EMBL-ABR training: an interview with Daniel Park

Associate Professor Daniel J. Park, Principal Research Fellow, Head, Melbourne Bioinformatics Platform and Head, Genomic Technologies Group, The University of Melbourne

 

February 2018

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What role does bioinformatics play in your work, and why is bioinformatics important?

Bioinformatics is crucial to my research. I do a lot of work that involves analysing massively parallel sequencing datasets across thousands of specimens. Such analyses require collections of bioinformatics tools bolted together into ‘pipelines’ – each tool doing a particular job around removing false or low-confidence signals, making genetic variant calls, annotation and testing for signal enrichments. Much of this has to happen in automated fashion.

Part of my work is centred on novel genomics technology development, particularly targeted sequencing approaches – this requires an integration of molecular biological methods design and bioinformatics algorithm and software development. I could not do this effectively without having acquired programming skills and an awareness of pre-existing bioinformatics algorithms and tools.

With Melbourne Bioinformatics, I have a networking role to link life scientists across a broad range of disciplines with bioinformaticians skilled in relevant areas, as well as to direct them to suitable training resources. This has reinforced my view that the majority of current high-profile life science research projects depend upon the guidance and leadership of expert bioinformaticians.

Is there a bioinformatics skills shortage in Australia and how do you experience this in your own research or organisation?

Absolutely. We encounter a good number of life scientists who have generated large amounts of data without a real plan as to what to do next. Existing bioinformaticians are fully booked, making it a real challenge to establish new collaborations. A lot of excellent work has been done here at the University of Melbourne through the Masters of Science (Bioinformatics) and around online training and workshops. We have collaborated with colleagues in Queensland to develop a simple web interface to allow life scientists to conduct commonly performed complex analyses without the need to learn how to program or work at the command line: the Genomics Virtual Laboratory (which includes the popular platform, Galaxy). However, such initiatives will not satisfy many bespoke demands or deeper collaborative engagements. Only significantly increased investment will allow these gaps to be closed. Our institution, probably like many others, has been relatively slow to recognise or embrace this at scale.

Why has training and skills development in bioinformatics become so important in life science research?

The mode of engagement in life science research has suddenly and dramatically changed. With the advent of ‘postal genomics’ and instrumentation of various types pumping out information orders of magnitude faster than just a few years ago, life science has become a predominantly data science. This transition necessarily requires more importance to be placed on the gaps in bioinformatics skills and supporting computing infrastructure to continue to produce globally competitive research.

How do you see such a skills shortage impacting health outcomes, in particular, in Australia?

The shortage of bioinformaticians, left unaddressed, will continue to present a serious bottleneck to progress in many areas from discovery to translation. Without serious investment in this area, Australian life scientists will slide in terms of their global relevance except for a relatively small number of well-funded individuals. Without such investment, the substantial majority will become followers and bit-part players rather than leaders on many international consortium-based projects. In terms of clinical applications, we become a consumer rather than a producer, with obvious cost implications.

What difference might be made to our performance in markets such as health, agriculture, education and biotechnology, if we find ways to address this skills shortage?

Addressing the bioinformatics skills shortage along with the availability of appropriate computing and data storage infrastructure will increase productivity dramatically across these sectors. This is basically a bandwidth problem. Currently, we are trying to do bioinformatics using dial-up.

What role do you see for the EMBL-ABR network?

The EMBL-ABR network can make important contributions in the areas of networking, particularly around training content and workshops, and advocacy.

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Biosketch: Danny studied Natural Sciences at The University of Cambridge from 1992-1995, before continuing there to complete his PhD in Biochemistry. Since then, he has worked on a range of projects based in London and Melbourne, mostly based around diagnostics or genetics-based discovery – a recurring theme has been the development of novel technologies. Recently, these have involved the integration of molecular biological and algorithmic approaches. Notably, a variety of platforms that he developed and/or conceived are in current clinical practice, including those applied to screening for tuberculosis, cervical cancer and breast cancer. Danny began the transition to bioinformatics-beyond-Primer 3 around 2010 while based at the Genetic Epidemiology Lab, inspired by the need to derive meaning from new “whole-exome” datasets, and in collaboration with colleagues from what is now Melbourne Bioinformatics.