By Liz McGrath
Bioinformatician and Forrest Fellow Philipp Bayer is a valuable commodity in today’s world – a biologist with ‘a knack’ for computational analysis and a desire to tackle one of the most pressing and complex problems on the planet.
“Climate change is real and climate change is here and the world is running out of food,” the German-born scientist says starkly. “Particularly with a growing population. And we know that because of climate change, this problem will only get worse. So the question I’m trying to solve, along with many other people, is to how to feed a future world.”
With elevated temperatures and water stress already having an adverse effect on food production and food quality across the globe, Philipp says farmers and plant breeders desperately need crops that will be able to be grown under drastically different conditions than those of the past.
“Take the wheatbelt in Western Australia for example, which is being reshaped due to climate change which is affecting wind patterns in the southwest of the state leading to changes in rain patterns.
“In simplest terms, my research involves using computational techniques to find new novel combinations of plants that are more resilient that we can very quickly get out so they can become part of the breeding process.
Indoors with a computer and I’m happy
He’s lived in some of the most beautiful places in the world but Philipp admits he’s not a person who needs to be outside in nature.
“I’m more a computers and inside sort of guy and have been since I was a child,” the Postdoctoral researcher says, admitting that two busy young sons with wife Keiko don’t always make that easy these days.
“They love living in Forrest Hall because we’re so close to the river and the Matilda Bay foreshore and they can run around like crazy,” he laughs, adding while three-year-old Alex and Charlie, one, are too young to be showing any talent for technology just yet, “my younger child did break a laptop by dropping it from the couch, if that counts!”
Growing up in Germany, close to some of neighbouring France’s most beautiful wine towns, was ‘happy’ with a doctor dad, mum and a sister who has moved into medicine and now lives in Switzerland.
It was during his undergrad days (a BSc Biology at the University of Muenster) where he worked on the evolution of HIV and SIV and heat shock resistance in sea grasses, that Philipp’s interest in bioinformatics – the mathematical and computational approaches used to glean understanding of biological processes – began.
“Turns out I have a knack for computational analysis – in bioinformatics we use massive computing systems to analyse genetic variation data from hundreds of plant cultivars,” he explains. “And that fascination was something that just grew and grew.”
Australia and diverse opportunities
After finishing his undergrad, Philipp decided he needed to further his IT skills and cast his net wide.
“I basically applied all over the world, and Australia said yes,” he says. And so began a Master of IT at Bond University on the Gold Coast, where he graduated with a High Distinction, followed by a PhD in Applied Bioinformatics at the University of Queensland.
“What were my impressions when I got to Australia and Queensland? It was hot! And there were a lot of beautiful beaches.”
But there was little time for relaxing. On top of his study Philipp co-founded openSNP.org, an open repository for human genotyping datasets from customers of direct-to-consumer genotyping companies like 23andMe, known for its at home DNA testing kit.
His PhD was spent in the Edwards Group at UQ developing a novel low-coverage genotyping by sequencing pipeline, then used to assess genome assembly quality in Brassica napus (rapeseed/canola) and Cicer arietinum, which we know as chickpea.
Philipp’s current work as a post-doc is in the same group which has moved to UWA, focusing on knowledge networks, the assembly and analysis of pan-genomes of several crop series (legumes and cruciferous vegetables), genome-wide association studies, population genetics and so much more, along with student supervision and teaching duties.
The power of Pawsey
Plant breeding is fairly slow, the data whizz explains, while climate change is not. Which is why he, and scientists like him, are using some of the most powerful computers on the planet to crack the complex genetic codes of plants like canola and cabbage so as to make them stronger and more resistant to a hotter and drier world.
Proximity to the Pawsey Supercomputing Centre in the nearby suburb of Kensington (co-funded by the Australian and WA governments, the CSIRO and four WA universities – Curtin, Edith Cowan, Murdoch and UWA), with its massive data storage and visualisation infrastructure is a massive advantage for the Nedlands based scientist.
“Pawsey has had a massive impact on our work,” Philipp explains. “It’s got many CPU nodes for our day-to-day work, high memory nodes for our genome assembly workflows and GPU nodes for our machine learning and our deep learning work.
“We sequence hundreds or thousands of plant individuals which generates massive amounts of data on the petabyte scale. And we need supercomputers to look at that data. It’s helped us massively accelerate our workflows because analysis that would have taken a few years in the past, now takes maybe a month or even less than that.”
Happy Hacky Hour
Somehow Philipp has also found the time to set up ‘Hacky Hour’ at UWA, an informal weekly meet up where researchers (staff and students) from all disciplines workshop their problems related to code, data or digital tools in a friendly, welcoming environment.
“It started at the University of Melbourne, an idea by Damien Irving, and has taken off across the country,” he says. “It’s a great way to be able to help people and I really enjoy it. As long as I get a coffee I’m happy!”
While the coronavirus pandemic and accompanying social isolation mean the club is now run purely online via Zoom, the change has only added to the number of people using it, Philipp reports.
“We’ve had people calling in from Japan, Melbourne, and all over the place with their problems and requests, it’s been really interesting how far the concept has spread.”
Admitting he’s interested in ‘far too many things for my own good’, the certified Software and Data Carpentry instructor is also involved in organising and teaching the Bioinformatics courses for Masters students at UWA.
There’s no doubt that Philipp Bayer is someone we’ll be hearing a lot more of as Australia joins the world in trying to protect future food security amid disruption from increasingly extreme weather events.