A European infrastructure for farmed animal genotype to phenotype research

Risultati finali

Set of biobanking access rules for future TNA for input in WP2

The access procedures linking with WP2 in the form of a set of bio banking 'rules' will be developed for D4.2 to connect EuroFAANG repositories and standardise the requesting procedures, for tissues or cells for G2P research, via TNA applications to the EuroFAANG infrastructure.

Dissemination and communication plan

For D8.2 a communication and dissemination plan will be developed for the long term promotion of the EuroFAANG infrastructure through the EuroFAANG webpage, social media networks, and relevant conferences.

Outcomes of stakeholder workshops exploring TNA to genome editing technologies

To engage with stakeholders EFFAB will run an annual workshop, when the think-tank on genome editing will meet virtually and explore the use of genome editing, barriers to implementation, and importance of TNA to capabilities and facilities for application of the technology. Outcomes of these workshops will be consolidated for D5.5.

Report on Global EuroFAANG animal agriculture G2P networking event

D8.1 will provide a report on Global EuroFAANG animal agriculture G2P networking event that will be held at the Plant and Animal Genomes conference in San Diego

Template of collaboration agreements between EuroFAANG and INFRA projects for animal phenotyping

D7.3 will map the relevant projects from the INFRAIA, INFRA-DEV, INFRA-SERV, INFRA-TECH actions. Mapping of the national R.I Roadmaps in the field of phenomics and genomics for farm animals, will also be performed, to anticipate a possible future European organisation of national RIs in this field.

Results of survey of technological advancements in the field

To identify new potential partners to integrate with the EuroFAANG operating infrastructure, EFFAB and UEDIN will undertake a survey of scientific and technological developments in the field and of other international and national initiatives in animal agriculture, including those beyond the state of the art, and provide the results of the survey for D1.3.

List of existing biorepositories to be connected via a common portal for access to resources labs

For D4.1 the European facilities storing sample collections that are open to collaboration, their current users and the list of potential future users upon EuroFAANG upgrading will be mapped, and a list created, building on the gene bank survey performed by the former H2020 IMAGE project.

EuroFAANG infrastructure business plan

The business plan (D1.5) will be provided by FBN, as project coordinator, and will have three main objectives: i) to provide a breakdown of costs across partners, ii) to define the political and financial support required for the EuroFAANG infrastructure and iii) to determine the required logistical and administrative support for the infrastructure. Additional components of the business plan will include a ‘business model’, user strategy, value proposition, analysis of market trends and opportunities, and a communication plan.

Report on current data infrastructure gaps and proposals for required data infrastructure development including an update of the DMP

For D3.5 a report will be produced that identifies the gaps in existing FAANG and EuroFAANG data structure and infrastructure that will be required to support the developing EuroFAANG components (WP4-6), access requirements (WP2) and interoperability with other existing and developing infrastructures (WP7). The report will also cover requirements for development including design and technical preparatory work for the integration and e-infrastructure of the FAANG data platform to support new and emerging technologies and infrastructures for EuroFAANG.

Inventory of upcoming technologies and required inter- and transdisciplinary networks bridging the gap between genome/cellular/organoid and organism level information with respect to key challenges as outlined in the Green Deal and Farm to Fork strategy

D6.1 will provide an inventory of upcoming technologies and required inter- and transdisciplinary networks bridging the gap between genome/cellular/organoid and organism level information with respect to key challenges as outlined in the Green Deal and Farm to Fork strategy.

Roadmap to set up an animal science community within ELIXIR

D7.1 will study the potential added value and the feasibility of establishing an Animal Agriculture Community within Elixir, drawing from the experience of the existing Plant Science Community. For this, we will map the interest of data scientists across countries and Elixir nodes to collaborate in a community for farmed animal research.

Framework for access to HTP platforms

D5.1 will provide a framework for how stakeholders could test a causal variant or set of functional variants using high-throughput phenotyping (HTP) platforms with cellular models (developed in WP4).

Report on existing and required interfaces to the animal farming industry for integrating genome and phenotype information

D6.2 will provide a report on existing and required interfaces to the animal farming industry for integrating genome and phenotype information

List of barriers to implementation of genome editing technology in vitro and in vivo

D5.3 will summarize the status quo regarding existing barriers (legal, technical, societal) to implement genome editing in vivo and in vitro

List of services that can be proposed to RIA projects

D7.4 will provide a list of services that EuroFAANG could provide to other RIA projects, i.e. integrating their outputs into its services and making them sustainable in the long term, for instance in terms of protocols, pipeline, panels of reference samples and in vitro models, FAIR data sharing and data management processes, and taking advantage of the EuroFAANG Data Portal.

Formalised access policy for the infrastructure

D 2.1 is concerned with formalising an access policy for the EuroFAANG infrastructure based on scientific excellence for academia and based on feasibility and impact for industry. Criteria of selection will be soundness of concept and adequacy of the experimental design. Applicants and users’ profiles, geographical distribution and gender will be also considered; for example, access priority will be given to users who can rely only on limited resources locally and nationally.

Publish formalised EuroFAANG Data policy and access principles

For D3.2 a data policy and set of access principles will be developed for the future users of the EuroFAANG infrastructure that will define the data handling expectations and data access requirements for all users of the EuroFAANG infrastructure, with a focus on open science, FAIR data principles and existing European policies.

Publication of the EuroFAANG design study and sustainability plan

D8.3 will outline the design components necessary for the EuroFAANG infrastructure to provide services that offer new solutions for a transformed farmed animal production landscape in Europe. D8.3 will describe the available resources, stakeholder interest and support and also challenges for setting up a comprehensive EuroFAANG infrastructure. In addition to the status quo, the deliverable will provide a sustainability plan for EuroFAANG, i.e. perspectives how the EuroFAANG initiave will be operational beyond the lifetime of the current project.

List of labs/institutions dedicated to application of artificial intelligence for G2P prediction

D6.3 will provide list of labs/institutions dedicated to application of artificial intelligence for G2P prediction to establish interconnected nodes with appropriate AI expertise as a platform for research based on functional genome and phenome information at cellular, organismal and population level to address key challenges in animal farming.

Plan describing the different options for transnational access to the infrastructure and how they can be implemented

How distribution of transnational access to the EuroFAANG infrastructure will be set up and managed via different options including on-site, remote or virtual means will be devised in D2.2 and a plan describing TNA to the infrastructure published.

Report on possible collaboration between EuroFAANG and other ESFRI infrastructures

D7.2 will map the relevant RIs in the ESFRI Roadmap and provide a report on possible collaboration between EuroFAANG and other ESFRI infrastructures, based on specific workshops to be organised in Task 7.1.

Framework for equitable partnership and connecting industry for pre-competitive research

D4.6 will establish a collaborative framework with industry users focused on the use of in vitro models and tools under the 3Rs principle for pre-competitive research by relying on multiple measures of communications and outreach.

Open samples policy

D4.3 links with WP2 and will develop an “open samples” policy, built on the “open data” philosophy of EuroFAANG, aimed to achieve the equitable sharing of created models for building new scientific knowledge and for facilitating bilateral competitive G2P research for the breeding industry stakeholders. This open sample policy will be elaborated and integrated in the TNA model of the infrastructure devised in WP2.

Survey form for feedback from users, hosts and stakeholders accessing the infrastructure

After each access provision, the quality of the access given will be evaluated through a satisfaction survey, developed for D2.3, for users, hosts and stakeholders of the EuroFAANG infrastructure.

Publish metadata standard requirements to support proposed infrastructures

For D3.4 a set of metadata standards will be published for the EuroFAANG infrastructure which requires development of rich metadata standards, in line with FAIR and Elixir principles, and provision of efficient data curation and information brokering platforms to ensure long term preservation of generated data in the public INSDC archives and FAANG data portals.

Report on EuroFAANG and Elixir on shared information management strategy including an update of the DMP

A shared strategy for management and standardisation of animal agricultural data will be developed between Elixir and EuroFAANG, for D3.3, that will clarify synergies and responsibilities for data management, data production, data sharing and data standards.

Collaborative framework with EUGENA and industry users

D4.5 will establish a connection with European organisations such as EUGENA (the European animal gene bank network, managed by the European Regional Focal point) with the aim to contribute to safeguarding genetic diversity through biobanking.

Consolidated list of all labs using genome editing in Europe

D5.2 will help to facilitate access to genome editing technology in vivo and in vitro by providing a list of all the animal research facilities currently generating genome edited animals, as well as those performing genome editing in vitro using organoids and cell lines to help facilitate connection and consolidate research effort.

EuroFAANG Data Management Plan

A Data Management Plan (DMP) will be developed and published for EuroFAANG in accordance with Horizon guidelines for D3.1. The DMP will cover all data generated as part of the concept development stage of EuroFAANG.

Pubblicazioni

EuroFAANG Data Policy and Access Principles

Autori: Clark Emily , Solokov Alexey, Peter Harrison
Pubblicato in: 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18550511

An Open Sample Policy for a European infrastructure for farmed animal genotype to phenotype research

Autori: Ige T-O, Tixier Boichard M, Guiffra E
Pubblicato in: 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18602790

Plan describing the different options for transnational access to the infrastructure and how they can be implemented

Pubblicato in: 2023
Editore: EUROFAANG

Empowering bioinformatics communities with Nextflow and nf-core

Autori: Langer, Björn; Amaral, Andreia; Baudement, Marie-Odile; Bonath, Franziska; Charles, Mathieu; Chitneedi, Praveen; Clark, Emily; Di Tommaso, Paolo; Djebali, Sarah; Ewels, Philip; Eynard, Sonia; Yates, James; Fischer, Daniel; Floden, Evan; Foissac, Sylvain; Gabernet, Gisela; Garcia, Maxime; Gillard, Gareth; Gundappa, Manu; Guyomar, Cervin; Hakkaart, Christopher; Hanssen, Friederike; Harrison, Peter; Hörtenhuber, Matthias; Kurylo, Cyril; Kühn, Christa; Lagarrigue, Sandrine; Lallias, Delphine; Macqueen, Daniel; Miller, Edmund; Mir-Pedrol, Júlia; Moreira, Gabriel; Nahnsen, Sven; Patel, Harshil; Peltzer, Alexander; Pitel, Frederique; Ramayo-Caldas, Yuliaxis; da Câmara Ribeiro-Dantas, Marcel; Rocha, Dominique; Salavati, Mazdak; Sokolov, Alexey; Espinosa-Carrasco, Jose; Notredame, Cedric
Pubblicato in: BMC Genome Biology, 2025, ISSN 1474-760X
Editore: Springer Nature
DOI: 10.1186/S13059-025-03673-9

Survey form for feedback for Trans-National Access (TNA) applications access

Autori: Godia M
Pubblicato in: 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18506353

EuroFAANG Research infrastructure business plan

Autori: Hartwig T, Tixier-Boichard M, Clark E
Pubblicato in: 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18772032

Gene Editing in European Agriculture - EuroFAANG RI

Autori: Cartick G, Clark E
Pubblicato in: 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18611798

EuroFAANG Research Infrastructure Data Management Plan

Autori: Clark Emily , Solokov Alexey
Pubblicato in: Zenodo, 2026
Editore: Zenodo
DOI: 10.5281/ZENODO.18548947

Genomics

Autori: Clark, Emily L
Pubblicato in: Genomics, Numero 111220, 2026, ISSN 0888-7543
Editore: Elsevier
DOI: 10.1016/J.YGENO.2026.111220

Aquaculture

Autori: Johnston I. A.; Kent M. P.; Boudinot P.; Looseley M.; Bargelloni L.; Faggion S.; Merino G. A.; Ilsley G. R.; Bobe J.; Tsigenopoulos C. S.; Robertson J.; Harrison P. W.; Martinez P.; Robledo D.; Macqueen D. J.; Lien S.
Pubblicato in: Aquaculture, Numero 583;740589, 2024, ISSN 0044-8486
Editore: Elsevier
DOI: 10.1016/J.AQUACULTURE.2024.740589

Risultati finali

Pubblicazioni

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