News / 31 May 2024

The European Molecular Biology Laboratory’s (EMBL) European Bioinformatics Institute (EMBL-EBI) serves as a hub for biological data resources and bioinformatics tools, facilitating research worldwide. EMBL-EBI provides access to vast databases, tools and training to enable scientists to analyse, interpret and share biological data, ultimately advancing understanding in fields such as genomics, proteomics and bioinformatics.

Rolf Apweiler, Associate Director of EMBL-EBI recently visited Australia to speak at the World Health Summit Regional Meeting in Melbourne and a proteomics workshop, ‘Future-proofing Computational Proteomics’, hosted by EMBL Australia and Bioplatforms Australia.

We took the opportunity to talk to Dr Apweiler about the role of EMBL-EBI in the Australian context, opportunities for collaboration and the future of bioinformatics.

Tell us a bit about what EMBL-EBI does and why collaboration with EMBL-EBI is beneficial for advancing scientific endeavours in Australia.

We offer bioinformatics training for scientists at all levels, from PhD students to principal investigators. Renowned for our first-class scientific services, we disseminate biological data globally, with our website attracting more than 100 million hits daily and 40 million unique visitors annually – with over 950,000 of those coming from Australia. Additionally, we collaborate with industries to optimise bioinformatics tools and services and play a key role in coordinating Europe’s bioinformatics research infrastructure.

EMBL-EBI plays a crucial role in providing data resources and tools for life sciences research worldwide. What do you view as its most significant contributions?

I think our most important contributions are our databases and our efforts in teaching users how to use them. This includes our oldest databases: the European Nucleotide Archive, which collects nucleotide sequences; UniProt, the world’s go-to for protein information; and Ensembl, a rich source of genomic data and PDBe. It also includes cutting-edge structural biology endeavours, like the AlphaFold database, which contains artificial intelligence-generated structure predictions for every known protein in the universe. These resources empower researchers worldwide, accelerating experiment planning and research progress – life in the lab wouldn’t be the same if researchers couldn’t access this data. This influence spans continents, benefiting labs across the world, but with particular attention to our member states, of which Australia is a part.

(L-R): Population Health Research Network CEO Dr Merran Smith, EMBL Australia Scientific Head Professor James Whisstock, EMBL-EBI Associate Director Dr Rolf Apweiler and Bioplatforms General Manager Andrew Gilbert at the World Health Summit Regional Meeting 2024 in Melbourne.

The intersection of biology and computing has led to ground-breaking discoveries and innovations. What emerging trends or technologies do you foresee shaping the future of bioinformatics and genomics?

In recent years, the most significant impact has stemmed from novel applications of artificial intelligence, a trend that will continue. Our role in this domain is twofold: providing crucial datasets for training large language models and other AI tools, which are essential for accurate predictions. Additionally, we’re leveraging these AI tools internally to expedite service delivery to users. This symbiotic relationship between AI and bioinformatics is expected to intensify, driving further innovation and acceleration.

Could you discuss the primary challenges and considerations surrounding data-sharing in scientific research today, and how EMBL-EBI addresses these to foster collaboration and knowledge dissemination?

I’m certain the success of modern biology lies in its foundation of open science and data-sharing. This ethos dates back to the early days of molecular biology, with nucleotide sequences and protein structures being openly shared since the 1980s, enabling rapid advancements in modern biology. However, with the exponential growth of users in diverse domains, challenges arise – particularly in fields like healthcare, where privacy concerns necessitate controlled, rather than open, access to data. Additionally, some disciplines may resist open data practices to protect individual interests, building up hurdles to sit longer on ‘their data’ (which is usually funded by taxpayers) and advance their own career at the expense of progressing the entire field. Convincing diverse communities of the long-term benefits of an altruistic approach to open data remains an ongoing effort but, in my view, is essential for advancing science collectively. EMBL-EBI advocates for open access, while acknowledging the need for controlled access in certain contexts.

For young researchers aspiring to enter the field of bioinformatics and genomics, what advice would you offer and what skills and qualities are crucial for success?

Certainly, proficiency in programming is essential in today’s landscape. But the most important attribute is a perpetual willingness to learn because the skills relevant today may not hold the same importance tomorrow.

“Collaboration is paramount because biology is a team sport, not so much a sport of individuals anymore, given the vast amounts of data produced and the need for diverse scientific expertise. So effective communication, being open to new ideas, and recognising one’s limitations while appreciating the contributions of others are all vital attributes for success.”

As Associate Director of EMBL-EBI, what are your primary goals and priorities for the institute in the coming years? 

My foremost aim is to emphasise the critical role of research infrastructures and ensure their sustainability, and their accessibility to all users. The challenge lies in reminding users that resources – such as those funded by EMBL Member States and via other funding sources – though freely available, require ongoing support. Just as electricity is taken for granted until it’s unavailable, the same applies to our databases and tools. Global coordination and sustained core funding are essential to prevent duplication of efforts. We need to foster a culture of shared responsibility and benefits among nations, institutions and users to sustain these invaluable resources.

 What do you think is most unique about Australia in the scientific context?

In the realm of bioinformatics, the significance of biodiversity and health is rapidly escalating. Australia stands out with its exceptionally diverse flora and fauna, presenting unique research opportunities. The growing focus on health, both globally and in Australia, underscores the importance of initiatives like genetic sequencing of cohorts. These endeavours enable individuals to better understand their genetic predispositions to diseases, facilitating proactive health management and lifestyle adjustments. Leveraging Australia’s biodiversity, coupled with advancements in health initiatives, promises significant strides in bioinformatics research. Through our current programme, Molecules to Ecosystems, EMBL – with Australia and our other Member States – is undertaking work that supports these activities. The programme expands EMBL’s scope to study the molecular basis of life in the context of changing environments, transforming our understanding of life on earth and informing potential solutions for some of society’s biggest challenges.

Read EMBL-EBI’s 2023 Highlight’s Report.

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