EMBL-ABR network: an interview with Lavinia Gordon

Lavinia Gordon is the Bioinformatics Manager at the Australian Genome Research Facility Ltd (AGRF). She is based at their office at The Walter and Eliza Hall Institute, Melbourne, Australia.

Lavinia Gordon

Lavinia Gordon

October 2016

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What is bioinformatics for you and why it does it matter?

Bioinformatics for me is choosing from a scientific palette of statistics, computing and biological knowledge to find answers to interesting biological questions.

What are the challenges you see for life scientists / medical researchers in the data driven science era?

Dealing with the data!  It is very easy to generate masses of data, but it takes time to design an approach that will produce data that directly answers your hypothesis.  Most methods of sharing data are flawed (e.g. transferring data on hard drives that can fail) and most scientists do not have sound processes for dealing with large amounts of data, in terms of storage and long term secure archiving.

Would you say this is different for actual bioinformaticians? Do they face different challenges?

There are many challenges that we have been dealing with for years and will continue to deal with – finding sufficient computation resources, troubleshooting external code, data munging to switch between different formats and getting software to work.  There are new challenges popping up every day which are hard to plan for and often need to be tackled in novel ways, for example the jump in data from exomes to calling variants on whole genomes.

What is open data, and what does it mean to you?

The ability to easily access data in a transparent manner, to obtain and use the data and to be confident that you know how the data that you are looking at has been handled. Is it raw or has it been processed? If it has been processed, what was done to it and can you reproduce it?

What is currently missing in the field of bioinformatics AND life sciences?

I don’t think that anything is missing but there are many things that are insufficiently supported or immature.  I would like to see a better relationship between the existing storage and compute capabilities and greater efforts for standardisation and consistency in best practice methods.

Are there specific needs when it comes to bioinformatics in Australia? 

Australia is at a disadvantage because of distance – both distance from other countries and distance between researchers across Australia.  We lament the lack of high profile conferences, and the difficulties with attending workshops that might be considered local but still require a plane trip!

How do you see AGRF benefiting and contributing to a national federated Bioinformatics infrastructure? 

We have a large client base who are open to sharing and collaborating so an infrastructure that is easy for them to access and is appropriately resourced would be massively beneficial.

It is early days yet, but what would you like to see EMBL-ABR become, achieve? 

I am delighted to see the interactions across states, the broad involvement of researchers across the EMBL-ABR team and the collaboration with other key resources and I hope to see this continue into the future, where EMBL-ABR is a resource known across Australia and with involvement across Australia.

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Biosketch: Ms Lavinia Gordon studied physiology and pharmacology, with a brief stint working for Novartis Pharma in Switzerland, before completing a Masters in Research in Bioinformatics at the University of York, including a collaborative project with GlaxoWellcome.  She subsequently worked at the Cambridge Institute for Medical Research, with collaborative projects at the Sanger Institute and EMBL-EBI, and then moved to Melbourne to take up a position in the bioinformatics group at Walter and Eliza Hall Institute of Medical Research.  After five years she moved to work as a senior bioinformatician at the Murdoch Children’s Research Institute in September 2006. In April 2014 she accepted a position as the Bioinformatics Manager at the Australian Genome Research Facility (AGRF), Australia’s largest provider of genomics services and solutions.

AGRF is one of the EMBL-ABR Nodes, unique in that it has five locations around Australia. Link here to learn more about how they are contributing to the resource.