Two decades ago, sequencing the entire human genome – that is the order of all 3.2 billion pairs of DNA letters in the helix – took years. Today, next-generation sequencing can do the same thing in 24 hours.
The ambitious and international Human Genome Project, which remains the world’s largest collaborative biological project, led to a huge demand for analysis and interpretation of the unprecedented wealth of biological data it generated.
Which was when the evolving science of bioinformatics, the interdisciplinary field that harnesses computer science, mathematics, physics and biology, entered the mainstream.
Third year PhD student Jacob Martin
Associate Professor Silvana Gaudieri, head of the Department of Anatomy, Physiology and Human Biology at UWA’s School of Human Sciences and an Executive member of UWA’s new Centre for Applied Bioinformatics, has seen firsthand the way bioinformatics is transforming research.
As the head of a research group examining hostviral interactions, including studies demonstrating the adaptation of viruses such as Hepatitis C, Hepatitis B and HIV to immune responses at a population level, she now depends on it.
“One of the things that we’re looking at is the way that the immune system responds to infection,” she says.
“We need to know which genes are turned on and turned off and how that may differ from person to person.
“For any one sample, and bearing in mind we’re looking at both the pathogen and the person, we’re probably looking at 100 gigabytes of data – that’s a deep, deep dive into data which requires a lot of computational ability and a forum or environment in which to communicate and collaborate.”
Which is where UWA’s Centre for Applied Bioinformatics comes in.
“While it’s still in its infancy, the idea is to provide an environment in which research groups – often working with big human-based data sets or non-human-based datasets that generate enormous gigabytes of data – can access the expertise and training they need to analyse that data,” Associate Professor Gaudieri explains.
“Many academics have gone through their careers being involved in lab work but without the training and skills needed for complex bioinformatic analysis, these are techniques that didn’t exist when they started out,” she says.
Helping researchers and students
Centre director Professor Dave Edwards said bioinformatics was now being applied to identify early-stage cancer from scans, discover the basis for rare genetic diseases from genome sequences, model environmental change on ecosystems and accelerate the breeding of improved crop varieties.
“Biology has changed incredibly over the last decade and the huge amount of additional data that is being generated has become very hard to analyse manually,” Professor Edwards says.
“The rapid growth of data spans everything from the sequencing and analysis of genomes through to the automated analysis of images in biomedicine and agriculture.”
He says the virtual hub, which brings together expertise from six UWA schools, as well as Harry Perkins Institute of Medical Research, The Kids Research Institute Australia and the Marshall Centre to support bioinformatics teaching and research, will also help meet the huge growth in demand for researchers with applied bioinformatics skills.
“Biology has changed incredibly over the last decade and the huge amount of additional data that is being generated has become very hard to analyse manually.”Professor Dave Edwards, Director, UWA’s Centre for Applied Bioinformatics
“The increase in biological data generation has led to high demand for researchers with applied bioinformatics skills – including training in high-performance computing and techniques such as machine learning – which is why at UWA we responded by establishing the centre together with a new Master of Bioinformatics,” he says.
For Associate Professor Gaudieri who is involved in teaching at both undergraduate and postgraduate level in genetics, immunology and biological anthropology, the new offering will act as a ‘research incubator’.
“It started this year and means that upcoming scientists can do their Bachelor’s and then a Master of Bioinformatics as they move from undergrad to postgrad which is really important because big data is becoming more and more prominent,” she says.
“Students will learn practical skills in biological data management and analysis and the application of high-performance computing to advance the understanding of biology – in demand skills which are also transferrable to diverse computational and data analytic fields.”
Providing connectivity across a diverse field
Professor Edwards says one of the challenges in establishing the centre and one of the reasons it’s a virtual centre is that bioinformatics is so diverse.
“Many researchers who need bioinformatics skills are isolated in different groups, sometimes doing a bit of laboratory work and generating a lot of data, and the challenge is that they lack the experience or the community to help them solve their problems, they’re often banging their heads against the wall to try and identify things,” he says.
“We’re bringing them together and showing them that UWA has this capability across a broad range of skills, and providing the connectivity which we can only really do as a major centre.
“Bioinformatics methods and applications change rapidly, and no single individual or group can stay ahead of all developments, but by collaborating through the centre we can support advances in this field across biological disciplines.”
The centre is working across universities, with state, national and international organisations to deliver applied bioinformatics training and research excellence to advance medical, environmental, and agricultural research in the state.
Download a print copy of Uniview Winter 2022 to read the full edition. An accessible version is also available.