Public services

The goal of this WP is to provide a collection of best practices and indicators for research software and workflows. To do this, the WP will engage with the 15 ELIXIR Communities, which will also provide use cases for the best practices.

WP2 is linked with the services and infrastructure developed in WP3, which will capture Community input to steer development and drive adoption of best practices.

WP4, which is about capacity building and training, will ensure ensure expertise/content from WP2 is disseminated across ELIXIR Nodes. WP2 will also provide support for the industry and scientific outreach activities in WP5.

Objectives

Tasks

Task 2.1 Building the technical toolkit for software best-practices

Task 2.2 Identifying efficiency indicators for research software and workflows

Task 2.3 Adoption of best practices through Community engagement

WP leaders

• ELIXIR-STEERS
• EU projects
• Back to the top

Uncovering new families and folds in the natural protein universeStructural bioinformatics provides methods and tools to analyse, predict, archive and validate the three-dimensional (3D) structure data of biomacromolecules such as proteins, RNA or DNA.

The specific 3D shapes of macromolecules allow them to perform many functions within cells. Understanding their structures is therefore crucial for understanding the interactions and functions of cells, which in turn opens up potential for innovations in biotechnology and drug development.

Enquiries

Please contact the Community Coordinator Katharina Heil (katharina.heil@elixir-europe.org).

A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning. Via A, Attwood TK, Fernandes PL, Morgan SL, Schneider MV, Palagi PM, Rustici G, Tractenberg RE. Brief Bioinform. 2019 Mar 22;20(2): 405-415.

WP1: Management and coordination 

WP3: Recognition and credit attribution of research contributions to data resources

Lead Partners: University of Padua (Italy)

This WP will support the recognition and credit attribution of activities which curate, annotate or otherwise contribute to the increase of data in relevant resources such as knowledge bases. Further, it will leverage the work of APICURON to provide an infrastructural component to use in different contexts beyond more traditional biocuration activities (e.g. knowledge bases), ranging from ELIXIR registries (e.g. bio.tools, RDMkit, FAIR Cookbook, FAIRsharing), to code contributions (e.g. in GitHub) and data management/stewardship (e.g. data brokering).

The resulting service will link the mapped data citations and credits for primary contributions to citation networks (e.g. OpenAIRE KG). Moreover, it will explore the possibility to generalise the approach and employ it in other contexts such as crediting trainers in Training Platform activities. In addition to the technological component, it will explore the “sociological” implications for the “person infrastructure”, including career pathways, fostering adoption and user engagement (e.g. with gamification techniques). 

Activity 1: Technical developments for recognition 

This task will continue the technical developments for implementing recognition and credit attribution mechanisms. The APICURON platform, currently restricted to curated databases, will be expanded to cover a wider range of activities, based on user input. On-boarding of additional ELIXIR resources will lead to technical changes, as well as requests for additional features supported by this task.

A major step will be the establishment of a prototype mechanism for harvesting GitHub contributions on a small subset of selected profiles, e.g., training materials developed using the GitHub template established by the Training Platform. The visualisation of additional statistics for curators both on the APICURON website and via widgets for third-party websites will be supported based on the outputs of WP3.2. In addition, work will be carried out to create appropriate Bioschemas entities for information in APICURON in order to connect to the OpenAIRE knowledge-graph.

Activity 2: Engagement and gamification for recognition

This task focuses on the sociological aspects related to recognition and credit attribution. It will define strategies for implementing gamification effectively, through the evaluation of use cases and establishment of guidelines.

The work will span two orthogonal views, from the resources implementing recognition and credit attribution mechanisms (resource view e.g. PomBase) as well as the individual contributors (people view, e.g. curators).

The resource view will help define best practices for the granularity of events to be captured in recognition and how to attribute credit for them. The people view will instead focus on how to promote engagement via gamification, i.e. how to build meaningful statistics based on the captured events.

Activity 3: Outreach and engagement with other initiatives

This task focuses on promoting alignment with and uptake of the recognition and credit infrastructure by other initiatives, both within and outside ELIXIR (e.g. Bionomia, LifeWatch). It will create opportunities for Community engagement by presenting the recognition work at different ELIXIR meetings (e.g. All Hands Meeting, BioHackathon), and within Platforms e.g. by aligning with related work in the contemporary activities of the Training Platform.

It will also provide the necessary coordination with relevant stakeholders for alternative career assessment, including EU projects (such as STEERS, EVERSE and GraspOS) and the EOSC task force on research careers.

WP4: Scalable curation support from the long tail of biological data

Lead Partners: SIB (Switzerland)

The backlog of supplementary data attached to published scientific reports, as well as generalist deposited contents, the so-called long tail of data, is a potential goldmine for research. Unfortunately, these data are buried in the contents of millions of semantically poor files. This long tail of data needs FAIR-ification using automatic methods.

Activity 1: Coordination of literature curation challenges and practices

The primary channel of communication in life science is and remains the literature. However, practices and standards for literature publication are evolving and a growing set of publications contains structured dataset descriptions (e.g., DOME) and links to specialised data repositories or general ones (e.g., Zenodo).

Further, and although CDR and Community Databases may exhibit very heterogeneous biological interests, we aim at defining some minimal data typology shared by all data resources: paper- vs. passage-centric curation, continuous vs. session-driven curation efforts, role of supplementary data or generalist repositories in curation guidelines, and named entities as in EuropePMC/SIBiLS annotations.

Activity 2: Turning the long tail of literature and supplementary data into FAIR digital objects

This subtask aims to complement the transformational efforts focusing on the FAIR-ification of literature using semantic web technologies. The idea is to leverage on-going efforts (e.g., PDF2JATS, RO-Crate, DOME, Zenodo) to both improve FAIR archiving standards and to explore how such formats can be discovered through an index or a Knowledge Graph.

First, we plan to establish a communication channel with related European initiatives. We will leverage EU research infrastructure projects, such as BiCIKL or FAIRClinical (ELIXIR-LU, CH, FR, UK), to coordinate efforts in and outside ELIXIR with lead stakeholders (e.g., CERN, LifeWatch, GBIF, GBC).

Second, the task will explore how these digital objects can be made available for discovery.

Activity 3: Accessing traceable author statements from curated databases

ELIXIR Core Data Resources and Community Databases tend to cross-reference articles to provide their end-users with access to the source of their knowledge. Unfortunately, the unit of evidence is generally the article, which may mean up to 20-30 pages of PDF.

Such granularity is often not sufficient to efficiently access an explicit traceable author statement. However, some databases and communities (e.g. System biology, Rare diseases, Biodiversity) propose to record evidence at a finer granularity. In particular GeneRiFs (Gene Reference Into Functions) and MINT/IntAct can track evidence at the level of a unique sentence. The same applies to biotic interactions.

Based on a sample of GBC, CDR and CDB (e.g., DisProt, CelloSaurus, MINT/IntAct, OLIDA), and together with WP3.1, we propose to explore how published evidence could be better captured, cross-referenced and displayed. Such a curation model will leverage methods to uniquely identify both sentences and sections in articles (e.g., Europe PMC SciLite, Biocuration Toolkit); thus evolving article and supplementary data representation standards such as JATS and BioC.

WP5: Establishing and shaping the landscape of Core and Community Biological Databases

Lead Partners: Sib (Switzerland), University of Padua (Italy)

Activity 1: Leverage the interactions with the Global Biodata Coalition to support the CDR and outreach

The aim of this task is the coordination of the interactions between ELIXIR Data Platform and Global Biodata Coalition. It also includes established processes of assessment for granting CDR/EDD status and Periodic Review of existing resources.

Activity 2: Establish guidelines for Community Database identification and monitoring

This task aims to establish a robust and simple procedure for the identification and badging of ELIXIR Community Databases. This entails landscape analysis, covering all ELIXIR Databases, based on Nodes’ service delivery plans (SDPs) to establish simple minimum quality criteria for Community Databases. The identified criteria should be a checklist that does not require additional discussion or complex assessment to be applied. At the end of the process, a first iteration of the ELIXIR Community Database badge should be awarded to all data resources meeting the criteria.

Activity 3: Apply and adapt monitoring methodology for indicators

The current criteria to define ELIXIR CDR include various bibliometric indicators. Such statistical indicators include the counting of mentions, citations and database accession numbers (e.g., identifiers.org). This acitvity will produce recommendations to establish an improved list of Key Performance Indicators (KPIs) to support the evaluation of ELIXIR databases. 

Beacons is a technological solution that enables the discovery and sharing of sensitive human data from multiple datasets around the world without compromising privacy. ELIXIR was a major contributor to the development of the Beacon specification, as a product of the Global Alliance for Genomics and Health initiative. The technology has now been adopted well beyond Europe, thereby enabling researchers to securely search for and explore the data they need in their work, before undertaking accreditation to have access to them.

Biodiversity represents the full spectrum of organisms on Earth, at population, community, and ecosystem levels. The loss and decline of biological diversity are recognised by scientists and the public as a critical challenge for humankind to address. Addressing this global crisis requires knowledge of the diversity of life on Earth, how that diversity functions and interacts, and how it responds to changing environmental pressures. This is why research that transforms our understanding of the variety of life on Earth, at phenotypic or genetic levels, is so important.

Current biodiversity data infrastructures and resources are a testament to the long-standing recognition by multiple stakeholders of their importance. However, their heterogeneity poses many challenges. These challenges are both technical, in terms of data analysis and data integration, and at the level of the scientific community, which faces a complex landscape of tools and data that can be difficult to navigate. Building connections across the many infrastructures and services active in biodiversity research is key to overcoming these challenges. These endeavours support the broader ELIXIR framework of striving to bring data science solutions to the priority area of Biodiversity, Food Security, and Pathogens. 

For more information, have a look at the Biodiversity Focus Group page, as well as the published Biodiversity Community white paper. 

Goals of the Community

Leadership

The Linking Data theme of the Science tier focus area of the Human Data and Translational Research is now open. Below is all the information you need to apply.

Objectives and call requirements

The Human Data and Translational Research ambition of the ELIXIR 2024–2028 Scientific Programme is to provide the infrastructure to support the discovery, access, sharing and analysis of human genomics data and linked data on a massive scale, building on progress made in this priority area by ELIXIR since 2014.

We will achieve our ambition via projects focussed around three themes, which will be implemented as part of the new HDTR project plan. The recently funded projects (from the previous 2024 open call) cover the areas of Data Deposition and Federated Data Analysis.

Applicants are now invited to submit their proposals for the Linking Data theme.

General information

• Call opening: 30 September 2024
• Call closing: 10 November 2024, 17:00 CET
• Expected Starting Date: 1 January 2025 – 31 March 2025
• Expected Completion Date: 31 December 2026 
• Duration: Up to 24 months
• Maximum number of funded projects: One
• Financial Allocation per project: Up to €200,000, including indirect costs

Linking Data theme

Data linking is understood to be the technical integration of heterogeneous data sources through identifiers or common attributes, enabling the aggregation, comparison and analysis of data across different domains, formats and structures to enhance data interoperability.

Objectives:

1. Partnerships linking human genomics data to other -omics and/or other heterogeneous data (for example, imaging) using/relying on existing ELIXIR-supported infrastructures/data portals/repositories/toolkits are well established.
2. Mechanisms for data deposition across data types are defined and agreed across Nodes/consensus is gained across Communities to ensure interoperability across ELIXIR-supported technical infrastructure.
3. Drive towards ontology-based data integration to effectively combine data or information from multiple heterogeneous sources.

Description:

The expected outcome is that other data types can be accessed and linked at scale to human genomic data research studies and that relevant data infrastructures and data spaces are interoperable. 

We encourage proposals that outline specific strategies for linking genomic data with other -omics and heterogeneous data types (for example, imaging), emphasising methods ensuring meta-data alignment. Proposals need to demonstrate achieving interoperability across different ELIXIR Nodes.  

While it is preferable to use real genomic data, if this is not available then synthetic data will be considered in order to move forward with demonstrating capabilities and solutions.

Call requirements 

The ELIXIR Hub will assess proposal eligibility before submitting the proposal for formal review. Applicants will be notified if there are issues with their submission. All steps of assessment, including review panel and evaluation criteria, can be found below.

Eligibility:

• Projects must be sponsored by at least one ELIXIR Community, and more where applicable. This sponsorship will be verified after submission by contacting relevant Community co-leads.
• Projects must include and fund at least three Nodes with a minimum level of funding equivalent to two person-months per funded Node, as well as a diverse mix of gender and geographical range. This is to encourage cross-Node collaboration in proposals.
• A balance of the involvement of the four Human Data Communities may be considered to ensure a portfolio spanning use cases.
• Any institute that receives more than one person-month of funding should be responsible for at least one deliverable or milestone.
• In-kind contributions are acceptable, but must be defined in terms of person-month equivalents, and can’t be more than 20% of the overall person-months budgeted in the proposal.
• Applicants must submit a fully-costed budget and also include person-month allocations (a minimum of 1PM ideally, and 0.5PM if the task allows). It should be attached as a spreadsheet (template) with a complete costing form during submission, following Section 3 of ELIXIR Guidelines for Commissioned Services, and adhere to budgeting principles outlined in the Guidelines.
  • Funding may be used for travel, where necessary, even for participants allocated zero person-months. However, amounts must be declared in the overall proposal budget (i.e. the total budget should also include travel and other costs, beyond the person-month allocation).
• Proposals must not duplicate existing funded efforts, such as Platform Work Plans or Implementation Studies, but can build on prior studies.
• Proposals should also consider how they complement, connect with and avoid duplication of activities within external partners and projects (international organisations, ESFRI, EU agencies and EC funded projects).
• Applicants may submit multiple applications but must ensure clear differentiation.
• Applicants may not submit an application identical to that submitted in any other funding call that is open at the same time.
• Only ELIXIR Node members covered by a Node’s Collaboration Agreement may receive funding through this call.
• Declarations of Support from Heads of Nodes are not required in advance; but submitted applications will be made known to the respective Head of Node (HoN) during the eligibility assessment.
• Deliverables and milestones must be realistic, but have to reach beyond typical coordination activities that exist within ELIXIR Community functions. For example, some encouraged outputs include:
  • Standards
  • Services
  • Guidelines
  • Training
  • Connections
  • Datasets
  • Benchmarks

Proposal details:

• Proposals should be concise and include ELIXIR context. Do not assume that all reviewers will be fully acquainted with ELIXIR context.
• Proposals should be made up of only a few key work packages, each with identified leaders that all align towards the one or two specific topics chosen to address.
• Proposals should have an appropriate number of milestones and deliverables, given the expected duration and budget.
• Proposals should provide a person-by-person justification for requested person-months, tying their expertise to specific deliverables.
• Proposals should put the Consortium of those applying in context. For example, why is this group of people the best for this project?

Submission process:

• Participants planning to submit a proposal must refer to the ELIXIR Guidelines for Commissioned Services, section 3.6 on open calls, and any other formal announcements made through the usual channels.
• Proposals must be submitted through the Oxford Abstracts platform link. Each section that will be completed, has its own word limit visible on the platform.
• For each proposal, one project lead should be nominated and agreed among the applicants responsible for submitting the application.

Review panel:

The Review panel reserves the right to propose small amendments to project budgets or time frames after review, but before issuing funding. This is in order to accommodate the overall restrictions of the call and maximise the number of funded projects.

Evaluation criteria:

Proposals will be assessed according to the following criteria.

• Ambition – The novelty, expected outcomes and impact of the proposed research; whether the proposal pushes the boundaries of current knowledge.
• Scope – The proposal's alignment with the call objectives and ELIXIR's objectives and research priorities in the 2024–28 Scientific Programme.
• Context – The extent to which the proposal complements, connects with and avoids duplication of activities within ELIXIR (Platforms, Communities or Services), and ELIXIR’s external partners and projects (international organisations, ESFRI, EU agencies and EC funded projects).
• Balance – Whether the proposal adequately balances the involvement of member Nodes and Communities, while staying within realistic resource limits. To what extent the proposal includes a diverse team, including a mix of gender, geographical range and new and mature Nodes.
• Implementation – Whether the budget is appropriate for the project's scope and goals and if the proposed timeline would allow for realistic project completion.
• Scientific and Technical Rigour – The scientific soundness, methodology and technical approach of the proposal.

The review process is described in the ELIXIR Guidelines for Commissioned Services, section 3.6 on open calls. In short: reviewers will be allocated to each proposal for assessment and scoring. The scored proposals will be assessed and ranked based on both overall score and alignment with the Science tier ambitions.

Cancer research is highly data intensive, making efficient data management essential to enabling precision medicine for European citizens.

The ELIXIR Cancer Data Community was established early in 2024, following the publication of the Community’s white paper. The Community brings together expertise and resources to gather, manage and analyse clinical and biomedical data. By joining forces with other initiatives focused on human data, including several Horizon Europe-funded projects, ELIXIR aims to enhance the data infrastructure, improving the accessibility, quality and interoperability of data, ultimately accelerating discoveries in biomedical research and enabling better decision-making.

Effective data management involves the adoption of standardised data formats, robust data privacy and the engagement of healthcare professionals. Broad interoperability of data, metadata, research software and computational infrastructure are all critical for data to make a difference to cancer prevention and treatment.

The scope of the Community includes running pilot projects, delivering training and lectures, providing a network of experts to respond to funding opportunities, and influencing the direction of policy development in cancer research.

For more information, have a look at the Cancer Data Focus Group page. 

Community goals

Leadership

The purpose of the  Capacity Building and Knowledge Exchange programme is to strengthen the links between ELIXIR Nodes, facilitate capacity building in ELIXIR Nodes and support the exchange of best practices in bioinformatics service provision.

This programme is expected to cover ad-hoc needs, accommodate innovative, emerging ideas, or newly onboarded people requiring capacity building and knowledge exchange outside of the activities already funded through ELIXIR Commissioned Services. The Capacity Building and Knowledge Exchange programme instruments can be applied for with separate forms below.

Applications that seek to interact with organisations beyond Europe, in support of implementing ELIXIR’s International Strategy, may also be considered. If interested in submitting such a proposal, in the first instance, the External Relations team at the Hub needs to be contacted.

You need to log in to view all the application forms.

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Many ELIXIR kick off meetings are happening in September and October. I agree with many comments in the last monthly meeting and I think we should have our F2F after the kick offs. This would help us to get an update about platforms to better plan our activities. By our F2F we should know if the platforms will have platform coordinators and if so we could invite them to our meeting.

I have created a doodle poll with few options to have our F2F meeting. Please vote. I would suggest we have it in Hinxton (UK) on Monday 16-17 Nov collocated with the BioMedBridges Symposium (17-18 Nov) followed by the CORBEL Kick Off (19 Nov).

This interactive map provides details of industry engagement by ELIXIR countries. Not shown on the map is EMBL-EBI, the European Node of ELIXIR, which runs a long-standing and successful industry programme. 

Commissioned Services are projects internal to ELIXIR, and funded through ELIXIR's own budget.  See the Commissioned Services Guidelines on the intranet.

The 2024-2028 Programme will focus on Commissioned Services projects aligning with the programme priorities. See this page for the pre-2024 Commissioned services.

• 

  Science

  Enables scientists to access and analyse life science data.

• 

  Technology

  Deliver services to support distributed data management and analytics.

Pages coming soon:

• 

  Nodes

  Equip national Nodes for successful long-term operations.

• 

  People

  Develop people and capacity to benefit science and society.

Equipping ELIXIR Nodes for successful long-term operations

ELIXIR is a distributed research infrastructure where each member state establishes an ELIXIR Node that connects leading institutes and universities, and provides bioinformatics services to the community. The services and scientific focus of ELIXIR Nodes are shaped by local needs and national priorities.

ELIXIR Nodes must be well-coordinated, professionally managed organisations, meeting their national stakeholders' needs by offering high-quality support, expertise and services.

Long-term success for ELIXIR Nodes requires strategic planning, effective communication, community engagement, technological innovation, skilled personnel, adaptability and a commitment to ethical and legal standards.

Nodes often face similar problems. This project provides the structure to share this extensive experience and institutional knowledge. It will provide tools and knowledge to empower Nodes to better measure their activities and environment, streamline approaches and enable communication.

Activities in the project include:

• Establishing metrics to define Node diversity, organisation and maturity
• Evaluating potential strengths and weaknesses in Node operations
• Enabling alignment with other research infrastructures
• Improving access to information relevant to funding applications and other requests for information from funders and stakeholders, fostering sustainability by ensuring efficient access to crucial resources
• Establishing a light tracking system of references to ELIXIR and its services in national open science policies and research data management policies
• Supporting development of Node RDM strategies that align with EU and national policies, including open science
• Increasing industry engagement at the Node level and establishing a common support strategy across ELIXIR

This project complements tasks in ELIXIR-STEERS, in strengthening and equipping ELIXIR Nodes and Node staff with key organisation, management and training skills and resources.

Developing people and capacity to benefit science and society

There are three projects in the People Tier: PeoplePulse,  Train the Trainer and ELEAD 2nd edition.

PeoplePulse

Start date: 1 July 2024
Duration: 30 months

ELIXIR’s continued success requires a dynamic and skilled workforce across all ELIXIR Nodes and roles. This project focuses on these critical aspects of people development:

• Improving the onboarding process – the gateway for people new to the ELIXIR network
• Delineating roles that cater for a spectrum of expertise
• Developing innovative training concepts tailored to the challenges of ELIXIR
• Sharing success stories and best practices from people development initiatives

The PeoplePulse project underscores ELIXIR's commitment to nurturing a skilled, diverse and collaborative community for staff. By addressing key aspects like onboarding, role definition, ELITMa training, equipping ELIXIR Node staff with organisation and management skills and training on impact assessment, ELIXIR aims to strengthen its internal capabilities as well as significantly advance bioinformatics research and innovation.

Train the Trainer

Start date: 1 July 2024
Duration: 30 months

ELIXIR's goal is to enable and support life science research through the provision of infrastructure, resources, tools, knowledge and skills. Training researchers how to use these resources is essential. The importance of computational biology in life sciences means there’s a myriad of life scientists who could benefit from bioinformatics training. Using a Train-the-trainer approach allows for better scaling of training provision.

The project aims to sustain and further develop the community of Train-the-trainer instructors brought together by ELIXIR-GOBLET, develop a mentorship programme and create new training modules that can be delivered by ELIXIR members.

ELEAD 2nd Edition: ELIXIR LEadership And Diversity mentoring programme 

Start date: 1 January 2025
Duration: 30 months

Building on the success of the ELIXIR Leadership And Diversity Mentoring Programme (ELEAD) Pilot, launched in 2023 to empower women in ELIXIR's middle management with leadership skills, the ELEAD 2nd edition aims to expand this transformative initiative. Running from 2023–2025 as a strategic implementation study, the ELEAD pilot provided a comprehensive training framework, including one-to-one mentoring and peer mentoring professional training on topics such as inclusion, mental health and effective communication. The programme successfully engaged 12 participants from 10 ELIXIR nodes, with senior mentors from within and beyond ELIXIR.

Feedback from mentees, mentors, trainers and the broader ELIXIR community gathered at the 2024 All Hands Workshop has shaped the 2nd edition (2025–2027). Key enhancements include:

1. Broader dissemination – to reach wider audiences in ELIXIR (updated WP4 and integration of ELIXIR UK) 
2. Expanded cohort – from 12 to 16 
3. Extended face-to-face engagement –  aiming for at least three full days 
4. Involving (more) men and other genders – both as participants and allies, to encourage diverse perspectives and experiences (with parts of the training content opened to the broader ELIXIR community) 
5. Longer programme duration – from 24 to 30 months to address impact and disseminate outcomes

This enriched ELEAD edition continues to focus on fostering mindful leadership among ELIXIR’s middle management, which remains predominantly occupied by women in roles such as Node Coordinators (NoCs). In contrast, leadership positions like Heads of Nodes (HoNs) and Deputy Heads of Nodes (DHoNs) are still mostly held by men. ELEAD’s goal is to drive progress towards a gender-balanced leadership structure across ELIXIR, promoting a diverse and inclusive environment where all members can thrive.

The ambitions for the Science tier of the Commissioned Services are:

Biodiversity, food security and pathogens

Start date: 1 January 2024

Duration: 36 months

Abstract 

In the priorities of the ELIXIR Scientific Programme 2024-2028, molecular science connecting biodiversity, food security and pathogens has been identified as a societal challenge and scientific opportunity set as a core domain that shapes ELIXIR's activities. The Programme stresses that the application of molecular techniques is critical to understand the diversity and breadth of life on Earth. In other words, the diversity of life, rapidly changing climate, increasing contact between the natural world and humans can influence emerging infectious agents which impact not only humans, but also farmed animals, crops and wildlife. 

The Commissioned Service contributes to that Priority through the provision of leadership, community engagement, and open project calls:

• Leadership and Strategy: A team drives strategy, supported by the ELIXIR Hub.
• Community Engagement: ELIXIR Community Members are engaged via meetings and calls.
• Pilot studies and Open Calls: Members submit projects aligned with the roadmap.

This effort connects the ELIXIR Communities and Nodes in their response to advances in biodiversity, food security and pathogens and enables these advances to contribute to wider research questions.

Cellular and molecular research

Start date: 1 January 2024

Duration: 36 months

Abstract 

In the priorities of the ELIXIR Scientific Programme 2024-2028, leveraging cellular and molecular biology advancements is identified as a core domain that shapes ELIXIR's activities. The Programme stresses bioinformatics and cellular/molecular biology's role in solving global challenges and seeks to build a data-centric infrastructure, requiring strategic planning, partnerships, and funding engagement.

The commissioned service contributes to that Priority through the provision of leadership, community engagement, and open project calls:

• Leadership and Strategy: A team drives strategy, supported by ELIXIR Hub.
• Community Engagement: ELIXIR Community Members are engaged via meetings and calls.
• Pilot studies and Open Calls: Members submit projects aligned with the roadmap.

This effort connects the ELIXIR Communities and Nodes in their response to advances in cellular and molecular research and enables these advances to contribute to wider research questions.

Human data and translational research

Proposed start date: 1 January 2024

Duration: 36 months

Abstract 

Human data and translational research is a high priority for ELIXIR and builds on the progress made in the previous programmes by the Human Data Communities. Within the Science tier of the ELIXIR 2024-2028 Programme, advances will be focussed on enabling researchers (including research clinicians) to use ELIXIR’s infrastructure, for human genomic, phenotypic, imaging and demographic data to support discovery, analysis, innovation and integration of research findings into the clinic and healthcare. More specifically, through our objectives we will ensure:

• Millions of human genomes are discoverable and exploited in a biomedical setting through ELIXIR-supported infrastructure and community-endorsed standards, software, workflows and analysis environments across ELIXIR Nodes
• Federated analysis of data is demonstrated for use, for example, in rare disease, cancer, common complex disease, preventative disease, pharmacogenomic studies
• Partnerships linking human data to other disciplines and infrastructures are well established and mechanisms for data deposition are defined and agreed across Nodes
• Industry supports the deployment of the EU data spaces by providing solutions based on ELIXIR-supported standards

To further genomics research capabilities, ELIXIR plans to continue to have a lead role in developing data services, management and practices in this area, supported by the ELIXIR platforms, ELIXIR Nodes and externally funded initiatives. By building upon the network of ELIXIR experts we will ensure interoperability across different data spaces and establish a FAIR and federated data ecosystem.

Through open calls, community face-to-face meetings, workshops, new community engagements and strategic partnerships we will enable scientists to access, deposit and analyse human genomic data, and to link data on a massive scale to ensure knowledge exchange and interoperability across Europe and beyond.

By mapping the needs in the genomic data space in conjunction with scientific groups, Nodes, Communities, and European and International Initiatives, we will join efforts to build a larger infrastructure where data can be securely accessed and used with the aim to improve health and have a positive impact on preventive medicine and healthcare overall.

The ambitions of the Technology tier of the ELIXIR Scientific Programme are:

ELIXIR Infrastructure Services (24-TECH-Infraserv)

Start date: 1 April 2024

Duration: 33 months

Abstract 

Through the previous ELIXIR Scientific Programme, a portfolio of key Infrastructure Services has been developed, on which a range of ELIXIR activities depend - the ELIXIR Authentication and Authorisation Infrastructure (AAI), Training e-Support System (TeSS), Beacon Network, and Research Software Ecosystem. This project will provide a new model of core operational, maintenance and governance funding for these services intended to complement feature development funding from other sources. This approach will be combined with active evaluation of the impact and value for money, develop a protocol for managing the portfolio of Infrastructure Services and their selection, and make recommendations for future continuation or modification of the funding model.

WP1: To establish a cross-Platform Committee to oversee the portfolio and consider Service development, Governance, Funding, Impact and other aspects.  

• WP1: To establish a cross-Platform Committee to oversee the portfolio and consider Service development, Governance, Funding, Impact and other aspects.
• Maintain AAI as an operational Service (LS-Login) with a responsive governance structure and developments to meet user requirements.
• WP3: Maintain TeSS as an operational Service with a responsive governance structure and an approach to Change Management for further development.
• WP4-5: To consider additional Infrastructure Services, in particular Beacon Network and Research Software Ecosystem.

ELIXIR Compute Platform (2024-TECHNOLOGY-Compute)

Start date: 1 January 2024

Duration: 36 months

Abstract 

The ELIXIR Compute Platform ensures that European cloud, compute, storage and access services fulfil the requirements and are available for the life-science research community. European regulation on health data processing is evolving, computing capacity in national clouds is increasing and international standards are improving interoperability between the compute environments.

Such capabilities are also increasingly important to service the growing volumes of biodiversity, food security and pathogen data which comprise complex data types and must be linked to climate data resources. Also, supercomputer investments - especially EuroHPC - provide completely new kinds of computing capacities for researchers across these domains.

All this shapes the landscape of European compute resources. Especially, computing on sensitive data near the data resources is becoming obligatory but the same is true for non-sensitive data e.g. plant phenotyping data and associated imaging data. In 2024-26, the Platform will build technological capability to enable compute in new European-wide federated and multi-cloud settings by building on existing development and utilising previous work, especially Life Science Login. Beyond this, the platform actively seeks sustainable ways to operate the developed services for European researchers.

The Platform will deliver the services to support federated data management and analytics in life science through four complementary WPs:

• WP2 - Advanced Service Access Control
• WP3 - Protected Access to Sensitive Data for Analysis
• WP4 - Multi Cloud Infrastructure Deployment
• WP5 - Sustainability, Accounting and Provenance for Federated Analytics

ELIXIR Data Platform (2024-TECHNOLOGY-Data)

Start date: 1 January 2024

Duration: 36 months

Abstract 

The ELIXIR Data Platform has successfully established a robust community interested in various aspects of life science data, and defined sustainable Core Data Resources (CDRs) of exceptional quality. The Platform is now concentrating on developing and improving methods for brokering data contributions, promoting innovative credit attribution systems, and enhancing and automating data curation practices for FAIRification of existing data.

It seeks to expand its work on sustainability to more diverse biological databases and to create a diverse ecosystem of Node Data Resources, fostering collaborations through its extensive ELIXIR member network, while aligning efforts globally and ensuring impactful contributions to European research innovation.

ELIXIR Interoperability Platform (2024-TECHNOLOGY-Interoprability)

Start date: 1 January 2024

Duration: 36 months

Abstract 

The ELIXIR Interoperability Platform's mission has evolved beyond technical and semantic interoperability, responding to changing needs and life sciences standards. It has already created an ecosystem uniting expertise and information.

Aligned with ELIXIR's priorities, it introduced peer-reviewed Recommended Interoperability Resources, established the ELIXIR Knowledge Hub, and fostered recognition of Research Data Management (RDM). Now it is transitioning to a sustainable framework for enabling real-world data integration and reuse by promoting and supporting interoperability, data management and FAIR principles.

The strategy centres on "The 3 Ps": Products, Processes, and Practices.

• Products entail mapping and coordinating FAIR resources, minimising duplication, and enhancing user experience.
• Processes align products with user needs, ELIXIR Nodes, and global partners.
• Practices convert insights into actionable guidance, empowering users through the connection and use of diverse resources.

These initiatives reinforce the Platform's dedication to interoperability, data stewardship, and efficient resource utilisation. Aligned with Open Science and FAIR principles, they cement the role of ELIXIR in the EOSC ecosystem.

ELIXIR Tools Platform (2024-TECHNOLOGY-Tools)

Start date: 1 January 2024

Duration: 36 months

Abstract 

The ELIXIR Tools Platform provides services that enable findability, accessibility, interoperability, and reusability of computational tools: including research software, workflows, remote digital services, and trained machine-learning (ML) models.

These services aim at being optimised for the needs of molecular life sciences, while at the same time suit a broad range of interdisciplinary applications and scientific communities, including EOSC. The overall goal of the Tools Platform is to sustain the required services and expand them to fulfil the needs of the ELIXIR Programme 2024-2028.

The Tools Platform aims to:

• Allow researchers (end-users) to find well-described and fit-for-purpose research software, providing alternatives when available, that can be used in heterogeneous computational setups from a laptop to a cloud installation to an HPC centre
• Serve as reference point for individual research software engineers on how to develop better, more sustainable, and recognizable software by providing best practices and services supporting such endeavour
• Provide scientific-communities with a reference place for tackling common challenges deriving their own best practices for software development

The Platform will deliver this work through four Work Packages:

• WP2 - The ELIXIR Research Software Ecosystem
• WP3 - Software Management, Stewardship and Standards
• WP4 - Improving Software Quality for reproducible and distributed analysis
• WP5 - Democratised access to reusable complex workflows

ELIXIR Training Platform (2024-TECHNOLOGY-Training)

Start date: 1 January 2024

Duration: 36 months

Abstract 

The ELIXIR Training Platform (TrP) is building a network of training resources and services, aiming for collaboration, visibility, and standardisation. SPLASH, a digital hub, showcases core services like TeSS, enhancing the training life cycle. Work Packages focus on infrastructure, guidelines, and Train-the-Trainer resources. Collaboration across ELIXIR entities is essential, as are standardised guidelines and a supportive community for knowledge sharing. The project's success will transform training delivery within the community.

Technical Coordinators Group link

This group promotes connections among Nodes and Platforms, exploring technical opportunities and issues to provide advice and recommendations. Technical Coordinators are often involved in Implementation Studies or Communities.

Training Coordinators Group link

Constituting of training representatives of each of theELIXIR Nodes. TrCG meets regularly to share information, expertise and to coordinate and lead the implementation of the ELIXIR training strategy across Europe.

Node Coordinators link

This Group facilitates inter-Node communication on topics relevant to the administrative and operational running of the Nodes.

Data Management Coordinators link

Established as part of ELIXIR-CONVERGE project (WP1) this group is involved with the development of the Data Management Tooklit (WP3) and in developing best practices to ensure the infrastructure is sustainable in the long term.

Activities:

The concept of the "Coordinators Triangle" was initially raised at a workshop at the All Hands Meeting in 2021 (document) and picked up at the TeCG (and others) in-person meeting link

CDR Periodic Review 2024

CDR Annual Indicator Monitoring (AIM) 2024

Support

• Please contact Eduardo Esteves and Fabio Liberante at core-resources@elixir-europe.org for queries and support relating to the ELIXIR CDR process.
• Please also note only ELIXIR Node biodata resources are eligible to participate in the ELIXIR CDR/EDD process.

Information on the Global Biodata Coalition (GBC)

• The Global Biodata Coalition (GBC) has created an independent process for the selection and monitoring of the Global Core Biodata Resources (GCBR).
• While independent, the two groups have continued to keep their activities aligned to simplify the participation of ELIXIR members in both the CDR and the GCBR processes.
• Please find key dates and information on the GBC selection process here.

Publications written by members of ELIXIR Nodes. The papers are ordered by the surname of the first author.

• A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development.
  Alexander SPH, Armstrong J, Davenport AP, et al. (2020)  IUPHAR Review 29 [published online ahead of print, 2020 May 1].
  Br J Pharmacol. 10.1111/bph.15094. (https://doi.org/10.1111/bph.15094)
• Clinical population genetic analysis of variants in the SARS-CoV-2 receptor ACE2
  Ardeshirdavani A, Zakeri P, Mehrtash A, Hosseini SM, Li G, et al. (2020)
  medRxiv 2020.05.27.20115071 (https://doi.org/10.1101/2020.05.27.20115071)
• Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic. 
  Blomberg, N, Lauer, KB (2020).
  Eur J Hum Genet 28, 719–723. (https://doi.org/10.1038/s41431-020-0637-5)
• The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor. 
  Brielle ES, Schneidman-Duhovny D, Linial M (2020).
  Viruses 12 (5) 2020 (https://doi.org/10.1101/2020.03.10.986398).
• Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2
  Chiara M, Horner DS, Gissi C, Pesole G (2021).
  Molecular Biology and Evolution, msab049 (https://doi.org/10.1093/molbev/msab049).
• Comparative genomics provides an operational classification system and reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2
  Chiara M, Horner DS, Gissi C, Pesole G (2020).
  bioRxiv (https://doi.org/10.1101/2020.06.26.172924).
• Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-CoV-2
  Chiara M, Horner DS, Gissi C, Pesole G (2020).
  bioRxiv (https://doi.org/10.1101/2020.03.30.016790).
• Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
  Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, et al. (2020).
  Briefings in Bioinformatics, bbaa297 (https://doi.org/10.1093/bib/bbaa297).
• CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
  Chiara M, Zambelli F, Tangaro MA, Mandreoli P, Horner DS, Pesole G (2020).
  Bioinformatics, btaa1047 (https://doi.org/10.1093/bioinformatics/btaa1047).
• Comparative Genomics Reveals Early Emergence and BiasedSpatiotemporal Distribution of SARS-CoV-2
  Chiara M, Horner DS, Gissi C, Pesole G (2021)
  Molecular Biology and Evolution, Volume 38, Issue 6 (https://doi.org/10.1093/molbev/msab049)
• A review on drug repurposing applicable to COVID-19 
  Dotolo S, Marabotti A, Facchiano A, Tagliaferri R (2020).
  Briefings in Bioinformatics, bbaa288 (https://doi.org/10.1093/bib/bbaa288).
• Translating Scientific Knowledge to Government Decision Makers Has Crucial Importance in the Management of the COVID-19 Pandemic.  
  Gombos K, Herczeg R, Erőss B, Kovács SZ, Uzzoli A, Nagy T, et al. (2021)
  Popul Health Manag. Feb;24(1):35-45. (https://doi.org/10.1089/pop.2020.0159)
• Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity 
  Graudenzi A, Maspero D, Angaroni F, Piazza R, Ramazzotti D (2021)
  iScience 24, 102116 (https://doi.org/10.1016/j.isci.2021.102116)
• Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix. 
  Kemenesi G, Zeghbib S, Somogyi BA, et al (2020).
  Viruses 12(12):1401 (doi: https://doi.org/10.3390/v12121401).
• SARS‑CoV‑2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. 
  Lam SD, Bordin N, Waman VP, Scholes HM, Ashford P, Sen H, van Dorp L, Rauer C, Dawson NL, Pang CSM, Abbasian M, Sillitoe I, Edwards SJL, Fraternali F, Lees JG, Santini JM & Orengo (2020)
  Nature Scientific Reports 10:16471 (https://doi.org/10.1038/s41598-020-71936-5)
• Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
  Maier W, Bray S, van den Beek M, Bouvier D, Coraor N et al. (2021)
  bioRxiv [Preprint]. 2021 Mar 25:2021.03.25.437046 (https://doi.org/10.1101/2021.03.25.437046).
• Modeling COVID-19 pandemic using Bayesian analysis with application to Slovene data. 
  Manevski D, Gorenjec NR, Kejžar N, Blagus R (2020)
  Mathematical Biosciences, Volume 329 (https://doi.org/10.1016/j.mbs.2020.108466).
• SARS-CoV-2-Specific Antibody Profiles Distinguish Patients with Moderate from Severe COVID-19 
  Mata LC, Piñero J, Vaquero ST, Tachó-Piñot R, Kuksin M et al. (2020)
  medRxiv 2020.12.18.20248461 (https://doi.org/10.1101/2020.12.18.20248461).
• FAIR, ethical, and coordinated data sharing for COVID-19 response: a review of COVID-19 data sharing platforms and registries
  Maxwell L, Shreedhar P, Dauga D, McQuilton P, Terry R et al. (2020)
  Research Square (pre-print) (https://doi.org/10.21203/rs.3.rs-1045632/v1).
• Characterization of accessory genes in coronavirus genomes. 
  Michel CJ, Mayer C, Poch O, Thompson JD (2020)
  Virology Journal volume 17, Article number: 131 (https://doi.org/10.1186/s12985-020-01402-1).
• The landscape of SARS-CoV-2 RNA modifications.
  Milad M, Fuchs J, Maier W, Weigang S, Díaz i Pedrosa N, Weiss L, Lother A, Nekrutenko A, Ruzsics Z, Panning M, Kochs G, Gilsbach R, Grüning B (2020) 
  bioRxiv 2020.07.18.204362 (https://doi.org/10.1101/2020.07.18.204362)
• Detailed disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic: An exploratory analysis
  Modrák M, Bürkner P, Sieger T, Slisz T, Vašáková M, et al. (2020) 
  medRxiv 2020.12.03.20239863 (https://doi.org/10.1101/2020.12.03.20239863)
• Different mutations in SARS-CoV-2 associate with severe and mild outcome.
  Nagy Á, Pongor S, Győrffy B. (2021)
  Int J Antimicrob Agents 57(2):106272. (https://doi.org/10.1016/j.ijantimicag.2020.106272).
• From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance
  Ortuño FM, Loucera C, Casimiro-Soriguer CS, Lepe JA, Martinez PC, Diaz LM et al. (2021)
  bioRxiv 2021.04.13.439668 (https://doi.org/10.1101/2021.04.13.439668)
• Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece
  Pechlivanis N, Tsagiopoulou M, Maniou M, Togkousidis A, Mouchtaropoulou E et al. (2021)
  Scientific Reports (https://doi.org/10.21203/rs.3.rs-677811/v1)
• Detection of A-to-I RNA Editing in SARS-COV-2
  Picardi E, Mansi L, Pesole G (2021)
  Genes (Basel) Dec 23;13(1):41. (https://doi.org/10.3390/genes13010041).
• Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion
  Russell YN, Nikos CK, Christos AO (2021). 
  mBio Jan 2021, 12 (1) e03014-20. (https://doi.org/10.1128/mBio.03014-20)
• Galaxy and HyPhy developments teams. No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics.
  Nekrutenko A, Pond SLK (2020). 
  bioRxiv 2020.02.21.959973 (https://doi.org/10.1101/2020.02.21.959973)
• COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
  Ostaszewski, M, Mazein, A, Gillespie, ME et al. (2020).
  Sci Data 7, 136. (https://doi.org/10.1038/s41597-020-0477-8)
• Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece
  Pechlivanis N, Tsagiopoulou M, Maniou MC, Tougkousidis A, Laidou S et al. (2021)
  medRxiv 2021.03.17.21252673 (https://doi.org/10.1101/2021.03.17.21252673)
• A-to-I RNA editing in SARS-COV-2: real or artifact? 
  Picardi E, Mansi L, Pesole G. (2020)
  bioRxiv. (https://doi.org/10.1101/2020.07.27.223172).
• VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
  Ramazzotti D, Angaroni F, Maspero D, Antoniotti M, Graudenzi G, Piazza R (2021)
  Patterns 2 (https://doi.org/10.1016/j.patter.2021.100212).
• A-to-I RNA editing in SARS-COV-2: real or artifact? 
  Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J (2020)
  bioRxiv. (https://doi.org/10.1101/2020.04.12.025577).
• Mechanistic modeling of the SARS-CoV-2 disease map
  Rian K, Esteban-Medina M, Hidalgo MR, Çubuk C, Falco MM, Loucera C, Gunyel D, Ostaszewski M, Peña-Chilet M, Dopazo J (2021)
  BioData Mining volume 14, Article number: 5 (https://doi.org/10.1186/s13040-021-00234-1).
• Role of the early secretory pathway in SARS-CoV-2 infection.
  Sicari D, Chatziioannou A, Koutsandreas T, Sitia R, Chevet E. (2020) 
  The Journal of Cell Biology Sep;219(9). (https://doi.org/10.1083/jcb.202006005).
• Prevalence of SARS-CoV-2 infection in the Luxembourgish population – the CON-VINCE study
  Snoeck CJ, Vaillant M, Abdelrahman T, Satagopam VP, Turner JD, Beaumont K et al. (2020) 
  medRxiv. (https://doi.org/10.1101/2020.05.11.20092916).
• Recombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein S.
  Tagliamonte MS, Abid N, Ostrov DA, et al. (2020) 
  bioRxiv. (https://doi.org/10.1101/2020.03.30.015685).
• BIP4COVID19: Impact metrics and indicators for coronavirus related publications (Version 0.1) [Data set]
  Vergoulis T, Kanellos I, Chatzopoulos S, Karidi DP Dalamagas T (2020). 
  Zenodo (https://doi.org/10.5281/zenodo.3723282)
• Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy
  Voigt A, Omholt S, Almaas E (2022). 
  PLOS One (https://doi.org/10.1371/journal.pone.0263155)

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