its supercomputing resources (Cray XC40 Magnus and Cray XC30 Galaxy) through a number of national and stakeholder merit allocation schemes. These schemes were for the 2016–17 period:

  • 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.
  • Geosciences Merit Allocation Scheme and 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 made available with small (<0.1 per cent of available resource time), 3-month allocations.
  • Radio-astronomy operational commitment – 25 per cent of Pawsey resources allocated (100 per cent of Cray XC30 Galaxy). Priority access to these resources was to support MWA operations and ASKAP commissioning. Additional radio-astronomy science projects were allocated where resources were available.
Table 2.14: Allocation of the Pawsey supercomputers and data storage in %

SUPERCOMPUTERS ALLOCATION

2015–16

2016–17

NCMAS

15

25

Focused domain (Geoscience)

25

15

Partner share (allocated through merit process)

30

30

Director’s discretion

5

5

Radio astronomy (ASKAP and MWA)

25

25

DATA STORAGE ALLOCATION

Radio-astronomy

80

80

General science

20

20

Pawsey helps researchers power the world with waves

It’s a given that supercomputers are powerful, but for most people the terms ‘powerful’ and ‘supercomputer’ rarely offer up any context. This year, the supercomputers of Pawsey helped over 80 organisations undertake everything from investigating the genetic compounds of an insect that is destroying African crops, to supporting the Australian radio telescope precursors to the Square Kilometre Array.

Pawsey’s supercomputer has played an important role in assessing something many across the globe are monitoring – wave energy. If wave energy can be successfully harnessed we will have an infinite, sustainable energy source on our hands. The people closest to making it happen, the team at Carnegie Clean Energy (CCE) are relying on Pawsey’s supercomputer, Magnus, to achieve this.

Throughout this year, researchers from CCE and its partner, the University of Western Australia’s Centre for Offshore Foundation Systems, used Pawsey to simulate the environments their wave farms face in real-world climates. Their High End Computational Modelling of CETO Wave Energy Converter project, conducted on Magnus, studies the wave interaction of wave energy converters in the ocean. Researchers use code to remotely access Magnus and allow it to process complicated calculations and answer complex questions such as how weather extremities influence the wave farms and their energy outputs to the grid.

Much progress has been made in the last 12 months. Simulations from Magnus have allowed the teams to increase the amount of energy captured (up 50 per cent) by moderate waves and improve their device’s chances of survival in extreme waves.

An array of CETO devices tethered to the sea floor.  ©Carnegie Clean Energy

It is complex work, but one with many pay offs. The computational fluid dynamics (CFD) simulations have been used to improve predictions of day-to-day device performance and boost reliability of the energy-generating devices in large sea areas. Those outcomes will help CCE reduce the running costs of its innovative equipment, while increasing its lifespan in the ocean.

Were it not for the facilities at the Pawsey Centre, CCE’s work would have looked very different. Traditionally, such outcomes would have been achieved via wave basin (field) testing, but due to the CFD capabilities of Magnus, simulations were able to deliver the same outcomes much faster and at a far lower cost.

Of course, ‘fast’ in a project like this is relative. Even with Magnus’ power, the project has been time-consuming. This year alone the project used more than two million core hours on Pawsey’s supercomputer.

National Research Collections of Australia

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 a number of 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. NRCA also hosts the NCRIS supported Atlas of Living Australia (ALA), a modern 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.

Digitisation is important to making biological collections widely available. It can span capturing a specimen’s metadata through to including images and genomic information. NRCA is deploying a new collections-management system in the Australian National Insect Collection (ANIC) and Australian National Herbarium (ANH) that will lead to increased efficiency and security in data handling. Improvements made to digitisation processes within the collections have also delivered reductions in the cost and time it takes to digitise specimens.

Maintain or increase the collections available and utilised

This year, the ANH contributed to national and global research through loans and exchanges with more 46 herbaria in 18 countries. The ANH-developed Weed Seed Key is helping the Department of Agriculture and Water Resources (DAWR) staff to rapidly identify weed biosecurity risks for imported cargo. A new collaboration with the Gas Industry Social and Environmental Research Alliance (GISERA) is developing novel approaches to the conservation and management of rare plants. More than 80 per cent of specimen records are digitised and available through the Virtual Herbarium and the ALA. Imaging of all ANH type specimens (>9,000) has been completed, with images now publicly available through the Global Plants Initiative hosted by the digital library JSTOR.

This year ANIC hosted almost 100 national and international researchers and loaned more than 10,000 specimens. Two DAWR staff work as part of ANIC to identify hundreds of insects intercepted at Australia’s borders each year. In 2016–17, ANIC reviewed Australia’s biosecurity diagnostic system and ran training courses that build national biosecurity capacity. A large-scale project was launched focusing on the digitisation of more than 36,000 specimens of Australian bees and 7,500 Australian wasps, which represent important pollinator groups for both native plants and crops. The records are being transcribed by digital volunteers though the DigiVol portal and will be made available for collection management and research outcomes.

The Australian National Wildlife Collection (ANWC), especially its cryo-frozen tissue collection, is a major research resource for the international community, with 416 samples sent for DNA sequence-based research during 2016–17. ANWC digitised 4,420 specimens and 2,401 genetic samples. These primarily involved bird specimens collected from the savannas of Papua New Guinea and northern Australia, and herpetology specimens from Papua New Guinea and northern Australia donated by researchers at the Australian National University. The ANWC subfossil collection was also digitised, adding 785 records to the database. A research project into the feasibility of eggshell thickness as an indicator of environmental stress resulted in the digitisation of 827 clutches of eggs.

The 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 2016–2017, ANASS supplied a total of 330 living microalgae cultures to 89 customers (71 per cent Australian and 29 per cent international). Core culture and accession information is digitised for all ANACC specimens, while 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 2016–17, ATSC filled 86 seed orders (49 per cent Australian and 51 per cent international) to 68 customers. This year, ATSC focused on digitising archival records. Fifty per cent of germination sheets and record cards have been scanned to PDF and are now searchable from the ATSC’s web-served database.

The 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. Work has 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 Atlas of Living Australia is recognised as a global biodiversity platform, adopted by 10 countries around the world. It is also the primary mechanism through which NRCA’s digitised biological collection data is made freely available. The Atlas holds more than 70 million records provided by partnering with museums, state and local governments, non-government organisations, universities and CSIRO. During 2016–17, 3.6 billion records were downloaded for uses in education, research and management. Approximately 88 million of the records downloaded were provided by NRCA.

TABLE 2.15: COMBINED UTILISATION OF NATIONAL RESEARCH COLLECTIONS1

USE OF NRCA

2012–13

2013–14

2014–15

2015–16

2016–17

Number of specimens dispatched

13,660

30,514

20,156

18,588

16,946

Outward-going loans

153

222

171

177

143

Tissue samples sent

2,415

8,461

4,033

2,884

3,032

Tissue sample grants

74

34

61

74

58

Number of visitors hosted

417

404

329

Total visitor research days

651

1,018

828

Number of tours hosted

90

126

116

Total number of visitors on tours

695

888

1,133

TABLE 2.16: DIGITISATION OF THE NATIONAL BIOLOGICAL COLLECTIONS

COLLECTION

PROPORTION DIGITISED (%)

2012–13

2013–14

2014–15

2015–16

2016–17

Australian National Insect Collection

5.0

5.0

5.0

5.0

5.3

Australian National Wildlife Collection (excluding sound archive)

92.0

92.0

92.0

99.9

96.0

Australian National Fish Collection

100.0

100.0

85.0

85.0

85.0

Australian National Herbarium

76.0

76.0

76.0

80.0

80.0

Australian National Algae Culture Collection

-

-

100.0

100.0

100.0

Australian Tree Seed Centre

67.0

68.0

70.0

70.0

75.0

Digitising the bees of the Australian National Insect Collection

Biodiversity and food security depend on pollination of native plants and crops. Globally, pollinators are in decline due to habitat changes such as land clearing, habitat fragmentation, pesticides, diseases and climate change. Bees play a particularly vital role in pollination. While the European honeybee is the most well-known, Australia has more than 1,500 species of native bees that, alongside other insects, birds and even some mammals, actually pollinate the majority our native plants and agricultural crops.

The ANIC in Canberra holds more than 50,000 bee specimens collected from across the continent during the past 80 years. These specimens tell us where different species live, whether their distributions have changed over time and often what plants they lived on and pollinated. This information is crucial to predicting future trends in pollinator abundance and activity and the implications for both native biodiversity and pollinator-dependent industries.

To maximise its value for research, CSIRO is undertaking a project to digitise its collection using high-resolution imaging and capturing metadata. So far, the bee digitisation project has captured information from 36,000 bee specimens, unlocking the rich biodiversity information held in the National Research Collections Australia and making it freely available to both the research and industry communities. CSIRO is using volunteers and students as the workforce behind the digitisation program. The project has built core capability among volunteers and casual staff in digitisation and curation.

To implement innovative methods to rapidly digitise ANIC’s collection of 50,000 bee specimens, the team sought help from citizen scientists, strengthening community involvement and increasing scientific awareness and knowledge about biodiversity. Citizen scientists transcribed ANIC’s bee specimen labels using the online volunteering portal DigiVol, a collaboration between the Australian Museum and the Atlas of Living Australia.

A native blue-banded bee, collected in 1971, still has pollen stuck to its legs.

CSIRO is also collaborating with external parties to assist the digitisation effort and to accelerate the delivery of data held within the National Research Collections Australia. Prior to commencing this digitisation project, CSIRO partnered with the Australian Museum to curate ANIC’s bee collection. Taxonomic classification requires detailed knowledge and is a skill essential to managing Australia’s biodiversity into the future.

CSIRO’s bee digitisation project has added to knowledge about the distribution and diversity of Australia’s bees. It is part of a worldwide effort to understand bee diversity that includes partners such as the Smithsonian National Museum of Natural History. Access to CSIRO’s digitised collection data is available through the Atlas of Living Australia. The bee digitisation project has significantly increased the proportion of the National Research Collections Australia that is available for research, education and policy making. The project delivered productivity gains in collection specimen digitisation in a very short time, with costs being reduced from $4 or $5 per specimen to around $1 per specimen (excluding salaries).

  1. Excludes ATSC and ANACC, because the function of these collections is a supply service, not coverage

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