EMBL-ABR Training: an interview with Sonika Tyagi

Dr Sonika Tyagi, Manager, Monash Bioinformatics Platform at Monash University, Training Key Area Coordinator for EMBL-ABR.

 

April 2018

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

I am a bioinformatician by training and at my organisation I deal with solving biological questions using bioinformatics skills – therefore, Bioinformatics is an essential part of my work. Modern life science research is largely quantitative and with increasing diversity and complexity of data that is being generated from biological experiments, it challenges conventional methods for sharing, managing, and analysing that data. Bioinformatics is the interdisciplinary field that deals with multi-disciplinary processing, analysis and management of biological information by utilising computer science and information technologies. It is becoming core part of data-intensive biological research.

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

The problem is twofold. First is the lack of bioinformatics at the education level. In general biology and biomedical sciences curricula, although recognised as being more formally quantitative, it almost universally provides limited or no formal training in computational and high-volume data analysis skills. Instead, students are required to acquire task-specific skills as they undertake research projects, a highly inefficient process that runs the significant risk of propagating the same limited computational skill set as already present in the research lab or within the student’s pre-training. Secondly, given the speed at which technologies, data analysis practices and tools develop, there is lag in how these are incorporated into the undergraduate and postgraduate curricula or post-graduate training. It is concerning that in the research field these students/researchers will lack necessary computational skills to tackle complex problems and this may lead to limited research progress. It is therefore very important for a successful training regime to cover a breadth of subject matters in the fast evolving field of life sciences.

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

Life science researchers now commonly deal with large volumes of heterogeneous data in various digital formats. Analysis of these datasets often requires consideration of multiple variables and multi-dimensional visualisations. The latter means that without special efforts and skills in data management and evaluation, critical discoveries will be missed, resulting in much waste of resources in doing unnecessary research to gain already available information.

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

At the research level, biomedical scientists are using bioinformatics tools to solve research problems. However, they usually treat them as inputting data into a “black box” and reporting the results without an adequate understanding of the limitations of the models that run the analytical tools. It is becoming far too common an event that publications, even in major journals, are being retracted or corrected due to analysis errors. Users would benefit from the full power of the tools for research outcomes if they could gain a better understanding of the analytical processes used in these tools.

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?

Skilled bioinformaticians understand the value of carefully curated, managed and accessible data. Imagine the kinds of discoveries there are to be made with existing data that we can get access to – let alone by generating new data. ELIXIR, an intergovernmental organisation that brings together life science resources from across Europe, has just today published a report that explores how open data contributes to innovation and generates business value. I commend you to read it if you need further evidence of the value to the economy made possible by expertise in bioinformatics.

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

As I said, curricula development at educational institutes is slow to adapt to the fast changing life science technologies and therefore Bioinformatics training programs on the best practices of software use, development, and data analysis are a great way to address the skills gap. The efforts from Bioplatforms Australia to develop BTP (BPA-CSIRO training platform) in collaboration with the EBI was such an effort to launch a training program at national level in 2012, which has been running successfully. There are several other regular training activities are run by ABACBS, COMBINE, Melbourne Bioinformatics and the Monash Bioinformatics platform. At Monash University we have started an initiative called Data Fluency for Research to form a community of practice around the development of digital data skill across the faculties. The workshops run under this initiative are accessible to graduate students as part of the learning curriculum.

Training is one of the key focus area for the EMBL-ABR and its effort to network with various Australian who develop and run bioinformatics training activities is going to help in standardising, sharing and reusing bioinformatics training resources. EMBL-ABR’s affiliations with international bodies such as GOBLET, ELIXIR, NIH-BD2K, BD2KTCC etc. will help keeping pace international best practices in training standards and programs.

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Biosketch: Sonika currently manages the Monash Bioinformatics Platform at Monash University in Melbourne, Australia. After obtaining her PhD in Bioinformatics in 2007, Sonika completed postdoctoral work at UQ, QIMR and APCRC-Q in Brisbane. She later moved to Melbourne to join AGRF where she worked for six years before joining Monash University. Sonika’s research interests are in genomics and transcriptomics and particularly in studying the non-coding part of the genome. Sonika is also active in bioinformatics training and is member of various national and international bioinformatics education and training networks such as BPA-CSIRO, EMBL-EBI, ABACBS, EMBL-ABR and GOBLET.