EMBL-ABR network: an interview with Pedro Fernandes

Pedro L. Fernandes,  Coordinator, Gulbenkian Training Programme in Bioinformatics, Oeiras, Portugal.

June 2016

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How did you get into bioinformatics?

I have always been very interested in understanding how biological information is used in nature, how evolution is driven by it and how health and disease can find explanations there. I started working in bioinformatics by providing services at a national level in Portugal in 1982, establishing computational and updated data resources for researchers. Belonging to an international community was very important, so we joined the EMBnet. Very soon, I realised that training was an essential component and that it was missing almost everywhere. So in 1987 I started organising training courses. As the volume and diversity of themes increased and the need for a systematic approach arose, I invested in creating a training program in 1999 – the Gulbenkian Training Programme in Bioinformatics (GTPB). So far it has trained more than 4800 people.  Bioinformatics training takes most of my time and effort these days.

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

Data driven science has expanded sharply in the last ten years. The major challenge for life scientists is strongly connected to their education. Future life scientists, some of them already in their higher studies, are demanding that their curricula includes more data science content. But, more importantly, they are entering collaborative environments where contact with data driven science is already there. Established life scientists often discover that they are missing an important set of skills and competencies in this area. It is a fantastic opportunity for training providers, worldwide.

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

Bioinformaticians have a benefit here, as they have seen the emergence of data driven science from within their practice. Data driven challenges have ramped-up, especially with the advent of massively parallelised acquisition of new sequencing data. But I believe that the biggest challenges will come from other sectors, not from within bioinformatics itself. For example, the emergence of DNA and RNA editing with CRISPR, together with a more common use of synthetic DNA, will create much heavier needs for large scale responsiveness in bioinformatics. Health-related programs will be seeking responses that involve bioinformatics very extensively. Instead of counting on it to better understand health and disease, the health sector will want bioinformatics to provide decision-making aids at a high speed, by using evidence extracted from big datasets. Likewise, environmental decision makers will be seeking evidence from large scale datasets that hold molecular data that is being used to trace and monitor changes in ecosystems. Finally, systems biology has been raising the level of demand for access to molecular data for large scale modelling of signalling and gene regulatory networks.

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

Open data is the free access to data, by anyone, anywhere and at any time. It results from the removal of access barriers such as copyright, commercial rules, etc. Only ethical rules apply. For me, open data, together with open access and open science in general, are not utopian. Today, I see it as an emerging trend. As I am involved in education, I see it as my duty to defend it on logical grounds, in spite of resistance. It will require a profound social adaptation, and education is key. Open science also requires a lot of persistent advocacy by non-scientists that are, or need to be, educated about its benefits and pitfalls.

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

What we need worldwide, which would have a significant impact in this area, is a revolutionary change in education: creating a better balance between formal and continuous non-formal education. Free education on demand is a must as most of the transformations that are needed in science cannot cope with the low pace and high cost of the existing educational system. Particularly in the life sciences, barriers of various types that we see in the use of data and computational resources need to be lowered. And we need to orient infrastructures globally towards greater standardisation of datasets and their annotation, to be made discoverable by placing them in coherent public repositories.

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

EMBL-ABR faces very interesting challenges. By harbouring programs devoted to development, training and service provision, EMBL-ABR can play a major role in strengthening the links to foreign platforms by supporting intensive and extensive collaborations. By raising the level of demand in resources it can also help to make the case for national investments in better communications resources to link Australia to the other continents. I am already hopeful about the improvements in the training sector that it can foster, but I would also envisage EMBL-ABR could play a valuable role in promoting the public understanding of bioinformatics and its crucial role in science.

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Biosketch: Pedro L. Fernandes graduated in Electronics and Telecommunications Engineering at IST (U.T. Lisboa). He worked in Biomedical Engineering, Biophysics and Physiology and changed to Bioinformatics in 1990. He established the first user community in Portugal around the national service provided by the Portuguese node of the EMBnet. In 1998 he created the Gulbenkian Training Programme in Bioinformatics. Together with Mario Silva from the Universidade of Lisboa, he designed a graduate Programme in Bioinformatics with provision for MSc and PhD degrees. He currently teaches Bioinformatics in graduate and undergraduate programmes in Portugal. He is the Head of the Education and Training SIG in EMBnet, the Training Coordinator for ELIXIR-PT and a founding member of GOBLET. Affiliation: Instituto Gulbenkian de Ciência, Oeiras, PT. 

Researcher ID: A-9618-2010 | ORCID ID: 0000-0003-2124-0241.