Driving Beacon Version 2 development with an invaluable ELIXIR internship

The Centre for Genomic Regulation (ELIXIR-Spain) shares its experience with the intern, Marta Ferri, who helped to propel the Beacon v.2 development this year.

PRBB Barcelona

The Beacon project was born at the heart of the Global Alliance for Genomics and Health (GA4GH), a worldwide initiative to break the barriers of genomics and health data sharing. Beacon aims both to make health data more accessible and to reduce sharing restrictions without compromising the confidentiality of sensitive human data. 

The interconnectedBeacon Network combines the efforts of an abundance of institutes across the globe. We spoke with Jordi Rambla, Team Leader at the Centre for Genomic Regulation (CRG; ELIXIR-ES) that leads the development of the Beacon protocol. It is located at the Barcelona Biomedical Research Park, one of the largest research infrastructures in Southern Europe, where the CRG's top-notch international scope can benefit from this thriving research environment. 

Talking to Rambla, we learned more about the origin of the Beacon initiative, its roots, latest developments, including the second version and, above all, about one of their newest additions to the team, Marta Ferri — a highly-successful intern that was key to developing the Beacon v.2.

Beacon, the Beacon Network, and ELIXIR's role

ELIXIR joined the GA4GH efforts early in the development of the Beacon Project. Today, many ELIXIR members are key contributors to the development and implementation of the GA4GH standards. Also, 9 ELIXIR Nodes contribute to the ELIXIR Beacon Network service.  

As Rambla describes, 'The funding [that ELIXIR offered] was essential, but I must remark that ELIXIR helped to transform ideas into a reality, and created the needed connections. There are many aspects where ELIXIR has helped, and that we can leverage today.'

Moving to Beacon Version 2 

For the discovery of genetic variation data, Beacon offers a straightforward secure protocol to defeat the fear of sharing sensitive information. Although the platform allows users to formulate closed questions (yes/no) that represent the minimal expression of sharing, 'It paves the way to overcoming the fear of sharing', says Rambla.

The Beacon has helped many hospitals to start sharing data and contribute to the global pool of invaluable information to propel biomedicine research. Yet, the CRG unveiled areas with room for improvement, which are being matured into the Beacon v.2. 

The Beacon's conversation with the end-users

'We are finding out in which ways the community is comfortable with sharing sensitive data, and this is one of the reasons why we are part of the Beacon initiative', claims Rambla. With a great effort to gather information from the real end-users of the Beacon service, the CRG has been interacting, repeatedly and successfully, with several medical research infrastructures and hospitals.

Starting with the GA4GH partners, and expanding the conversations to other ELIXIR members, the CRG understood that there was a need for a revamped version — the end-users wanted to get more from sharing their data. 

'Once we gathered some information, we created a draft idea of what this Beacon version 2 could be; but we wanted to know what the users tried to say when saying they wanted more', Rambla says. Remarkably, the CRG decided to get raw feedback from face to face interactions and began a co-design process with the real end-users, to help with the relevance and subsequent uptake of the new functionality. 

They began the conversations with "Fundación Progreso y Salud" (part of the regional government of Andalucía, Spain), moved fast through the country, into Switzerland and France, and recently in Japan. The CRG conducted workshops and participated in multiple forums that helped to depict the concept of what the Beacon v.2 would be.

The internship's influence on Beacon Network v.2 

From ELIXIR Hub, we proposed to create a Beacon Internship to add a full-time dedicated team member to the Beacon Project. This is where Marta Ferri came into play. 

'She helped us move from the first draft of the Beacon to the Beacon v.2 that was released this January', says Jordi Rambla. He concludes, 'I would say that having Marta on board has been key to making this possible, hadn't she joined, we would be probably still struggling with putting this together.’

Rambla emphasises that the protocol has undergone substantial changes with Beacon v.2 thanks to Marta's involvement. Beacon is now able to support more detailed queries, provide richer responses, and provides data at different tiers using ELIXIR AAI to control data access with user-specific credentials. 

Click here to know more about Marta's personal experience

He told us about the "shoe shopper metaphor" he uses to explain the new update to different institutions and hospitals. He explains that the first version allowed the user to ask a footwear retailer for a particular size, without specifying the type of shoe. Now, the second version allows the user to access the shop virtually, and search for sizes, type of shoe, colour and material, which are real time-saving new features. 'This is the magnitude of the changes that the new update is offering', closes Rambla. 

The Beacon's Prospects

Beacon v.2 implies a big step in the right direction to help institutions, clinics, hospitals, and national genomics initiatives share and leverage the potential of human genetic variation data, yet there remains more room for improvement. CRG's interaction with hospitals unveiled areas that the Beacon has still not reached. Rambla claims that the recent hospital interactions have shown that their requirements are far more significant than what they imagined at the beginning.

The CRG discovered that while some hospitals had the foundations in place to start sharing data, many others still kept their data in PDF documents. Thus, demonstrating that the Beacon Network —while undoubtedly useful— ought to adapt to meet the needs of end-users that are currently unable to share their data. The Beacon, however, is continuing to address this issue and will continue to evolve to meet the users’ needs.

Throughout the entire evolution process of Beacon version 2, the ELIXIR Internship was crucial to find the end-users real needs and transform a prototype into a shaped product. Yet, as Rambla says, ‘None of this was an accident, all planets were aligned: a good proactive intern candidate with the right can-do attitude, a good technical mentor going beyond his job description, a good project with funding and international meetings happening all at the right time’.

Wed 6 May 2020