EMBL-ABR network: an interview with Rudi Appels

Rudi Appels, Professor, Gene discovery and genetic modification, Murdoch University, Western Australia and Honorary Cereal Scientist, University of Melbourne

Prof Rudi Appels IWGSC

Prof Rudi Appels IWGSC

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

Bioinformatics provides the framework for the storage and recovery of large datasets, as well as the analysis and integration of the data. The sharing of data and the capacity of bioinformatics infrastructure to allow re-use of data to validate or generate new ideas is driving a revolution in the biological sciences.

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

The speed of analysis and the rate of change in technology are major challenges for the life sciences which are traditionally based in laboratory run experiments and data generation. The out-sourcing of tasks such as DNA sequencing, RNAseq and proteomics studies mean that very large datasets are generated very efficiently and that life science researchers are required to form teams which are quite different in composition in human skills from those 10 – 20 years ago.

Would you say these are different for those working on plants? Agriculture, in particular, wheat? Do these face different challenges?

No.  At the data analysis/bioinformatics levels the challenges are no different in plants compared to research in microbes, insects and animals.  In fact the human genome project has been, and continues to be, an inspiration for researchers in other organisms, however, the wet chemistry and funding of research in plants can be more challenging than for other organisms.

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

Open data is where (large) datasets are made available through an accessible website, accompanied by accurate descriptions of the protocols used to generate the data. What this means to me is that working with colleagues who are familiar with the incredible diversity in analysis platforms in bioinformatics provides a capacity to answer significant biological questions in a way that was not previously possible. This is especially so when the available data is integrated into new datasets generated in-house to address very specific questions.

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

What is missing is probably not the right question. Both the life sciences and bioinformatics are undergoing rapid change and there is a need for capturing the rigor of data storage/recovery and analysis in other more developed fields such as finance, and integrating this with the analysis of biological phenomena.

What do you see are the priorities when it comes to bioinformatics for researchers working on wheat research in Australia?

The shaping of life sciences research teams to include mathematicians and statisticians is a key priority for the integration of diverse data-sets that can be applied to solving classical issues in the life sciences as well as new issues that arise from discoveries in specific areas.

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

The EMBL-ABR as it is developing, is a much needed infrastructure for integrating the life sciences into the rigorous requirements for the storage, retrieval and analysis of large datasets.  It is also providing a natural infrastructure for running courses and workshops that form the basis of building capacity in the bioinformatics area in Australia. An additional development important to Australia is that EMBL-ABR can provide a pipeline to the large infrastructures in the Northern Hemisphere.

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Biosketch: Prof Appels is one of Australia’s leading cereal scientists with major links to the international community through his efforts in championing the role of Australia to be a participant in an international consortium to sequence the wheat genome (IWGSC). Australia, through his leadership, is sequencing chromosome 7A, a particularly useful chromosome from an agronomic point-of-view in that it has many traits including yield, quality, biotic and abiotic stress tolerance genes/markers. Rapid advances during 2016 have provided the foundation for publishing in a major journal (end of 2016) an advanced draft of the complete wheat genome, with the Australian chromosome 7A assembly being recognised internationally as finished in most regions of the genome assembly.

Link here for more information about how EMBL-ABR is working with plant researchers in Australia to build the wheat genome annotation platform.