DNAdigest interviews ELIXIR

This week we are interviewing Niklas Blomberg from the ELIXIR project.

Niklas

1. Please provide a short introduction to the work of ELIXIR? What are the aims and the mission of the project?

ELIXIR is Europe’s response to the challenges of big data in life science research. Over the recent years, the amount of data produced by life science experiments increased exponentially and it has been estimated that by 2020 these data will be generated at up to one million times the current rate. ELIXIR’s goal is to orchestrate the collection, quality control and archiving of these data across Europe.

For the first time, ELIXIR is creating an infrastructure that integrates research data from all corners of Europe and ensures a seamless service provision that is easily accessible to all.  ELIXIR’s services – biological data resources, tools, infrastructure, standards, compute and training – will benefit not only bioinformaticians and computational biologists, but also geneticists, biochemists, clinical specialists, and plant, environmental and marine scientists, both in academia and industry.

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2. What does ELIXIR’s structure and legal framework look like?

Rather than concentrating all of the expertise and resources in one place, ELIXIR has a distributed structure based on a hub and nodes model that draws on the strengths of its members.

The ELIXIR Hub – located alongside EMBL-EBI on the Wellcome Trust Genome Campus in Hinxton, UK – provides an administrative governance structure and coordinates the scientific, technical and administrative tasks and delivery of core services.

ELIXIR Nodes across the Member states play a leading role in the provision of technical services. Nodes are typically made up of universities and research institutes in they come together to form a national ELIXIR Node. Each Node has a unique set of expertise and core areas: the ELIXIR Node in Denmark, for example, focuses on tool utilisation and provision, the UK’s Node is currently focussed strongly on training, the Swedish Node runs the Human Protein Atlas, and so on.

At this moment, we have twelve members (Czech Republic, Denmark, Estonia, Finland, Israel, Netherlands, Norway, Portugal, Sweden, Switzerland, UK and EMBL-EBI). A further six countries (Belgium, France, Greece, Italy, Slovenia and Spain) are Observers, working towards becoming full members in the near future.

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3. What is your role in ELIXIR and how does your background support the work you are doing?

As ELIXIR Director, my task is to develop and implement the scientific vision and programme for ELIXIR, all within the overall strategy adopted by the ELIXIR Board and in consultation with the scientific representatives of the ELIXIR Nodes.

I spent a good deal of my career working in industry, and I have a first-hand experience of how world-class research infrastructure drives innovation and knowledge economy. I am very well aware of the value of a public bioinformatics infrastructure for today’s life-science research.

I believe Europe needs robust bioinformatics services to meet the needs of biomedical research in both the academic and industrial sectors. World-class research infrastructures provide the backbone of new discoveries and have a vital role to play in economic recovery and competitiveness. I am excited to apply my industry experience to build bridges between the bioinformatics communities throughout Europe.

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4. What is the ELIXIR Hub? Tell us about its tasks.

The ELIXIR Hub coordinates the infrastructure’s activities and provides technical and administrative basis for ELIXIR’s day-to-day operations. We are responsible for a variety of tasks, from implementing the ELIXIR Programme and servicing the various Boards and Committees to external relations, and administrative, legal and technical support.

We’ve expanded our staff significantly in 2014 and 2015 and are now in a very good position to deliver tangible services to our members and to the scientific community.

The ELIXIR Hub also supports partners in securing additional funding from the European Commission and other international and national sources. We’ve recently won a €19 million grant from HORIZON 2020, the EU’s research funding programme. In contrast with our previous grants, which focused on legal and administrative aspects of the organization, the new ELIXIR-EXCELERATE grant will provide the opportunity to accelerate the implementation of services and fast-track coordination. Due to kick-off in September, the project will integrate Europe’s bioinformatics resources, supporting all sectors of life science. It will also support four use cases focused on rare diseases, human data, marine science, and plant science, which will showcase the value of ELIXIR infrastructure to the specific communities.

ELIXIR’s progress, and the value of bioinformatics in general, has recently been recognised by the European Council, which selected ELIXIR as one of the three prioritised research infrastructures in Europe. This enabled ELIXIR to access a dedicated Horizon 2020 Call, which in turn had led to the ELIXIR-EXCELERATE grant.

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5. Can you tell us more about the ELIXIR Programme 2014-2018? How do you plan to roll out the ELIXIR around the world?

The ELIXIR Scientific programme for 2014-2018 sets out the strategy and objectives of ELIXIR over the next five years and provides foundation for building concrete projects and activities.  Over 100 people from across the ELIXIR Nodes contributed to the development of this document and I was delighted to see their enthusiasm and collective vision.

There are several strategic objectives within the Programme: sustained and secure data, best practices and standards, training, technical services and strategic partnerships. These objectives guide the day-to-day activities of ELIXIR and the projects we run. We currently run several Pilot Actions, funded directly by the Hub budget. These are scalable technical projects to test and showcase the value of the distributed infrastructure and include projects on proteomics, marine metagenomics, data and software carpentry. We are also setting up a Node development programme, which supports the establishment of ELIXIR Nodes through the sharing of best practice between partners on issues such as reaching out to local users, establishing the appropriate legal and governance structures and securing national funding. Our Innovation and SME programme supportsbiotech companies across Europe in accessing the services run by ELIXIR partners. All these activities have been designed and developed bearing in mind the objectives of the ELIXIR Scientific Programme.

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6. How does your work support data access and data sharing?

Let me give you an example. We’ve recently started collaboration with the Global Alliance for Genomics and Health (GA4GH) on the Beacon project. The Beacons have been originally developed by GA4GH and allow researchers to discover genomic data that are available through many participating institutions, providing a single point of access.
In collaboration with the Global alliance, ELIXIR will implement such beacons in the European Genome-phenome Archive (a joint project of EMBL-EBI and the CRG in Barcelona) and national resources in Finland, Sweden and the Netherlands.

The collaboration between ELIXIR and the GA4GH is a good example of how ELIXIR can help scale up existing standards and good practices in data sharing and data discovery. In addition to the beacons in Finland, Sweden and the Netherlands, we will also provide a technical reference and training to support the establishment of further Beacons across the ELIXIR infrastructure.

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7. What do you see as the greatest challenge for increasing the amount of data sharing in the research community?

We identified the key challenges in our Scientific Programme and structured ELIXIR’s objectives as our response to them. Many of the key issues can be summarised as ‘Growing, distributed, complex and sensitive data’.

The immense growth of biological data pose a challenge of how and where to store them, and require dedicated efforts and resources, especially at local and regional level. It is however clear that much of the data will need to be managed as a federation of resources. For example, human clinical data often can’t leave the home institute without additional ethical review and patient consent.

Besides the data deluge, growing complexity is another major challenge. Biological data are heterogeneous and fragmented, often differing in formats, annotations and standards. This creates a serious bottleneck in life science and significant barriers to data integration and reuse.
Finally, I should also mention the skills gap in life science data management. An analysis by McKinsey estimates that by 2018 there will be a talent gap in the US alone of between 140,000 and 190,000 trained experts to analyse the increasing amount of data. We need a strong training programme to bridge this skills gap and to fully exploit the potential of big data.

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8. How would you encourage researchers to make their data available and easily accessible? What best practices would you advise to a young researcher today?

Biology has a long tradition of well-curated data resources, which have provided the bedrock for many discoveries. A recent example is the identification of novel risk factors for Alzheimer’s disease based on a large-scaIe meta-analysis. I think these successes and the global collaborative projects such as the 1000 Genomes Project are the best arguments for open-access infrastructure: the scientific progress in practically all fields of life-sciences depends on carefully curated datasets extracted from public archives.

The vast amount of data being generated by life science is fundamentally changing how research is done. Researchers who know how to manipulate, analyse, store and reuse theirs (and others’) data are better equipped to meet the challenges of the data deluge and take advantage of it. I encourage all researchers to adopt these skills and make them part of their work.

We are working in partnership with Software Carpentry and Data Carpentry to build the ELIXIR Data and Software Carpentry initiative and teach researchers the basics of working with data. It is led by our colleagues at ELIXIR UK, but we are planning to roll it out across all the ELIXIR Nodes, so that researchers all over Europe can take part.

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2 Responses

  1. December 8, 2015

    […] data for personalised medicine Talk by Niklas Blomberg, ELIXIR on data sharing for personalised medicine: Identify bottlenecks in data sharing and learn how to […]

  2. October 21, 2016

    […] Please introduce yourself, your background and your specific role in ELIXIR. Our audience is familiar with ELIXIR already – we interviewed Niklas Blomberg a year ago. […]

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