From planets to pandemics: translating science in challenging times

After years of building NCRIS enabled software to address geodynamics problems, researcher and AuScoper from The University of Melbourne, Rohan Byrne, found an opportunity to turn his Everest code to help model COVID-19 mobility data during Melbourne’s 2020 and 2021 lockdown periods. Here, Rohan shares his story.

JC — Rohan, please tell us what you usually do as a planet builder?

RB — I use big computer simulations to study how the hot rocks deep beneath us shift and flow over billions of years. I’m trying to understand why planets that are born the same — like Earth and Venus — can go on to lead very different lives. And I want to apply that knowledge to the thousands of Earth-like planets we’ve discovered beyond our sun, to try to get a sense of whether ‘living’ planets like ours are common or rare in the universe.

It’s a big topic with many unknowns. In other fields with heaps of mysterious quantities, researchers try to cover their bases by running lots and lots of similar-but-different models. But I needed to run thousands of models, and no-one had done that before in my field.

The toolkit just wasn’t there, I had to create my own. The result was PlanetEngine, a ‘wrapper’ around AuScope’s Underworld geodynamic modelling code that makes it easier to orchestrate big, complex jobs.

“It slashed the labour required to do my research — but it wound up being the beginning of an even stranger journey.”

A snapshot of one of thousands of mantle convection models run by PlanetEngine so far; colour represents temperature, arrows are velocity, and contours show viscosity on a log scale. Image: Rohan Byrne

A snapshot of one of thousands of mantle convection models run by PlanetEngine so far; colour represents temperature, arrows are velocity, and contours show viscosity on a log scale. Image: Rohan Byrne


JC — What made you think of applying your code to new problems outside of geoscience?

RB — My eyes were really opened at the 2019 Australasian Leadership Computing Symposium (ALCS) led by the AuScope peer, the National Computational Infrastructure (NCI) in Canberra, 2019. Meeting so many wonderful people in diverse fields — from pharmacology to astrophysics — I was struck by the similarities of the challenges we faced.

“We have amazing resources in this country, but we struggle to make good use of them. And though we know we need to make our data FAIR, we can’t seem to find the hours in the day to do it. It’s part of what I call the ‘complexity crunch’, and I think it’s a big problem.”

I presented my work at ALCS and was totally overwhelmed by people’s positivity. There was a clear, strong appetite for creative and cross-disciplinary solutions. I took home best-in-stream and spent the summer ripping the guts out of PlanetEngine. That was the beginning of Everest: my attempt in code to tackle the ‘crunch’ for scientists of all stripes.


JC — How did you take the first leap into that journey? 

RB — Well, we all know what happened next. The pandemic hit and I found I just couldn’t concentrate on my thesis anymore. I emailed the Doherty Institute and the next thing I knew, I was part of a cross-faculty team advising the government on pandemic control.

Australian cities had been slammed into lockdown but we had no way of seeing the effects. It became my job to turn an ocean of Facebook user location data into a daily-updated Crisis Mobility Data Portal that would reveal whether the policies were holding in real time.

Melbourne’s journey through 2020 shown in the Crisis Mobility Data Portal; the red line shows COVID-19 cases, while the blue line shows the ‘mobility score’, a measure of lockdown effectiveness. Image: Rohan Byrne

Melbourne’s journey through 2020 shown in the Crisis Mobility Data Portal; the red line shows COVID-19 cases, while the blue line shows the ‘mobility score’, a measure of lockdown effectiveness. Image: Rohan Byrne

Using Everest, I was able to get our app up and running in six weeks flat. It remains today the only public-access resource for mobility tracking in this country.


JC — Four lockdowns later, how did you go? 

RB — What started as a sprint became a marathon. Along the way, I met some great people – like Dr Jason Thompson from Melbourne’s Faculty of Architecture, Building and Planning, one of the social modellers behind Victoria’s “roadmap” out of lockdown of September 2020.

“Jason and I had both been involved in the scientific response to COVID-19 from the early days. Comparing notes, we quickly agreed that the pandemic had revealed a big problem: science is just too slow. The ‘complexity crunch’, once an inconvenience, had proved deadly in a crisis.”

That experience went on to inform the University of Melbourne’s entry into the Trinity Challenge, a new international coalition which aims to fortify societies against future health emergencies using novel data-driven approaches. Dubbed CrisisEngine, our contribution— a powerful new agent-based ‘social model’ built with Everest — is in part a continuation of the journey that began all those years ago with PlanetEngine. The University’s proposal was awarded an honourable mention in the Challenge’s highly competitive first funding round and is now moving into formal development.

A snapshot from the early development of CrisisEngine. Blue particles represent individual humans; red particles are active COVID-19 cases; yellow particles are recovered cases. Image: Rohan Byrne

A snapshot from the early development of CrisisEngine. Blue particles represent individual humans; red particles are active COVID-19 cases; yellow particles are recovered cases. Image: Rohan Byrne


JC — What response has your work evoked?

RB — I’ve been really humbled by the response. The Age, the Herald Sun, 3AW radio, and Channel 7 have all featured the Crisis Mobility Data Portal at different times, and thousands of citizens have shown their support in person and through social media.

“Our conviction from the beginning has been that seeing is believing: that data, when it’s open and visible, can change the world.”

I’ve had complete strangers thank me for helping them through the lockdowns — just being able to see the city’s response on a line graph has been proof enough for many that we really are ‘all in this together’.


JC — What excites you most about your experience?

RB — The pandemic has been a real shock to the system. There’s electricity in the air; things that concerned us before seem trivial. People joke about ‘dark times’, but the jokes aren’t funny anymore.

“The good news is that we have science on our side. The universities’ response to COVID-19 has outed a secret army of restless talent. Now it’s up to AuScope and all of our NCRIS colleagues to give that army an arsenal equal to the fight. Whether it’s CrisisEngine modelling disasters in real time, or the Downward Looking Telescope unearthing the materials for a sustainable future — if we build it, society will use it. That’s how we make a difference.”


JC — What would you like to see happen in the future to enable more transdisciplinary research like this? And, what’s next for you?

RB — For me, my immediate future is my thesis. I have to capture what I’ve learned, package the capability I’ve developed, and share it everywhere I can.

Beyond that, it’s clear that the academy can’t afford the luxury of disciplines anymore. At the University of Melbourne, Earth Sciences has just been merged with Geography: another crisis, another opportunity.

“But it’s communities of methodology like NCRIS, NCI, ARDC, AARNet, and Melbourne Connect that will have to shoulder most of the burden: providing the training, networking, advocacy, and — yes — the money that will make transformative, translational research possible.”

If we do this right, we will retire with pride in a much better world than this one.

Dr Stuart Newman

Therapeutic Innovation Australia

Since completing a PhD in Antarctic Biology from the University of Tasmania, Stuart has built up considerable experience of science policy, pharmaceutical R&D, grant funding, IP management, business development and commercialisation in the university and not-for-profit sectors.|

Stuart joined TIA as CEO in 2017. Under his leadership, TIA has focussed investment on the gap between research and development of high-value therapeutics, including pharmaceuticals, biologics, vaccines and cell & gene therapies. He also devised an innovative infrastructure access voucher scheme. He is a graduate of the Australian Institute of Company Directors

Beryl Morris

Terrestrial Ecosystem Research Network

Merran Smith

Population Health Research Network

Merran is the inaugural Chief Executive of Australia’s Population Health Research Network and chairs the PHRN Participant Council. She is a past Director of the International Population Data Linkage Network (2019-2020) and current member of the Pawsey Supercomputing Centre Board.

Merran has an extensive background in science, health, and economics with strengths in strategic leadership and many years’ experience in Australia’s health and research infrastructure systems.  She is well versed in data management and oversaw the WA Department of Health’s Health Information Centre for more than 10 years. While with the Department, she established data linkage as a core service and served on Australia’s peak national health information committees. 

Prof Michael Dobbie

Phenomics Australia

Prof. Michael Dobbie has worked to establish and operate Phenomics Australia since its foundation in 2007, serving as CEO since 2013. Prior to leading the development and implementation of these national research infrastructures, Michael was a biomedical research with a PhD in Neurochemistry from the University of London and gained over 20 Years’ experience at the bench in field including genetics, vascular biology, cancer angiogenesis, neuroscience, metabolism, developmental biology, malaria and oxidative stress.

Mark Stickells

Pawsey Supercomputing Centre

Mark is a research executive with more than 20 years’ experience working at a senior level in innovative research and business development roles in complex, multi-stakeholder environments. Through national and international programs and joint-ventures, Mark had successfully led initiatives to accelerate the impact of research, development and education programs for Australia’s key energy, mining and agricultural sectors.
He is a former Chief Executive of an LNG research and development alliance of CSIRO, Curtin University and UWA, partnering with Chevron, Woodside and Shell. Prior to his appointment at Pawsey Mark led the innovation and industry engagement portfolio at The University of Western Australia. In addition, Mark is the current Chair of the Board of All Saints’ College and was appointed an adjunct Senior Fellow of the Perth USAsia Centre (an international policy think tank) in 2017.

Craig Humphrey

National Sea Simulator

Craig Humphrey has worked at AIMS for more than 25 years. He presently serves as the Director of the National Sea Simulator, a position he has held for the last two years. During the ten years preceding his directorial role, Craig was instrumental in the initial conceptualisation, creation, and implementation of the SeaSim. Prior to joining the SeaSim team, Craig worked as an experimental scientist at AIMS for 15 years, where he conducted research on various projects including fish ecotoxicology, inshore reef biological indicators of water quality, and coral reef climate-related studies.

Wojtek Goscinski

National Imaging Facility

Prof Wojtek Goscinski, with over two decades of leadership in research and innovation, heads the National Imaging Facility (NIF), Australia’s premier imaging network. As CEO, he oversees NIF’s collaboration among universities, research institutes, and government agencies. An Adjunct Professor at Monash University, he contributes to the Faculty of Medicine, Nursing and Health Sciences. Prof Goscinski’s notable past roles include founding MASSIVE, a high-impact national analytics facility. He also serves on the Scientific Advisory Committee for Euro Bioimaging ERIC and has led significant international neuroinformatics programs.

Prof Sean Smith

National Computational Infrastructure

Sean Smith commenced as Director of the NCI in January 2018 and is conjointly Professor of Computational Nanomaterials Science and Technology at ANU. He has extensive theoretical and computational research experience in chemistry, nanomaterials and nano-bio science and technology.

Dr Lisa Yen

Microscopy Australia

Lisa is currently Microscopy Australia’s Chief Operating Officer and has over 15 years of experience in university administration, strategic research management in Centres of Excellence, and operations and management of national collaborative research infrastructure. She has been with Microscopy Australia since 2019. Lisa has a doctorate in cognitive science and a first–class honours degree in psychology.

Tamin Darwish

National Deuteration Facility (ANSTO)

Tamim leads the National Deuteration Facility at ANSTO, managing its operations and scientific advancements. With a Ph.D. in Chemistry, his expertise spans deuterium labeling, NMR spectroscopy, and organic synthesis. Tamim’s research focuses on creating deuterated molecules for advanced analytical techniques. His career includes postdoctoral fellowships and contributions to the field as a member of prestigious science communities and committees. His dedication to chemistry and material science is evident in his extensive work and achievements in the field.

Michael Steer

Southern Coastal Research Vessel Fleet

Professor Mike Steer is the Research Director at the South Australian Research and Development Institute (SARDI), with over 20 years of expertise in marine science. He specialises in fish biology, fisheries science, cephalopod ecology, and fishery reform. Dr. Steer has led numerous research initiatives that have significantly advanced Australia’s seafood industry. He is known for fostering collaborations between academia and industry to address challenges in aquatic ecosystems. Prof. Steer holds a PhD from the University of Tasmania and serves on several national committees, including the National Coastal Research Vessels Working Group and the National Marine Science Committee.

Toni Moate

Marine National Facility (CSIRO)

Toni Moate is Director of the Marine National Facility and Director of CSIRO’s National Collections and Marine Infrastructure business unit. 

Toni is responsible for ensuring CSIRO’s national collections and marine infrastructure programs and research areas are effectively positioned, managed and utilised for long term financial sustainability and support science delivery in the national interest. 

Toni has extensive experience in strategic, financial, project and stakeholder management and has worked for CSIRO for over 30 years. In 2015 Toni was awarded the Public Service Medal for outstanding public service in Australian marine and atmospheric science, as part of the Queen’s Birthday Honours List. This was followed in 2017 when Toni was awarded the Tasmanian Telstra Business Woman of the Year. 

Dr Michelle Heupel

Integrated Marine Observing System

Michelle Heupel, with over two decades in marine science, leads Australia’s Integrated Marine Observing System (IMOS) at the University of Tasmania. Her work, pivotal in deploying oceanic observing equipment, supports marine and climate research. Heupel’s expertise in marine predator ecology, especially sharks, is recognized globally. She has a BSc in Zoology and a PhD in Marine Science, contributing to over 160 scientific papers. Her roles have included Vice Chair of Strategy for the IUCN Shark Specialist Group and advisor for the Ocean Tracking Network. Heupel’s dedication to marine conservation and management reflects her profound impact on the field.

Thomas McGoram

Heavy Ion Accelerators

James Whisstock

European Molecular Biology Laboratory Australia

Professor James Whisstock is based at Monash University, where he is currently an Australian Research Council Laureate Fellow, an Honorary National Health and Medical Research Council Senior Principal Research Fellow and Deputy Dean Research in the Faculty of Medicine Nursing and Health Sciences.

Ceri Brenner

Centre for Accelerator Science (ANSTO - Nuclear Science Facilities)

Andrew Gilbert

Bioplatforms Australia

Andrew Gilbert has been Bioplatforms Australia’s general manager since its inception in 2007.
He is a graduate of the Australian Institute of Company Directors. Andrew oversees the investment of $300 million in Commonwealth Government research infrastructure funding in the discovery sciences of genomics, proteomics and metabolomics.
Andrew has an extensive network of contacts from Commonwealth and State Governments, along with prominent universities, medical research institutes, agricultural research institutes and commercial entities. The Bioplatforms Australia network now supports 4500 users per annum across the spectrum of pure research to commercial production. In addition to managing the national infrastructure network, Andrew has also catalysed the formation of a series of strategic national scientific collaborations.
Each of these projects is by design multi-disciplinary, multi-institutional and contain both discovery implications and pathways to end use.

Prof Pascal Perez

Aurin

Professor Pascal Perez is a specialist of Integrative Social Simulation, using Multi-Agent Systems technologies to explore complex infrastructure systems. He is a Fellow of the Royal Society of NSW and the Modelling and Simulation Society of Australia and New Zealand (MSSANZ). 

Professor Perez has published 200 refereed articles and book chapters. In 2002, he received an ARC-International Linkage Fellowship to develop social modelling research at the Australian National University. In 2006, he co-edited with his colleague David Batten the book ‘Complex Science for a Complex World’ (ANU E Press).

Rosie Hicks

Australian Research Data Commons

Rosie has 20 years’ experience working in Australia’s research infrastructure sector. With a career spanning every aspect of scientific instrumentation from product development and technical marketing to managing multi-user facilities, she works across academic and industry domains to drive innovation and research translation.

Richard Dichmann

Australian Plant Phonemics Facility

Richard is committed to advancing Australian agriculture through strengthening sustainable industry partnerships and creating new business opportunities which capitalise on innovation. His career with Bayer spans more than 25 years and five countries in roles ranging from marketing, technology scouting and sustainability. Hailing from rural Victoria and educated in Melbourne, Richard obtained an honours degree in Forestry from Melbourne University and a master’s degree in Agriculture, focusing on satellite remote sensing, from the University of Sydney. Richard is a graduate of the Australian Institute of Company Directors. As Head of Public and Government Affairs ANZ for Bayer Australia and New Zealand, Richard is dedicated to increasing awareness and understanding among political stakeholders of the critical role innovation plays in meeting the food supply and health challenges of the future. Richard is a proud ambassador for Australian agriculture and is married with four children.

Dr Jane Fitzpatrick

Australian National Fabrication Facility

Jane led ANFF’s Queensland node for a number of years, joining the HQ team as its Chief Operating officer in 2012, before becoming CEO in 2021. Her responsibilities include ensuring the network performs as a cohesive and collaborative community, and maximising ANFF’s ability to support projects from academia and industry.

Prof Andy Hogg

Australian Earth System Simulator (ACCESS-NRI)

Professor Andy Hogg is a distinguished climate scientist leading the ACCESS-NRI, where he oversees the development of Australia’s advanced climate models. As a key figure in COSIMA, he contributes to ocean-sea ice model research. His role as a Chief Investigator at the ARC Centre of Excellence for Climate Extremes underscores his commitment to understanding climate dynamics and extremes. His work is pivotal in shaping Australia’s approach to climate science and modeling, reflecting his dedication to environmental research and innovation.

Jamie Schultz

Australian Centre for Neutron Scattering (ANSTO - Nuclear Science Facilities)

Dr Debbie Eagles

Australian Centre for Disease Preparedness (CSIRO)

Debbie Eagles is currently the Director of CSIRO’s Australian Centre for Disease Preparedness (ACDP). Prior to this, Debbie’s roles with ACDP included 4 years as ACDP Deputy Director and 3 years as the Research Director for the Diagnosis, Surveillance and Response (DSR) Program.

Debbie is a veterinarian by training and a World Organisation for Animal Health (WOAH) Reference Laboratory Expert on Bluetongue Virus. She is also enrolled as a WOAH and Australian Qualified Expert on the UN Secretary-General Mechanism’s (UNSGM) Roster for investigations of Alleged Use of Chemical, Biological or Toxin Weapons, has postgraduate qualifications in veterinary public health and has a special interest in interactions at the field/laboratory interface. Debbie has extensive experience in working in the Asia Pacific region, including in laboratory capacity building projects, in field investigations and through the provision of training courses.

Heath Marks

Australian Access Federation

Heath Marks was appointed by the Council of Australian University Directors of Information Technology (CAUDIT) in July 2009 to head a team to deliver the sustainable operations of Australia’s Trust and Identity services for Research and Education. This includes the national trust authentication framework the Australian Access Federation (AAF), and the Open Researcher and Contributor ID (ORCID) Consortium Lead for Australia. He is an IT professional with a wealth of management experience in the successful delivery of transformational Information Technology within the tertiary education and research sector supporting the National Collaborative Research Infrastructure Strategy (NCRIS). Heath participates in many national and international committees and working groups on trust, identity, cyber security, and company strategy. 

Tim Rawling

AuScope

Tim Rawling is the CEO of AuScope Limited. AuScope is Australia’s provider of research infrastructure to the national geoscience community working on fundamental geoscience questions and grand challenges — climate change, natural resources security and natural hazards. Prior to this role, he was Director of Infrastructure Development for AuScope’s Australian Geophysical Observing System (AGOS). His recent research has involved the development of regional/crustal-scale 3D and 4D geological models as well as new exploration methodologies involving 3D modelling and finite element simulation. Tim’s background is in structural geology and IT and he has previously worked as a consultant exploration geologist, as the manager of the 3D modelling and simulation programs at GeoScience Victoria (DPI), as the MCA funded lecturer at the University of Melbourne, a commercial programmer and as a researcher at Monash University and the University of Arizona.

Dr Andre Zerger

Atlas of living Australia

Dr. Andre Zerger is a key figure at the Atlas of Living Australia (ALA), where he leverages his expertise in spatial sciences and eco-informatics to advance biodiversity research. His work at CSIRO and the Bureau of Meteorology has been instrumental in developing national data infrastructures. At ALA, he’s excited to lead the team in harnessing digital technologies to manage Australia’s largest biodiversity database, fostering collaboration and innovation in the field.

Mark McAuley

Astronomy Australia

Mark McAuley has worked for thirty years in research and development environments, with responsibility for securing investments, facilitating collaborations, and executing projects. As CEO of Astronomy Australia Limited, he is responsible for the NCRIS astronomy programme. Mark has previously worked for CSIRO, and in private industry, including six years in computer-aided engineering. His experience ranges from explaining science to young children to leading financial strategy discussions concerning billion-dollar research infrastructure projects.

Mark holds a Master of Business Administration, Master of Arts (Ancient History), and Bachelor of Science with Honours (Astrophysics). Upon completion of his MBA, he received the Vice-Chancellor’s Medal from the University of Notre Dame, Australia.