Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities

The community establishment process

ELIXIR Communities follow a defined path to maturity, which is formally embedded in ELIXIR’s processes as a treaty-based intergovernmental organisation, and sets them up for self-organisation and collaboration (Figure 1). Importantly, the majority of ELIXIR Communities that exist today were formed through a bottom-up approach, which ensures broad grass-roots support and interest.

Figure 1. Stages in the development of ELIXIR Communities.

Timeline to show the progression of each ELIXIR Community through the stages of Community maturity, following the processes outlined along the top row. Once a community has reached the phase of Heads of Nodes approval (i.e. approval by the country-level bioinformatics leads), it becomes an official ELIXIR Community and can begin work on an internal project funded through ELIXIR’s core funds. The most mature Communities are shown in the top right (these were the four ELIXIR-EXCELERATE Use Cases), with the newest Communities shown in the bottom left (Communities portfolio as of December 2023).

The first step for a prospective ELIXIR Community is for an initial group of interested parties to put forward a proposal highlighting the relevance and impact of the scientific area, as well as demonstrating broad benefit and buy-in across the ELIXIR country-level “Nodes” and beyond. The group will then give a formal presentation to the Heads of Nodes governance body of ELIXIR, which is composed of national bioinformatics representatives. Following consultation and approval, the group is invited to write a white paper outlining their community goals and strategic position in the scientific landscape. Examples of such white papers can be found in Table 2. The white paper is circulated for feedback, and finally, the Heads of Nodes are formally consulted on the white paper. At this point, the ELIXIR Community may be formally established and become eligible to receive ELIXIR support (such as funding through internal projects, or for knowledge exchanges) and participate in ELIXIR events and projects as an ELIXIR Community. They will then begin working towards the Community goals and represent their specific scientific domain within the ELIXIR research infrastructure. This process has evolved and matured over time in parallel with the formalisation and growth of the communities portfolio.

The community's establishment process helps its members to clarify their roles, responsibilities and overarching goals at an early stage and plays an important role in shaping the identity and function of the community. Notably, writing a white paper together and then being able to work towards these goals through an internal project, funded by ELIXIR’s core funds, offers an opportunity for community members to work together and become a cohesive group. The benefits of this process are also reflected in the literature, where having goals for the community and opportunities for collaborative participation have been highlighted as factors for community success.²

Networking opportunities and the human element

In any community, a sense of belonging is what keeps people involved.^19,20 Members of ELIXIR Communities have the opportunity to meet other experts, exchange ideas, and do meaningful work in their area of interest through project work. As part of this, community members build social capital, and gain leadership experience, e.g., through leading work packages, which helps their professional advancement.

ELIXIR supports this by providing and facilitating opportunities for connection, collaboration, and sharing ongoing work, such as at monthly virtual Community meetings, and annual events such as the ELIXIR All Hands Meetings, Community Face-to-Face meetings, and BioHackathon Europe.²¹ These events offer opportunities for people to work together on scientific literature, tools, services, standards, and training, at the same time building social capital. For example, ELIXIR Communities form a key part of BioHackathon Europe and its projects, and the event has been reported by participants to broaden one’s professional network.²¹

Proactive measures can also be taken to promote inclusion and thus belonging, such as the creation of psychological safety, upholding respect for others as a key value, and involving diverse members in the working group.²² Within ELIXIR, there are several mechanisms to support this including an Equality, Diversity and Inclusion working group at the ELIXIR Hub, an Equal Opportunity Strategy,²³ and ELIXIR’s Code of Conduct (https://elixir-europe.org/events/code-of-conduct) which aims to foster a culture of respect within the network, such as by having Code of Conduct allies at every ELIXIR event. Rewardingly, the Code of Conduct has also been used as a starting point for other organisations that are part of the ELIXIR network to begin to develop their own Codes of Conduct.

Additionally, ELIXIR organises outreach to increase the visibility and profile of its Communities, through events such as ELIXIR Webinars, the ELIXIR Communities track at the bi-annual European Conference on Computational Biology (ECCB) e.g., ECCB 2022 (https://elixir-europe.org/events/elixir-eccb-2022) and ECCB 2024 (https://elixir-europe.org/events/elixir-eccb-2024), and support for the joint ISMB/ECCB meeting in alternating years.

Co-leads and governance

ELIXIR ensures scientific leadership of each ELIXIR Community through its Community co-leads, who guide the scientific direction of the Community. This includes driving activities to fulfil the Community goals, engaging in projects related to the Community, and evolving the vision of the Community over time.

We conducted a survey of the ELIXIR Community co-leads in the fourth quarter of 2023 to assess the impact of having this role. The survey used a combination of open-ended questions and ranked questions using the Likert scale, from strongly agree to strongly disagree.²⁴ Out of 22 respondents (representing 42% of the overall co-lead group), 82% of co-leads agreed or strongly agreed that the position helped them to make an impact in their chosen field. Scientific impact was widely recognised as the main area of impact, with examples such as coordination of efforts through community building, and the ability to drive technological developments and strategic direction. Co-leads also described having more confidence in the success of grant proposals where they were able to cite their community’s involvement in the proposed activities.

The Community co-lead position was recognised as an opportunity for career development. Almost half (46%) of co-leads felt that the role had helped advance their career development or provided professional opportunities, with most of the remainder (41%) giving a neutral answer. While the survey was kept anonymous, based on our insights on the co-leads career stages we suggest that these values reflect the range of career stages of the co-leads and the possible benefits that can come with the role. It is likely that more established co-leads do not necessarily need the same level of career development, if any (in the case of senior co-leads), but still benefit from other aspects of the role. A common theme of the benefits of the co-lead role for visibility and profile was clear from the survey results and was cited as influencing co-lead promotion prospects.

The communities handbook

The Communities Handbook²⁵ is a reference tool that Community members use to understand various processes and day-to-day activities of an ELIXIR Community. This includes topics such as Community purpose and structure, benefits and impact, as well as eligibility criteria for joining an ELIXIR Community. These processes contribute to the sense of community and aim to facilitate the scientific work within the Community.

Community management

Each ELIXIR Community receives direct support from one designated staff member at the ELIXIR Hub, which is the coordinating secretariat of the distributed infrastructure, currently referred to as “Community liaison”. Although ELIXIR does not explicitly use the job title “Community Manager”, the skills portfolio required for people who support the Communities overlaps broadly with the skills for community managers laid out by the Center for Scientific Collaboration and Community Engagement (https://www.cscce.org/). These skills fall into five broad categories: technical, interpersonal, communication, programme management, and programme development.²⁶

As an illustration of this skills portfolio, staff supporting ELIXIR Communities have a high level of technical expertise, having attained an advanced scientific degree and/or worked in a technical role themselves before moving into a coordination role. This includes domain-specific expertise and hands-on experience, a combination vital to effective communication with community members. Secondly, since much of the work of ELIXIR Community management is facilitating collaboration across Europe, interpersonal skills such as cultural competence, engagement, and consultation are central to the role. Thirdly, to support the ELIXIR Communities effectively, there is a need for communication skills such as presenting, content creation, and knowledge brokering to foster connections between different groups. Finally, programme development and programme management skills are needed to successfully design, adapt, and implement the ELIXIR Communities programme. This spans the skillset from strategy development to the day-to-day time management, event planning, and meeting facilitation that keeps the communities running smoothly.

Portfolio management and monitoring community progress

As part of managing the portfolio of ELIXIR Communities, ELIXIR tracks Community activities and successes, including the areas where a Community might be facing challenges. This is monitored continuously, as well as in formal reviews by ELIXIR technical experts and governance bodies such as the Heads of Nodes and the Scientific Advisory Board.

Every few years, individual ELIXIR Communities are reviewed based on factors such as their leadership and membership, level of interconnectedness within the ELIXIR ecosystem, and whether the Community is meeting the goals initially proposed in its white paper. The Communities review form shows all currently established review criteria.²⁷ This review process is a helpful milestone for reflection and feedback and has assisted the Communities in maturing further.

The most active ELIXIR Communities have naturally created many useful and impactful outputs. However, some communities may become dormant due to various constraints such as time or funding, and others change their focus to better serve their members’ interests. For example, the established ELIXIR Marine Metagenomics Community has become dormant as its leads and members have developed a new Microbiome Community of similar but wider scope. This highlights the need to continually reshape the Communities portfolio to adapt to a changing research landscape.

Organising and FAIRifying biological data

The ELIXIR 3D-BioInfo Community in Structural Bioinformatics (https://elixir-europe.org/communities/3d-bioinfo) developed the Protein Data Bank in Europe - Knowledge Base (PDBe-KB; https://pdbe-kb.org) initially with BBSRC (UK) funding but subsequently expanded through ELIXIR project funding. It is an open, collaborative consortium for integrating 3D-structure data and functional annotations to enable basic and translational research. More than 30 research groups contribute to the PDBe-KB to increase the visibility and reduce the fragmentation of 3D-structure annotations available in specialist partner data resources and make these data findable, accessible, interoperable and reusable (FAIR).²⁸ The aim is to place macromolecular structure data in their biological context, to facilitate basic and translational research. The 3D-Beacons Network (https://3dbeacons.org), which is also enabled through a combination of ELIXIR and BBSRC funding, is integral to the PDBe-KB consortium activities, providing integrated access to experimental and predicted protein structure models and meta-information in a standardised data format.

Contributions to global efforts

The Galaxy project began at the Pennsylvania State University in 2006 and has since grown to become a global effort. The European Galaxy Server (https://usegalaxy.eu/), which underpins the ELIXIR Galaxy Community (https://elixir-europe.org/communities/galaxy), is one of just three major ‘usegalaxy’ instances supported by the NIH and the US National Science Foundation - the other two being in the US and Australia. In addition there are multiple growing international efforts, e.g., in India (https://www.galaxyproject.in), Africa (https://africa.usegalaxy.eu/) and recently Canada. The European Galaxy Server alone has had more than 90,000 users since November 2018²⁹ and has been cited in 547 publications between 2017 and 2023,³⁰ illustrating the wide-reaching impact of Galaxy on improving research efficiency.

The community receives national funding through the German Federal Ministry of Education and Research, and de. NBI (the German Node of ELIXIR; https://www.denbi.de/), which has been key in building and operating the European Galaxy Server infrastructure. The ELIXIR Galaxy Community has additionally created connections and facilitated knowledge exchange across borders - both within Europe, such as a knowledge exchange between the German Node and visiting researchers from Italy and Estonia, and beyond, such as the ELIXIR-funded staff exchange with Australia in 2023 (https://elixir-europe.org/news/australia_visit_2023 ).

Establishing community standards

A key challenge that is addressed by many ELIXIR Communities is the lack of community standards for different life science domains. A well-known example of this is the Minimum Information About Plant Phenotyping Experiments (MIAPPE)³¹ and Breeding API (Application Programming Interface)³² data standards that were developed through the ELIXIR Plant Sciences Community (https://elixir-europe.org/communities/plant-sciences ).

Another key example is the role that the Federated Human Data Community (https://elixir-europe.org/communities/human-data ), the Human Copy Number Variation (hCNV) Community (https://elixir-europe.org/communities/human-copy-number-variation ), and the Rare Disease Community (https://elixir-europe.org/communities/rare-diseases ) have played in driving genomic standards development through their work with GA4GH (https://www.ga4gh.org) in an effort to prevent silos in data sharing and ensuring that standards are endorsed by the wider scientific genomic community. One prominent example is Beacon V2 (https://docs.genomebeacons.org/), which enables the discovery of genomic variants and associated information without jeopardising the privacy of the dataset, and is being implemented in the European Genomic Data Infrastructure (https://gdi.onemilliongenomes.eu/) and more recently, the Federated EGA (https://ega-archive.github.io/FEGA-onboarding/). Interestingly, the ELIXIR Plant Sciences Community has developed extensions of the Beacon standards to make plant datasets discoverable, demonstrating further value of ELIXIR via shared developments across domains.

In the area of protein research, the IDP Community has developed the Minimum Information About Disorder Experiments (MIADE) guidelines³³ in collaboration with the HUPO-PSI initiative (https://www.psidev.info/), to maximise the interpretation and dissemination of IDP experiments. Similarly, the Proteomics Community created a metadata standard format for capturing the experimental design information in public datasets, the Sample and Data Relationship File (SRDF)-Proteomics format,³⁴ in collaboration with the EuBIC-MS community (https://eubic-ms.org/) and with HUPO-PSI. Three years after the first version of SDRF-Proteomics, the format is increasingly used and different tools are being developed supporting it,³⁵ including as a key point, the developments in the PRIDE database³⁶ to improve the metadata annotation of public datasets.

Finding and addressing user needs & training gaps

A common thread in the ELIXIR Communities is the goal to improve training within their domain. The Single-Cell Omics (https://elixir-europe.org/communities/single-cell-omics) and Systems Biology Communities (https://elixir-europe.org/communities/systems-biology ) are good examples of this, having each recently done a landscape survey of the training available in their field. They are currently working towards addressing the identified training gaps.

The creation of the Single-Cell Omics Community was largely driven by the demand from researchers for training in the rapidly developing single-cell and spatial technologies which have been accompanied by the active development of data analysis methods. This was coupled with the Europe-wide network of bioinformatics training providers seeing the benefits of working together through the ELIXIR framework. This demonstrates the crucial role that the grassroots, requirement-driven aspect of community development plays in curating the ‘right’ portfolio of ELIXIR Communities. Notably, dealing with the challenges in benchmarking, training and data standards is simply not possible without international collaboration.

Community similarities and distinctions

Communities are a common way of organising people in science and beyond.¹⁹ Some, like the ELIXIR Communities, are aligned with specific products or infrastructures, while others place emphasis on simply fostering communities of practice for like-minded people to come together. In both types of community, there is a common thread of shared goals and interests.

Initiatives like The Carpentries (https://carpentries.org/community/) and WILDLABS (https://wildlabs.net/) exemplify the philosophy of a community of practice. The Carpentries works to build both local and global communities of practice to build capacity in data analysis, computational thinking and research software development. Similarly, the WILDLABS community brings together conservation technology users and makers who want to find solutions to the many challenges facing nature today.

Similarly, communities that centre around an infrastructure or product also have an aspect of acting as a community of practice that brings together like-minded individuals who network and share knowledge, but in addition to this, they enhance the quality and relevance of the resources they are linked to. For example, the Australian BioCommons operates across diverse domains (https://www.biocommons.org.au/domains), facilitating communities geared towards fostering discussion and learning, along with identifying digital infrastructure gaps. This mirrors the ELIXIR Communities' function as a conduit for feedback. Additionally, communities such as Galaxy's Special Interest Groups (https://galaxyproject.org/community/sig) and GA4GH's Communities of Interest (https://www.ga4gh.org/what-we-do/communities-of-interest/) drive tailored solutions within their respective domains while pinpointing gaps in existing offerings.