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Project description
L’IFB-core pilote le projet PIA3 – Equipex, “Mutualised Digital Spaces for FAIR Life Sciences” (MUDIS4LS) afin de consolider ses orientations stratégiques et de les structurer autour de 5 projets thématiques (Implementation Studies – IS) qui s’appuient sur 4 WorkPackages (WP) technologiques. Ce projet vise à couvrir plus ou moins 30% des besoins en équipement pour l’ensemble des plateformes de l’IFB de 2021 à 2029, et réunit 17 établissements-partenaires. Partiellement orienté sur l’achat d’équipement, il constitue le socle de l’infrastructure numérique distribuée opérée par l’ensemble des plateformes et gérée par une “task force” mutualisée (WP2). Un axe majeur du projet est d’assurer l’orchestration des flux de données tout au long de leur vie (WP3), depuis leur production (avec les INBS) jusqu’à leur diffusion via des dépôts nationaux et internationaux. Il relève également le défi de l’IA pour les sciences de la vie en s’appuyant sur les ressources nationales de calcul intensif (WP4). Ses 5 implémentations studies visent à affronter le défi de l’intégration multi-omique, imagerie et phénomique (IS1) et à articuler les développements sur les besoins des communautés ciblées : écologie marine (IS2), santé (IS3), microbiologie (IS4) et agriculture (IS5).
WP1 – Coordination
Co-responsables : Jacques van Helden (AMU), Gildas Le Corguillé (SU/CNRS), Julien Seiler (CNRS), Rachida Chibani (CNRS), Hamid Ouahioune (CNRS)
Goals :
- Preparation of contractual documents
- Implementation and management of the governance framework
- Deployment of organizational tools
- Project reporting and monitoring
- Internal and external communication
WP2 – A Distributed data infrastructure for project-life-long secured storage and backup
Co-managers : Guillaume Seith, Olivier Sallou
Goals :
- Rationalize the equipment of IFB federated platforms by installing all equipment in certified regional or national data centers.
- Support the NNCR Core and Regional Nodes, combining HPC and secure storage in the medium term.
- Extend services to areas not yet covered by the NNCR IFB.
- Build a backup network between sites within the NNCR.
- Create shared data spaces (data lakes) allowing the integration of different types of data and their access by different IT technologies in a transparent manner.
WP3 – Orchestrating data flows for life sciences
Co-responsables : Julien Seiler (CNRS), Frédéric de Lamotte (INRAE)
Goals : Ensure data availability
- Develop procedures based on machine-readable data management plans (maDMP) for managing data flows between production infrastructures, computing centers, and repositories.
- Instrumenting data and computing infrastructures for metadata capture (including provenance) and feeding into maDMPs.
- Automatically update maDMPs throughout the research project lifecycle.
- Disseminate the maDMPs to the INBS in order to ensure data management complies with FAIR principles from the outset.
- Establish links with ELIXIR repository services for data brokerage.
- Providing environments that enable data curation by communities
- Increase the visibility of data hosted by the IFB and its partners.
Use cases:
- Submission of sequence data to EBI-ENA
- Data Fairization
WP4 – Intensive Computational Biology (HPC/AI)
Co-managers : Christophe Blanchet (IFB-core) et Philippe Hupé (Institut Curie)
Goals :
- Establish access to and use of national HPC/AI resources (IDRIS) for the life sciences community.
- Implement suitable research environments and useful bioinformatics resources (tools and reference data).
- Prototyping and evaluating performance at intermediate sites (CBP-PSMN)
- Train developers and users
Use cases:
- Deploying Healthcare Applications in an HPC/AI Environment (IS3)
- Deploy Microbiome Applications in an HPC/AI Environment (IS4)
- Evaluate applications with different computing resources (benchmark)
- Moving data between IDRIS and CCIN2P3 sites to make them accessible and interoperable (FITS project coll.)
IS1 – FAIR integration of imaging, multi-omics and phenomics data
Co-managers : Jean-François Dufayard (IFB), Perrine Paul-Gilloteaux (FBI) et Emmanuel Faure (FBI)
Goals :
- Preparing the roadmap for a national repository of scientific imaging
- Coordinate data flow with specific DMP (Data Management Plan) templates
- Ensure the FAIR aspect of imaging data management, and their integration with multi-omics data
- Provide specialized workflows for multi-scale integration
IS2 – Marine biology data integration and dissemination
Co-managers : Erwan Corre (IFB + EMBRC) – Lucas Leclère (EMBRC) – Eric Pelletier (CEA + FR-2022 GO-SEE)
Goals :
- Build specific Data Management Plans (DMPs) for marine organisms, inspired by the work initiated by the community working on marine metagenomic data within the ELIXIR project.
- Contribute to the development of a national infrastructure to ensure the regular processing and dissemination of data produced by marine stations and marine observatories.
- Promote the “FAIRfication” of data from marine models and augmented observatories and their dissemination in ecological data infrastructures (DataTerra, Emodnet Biology) and genomic and imaging data repositories (ENA, EuroBioImage).
IS3 – Bioinformatics solutions for processing health data
Co-managers : David Salgado (INSERM U1251- MMG-GBiT), Abdelkader Amzert (DSI-INSERM) et Boris Dintrans (CINES)
Goals :
- Health data is sensitive: it requires specific storage and computing environments to comply with regulatory policies
- Leverage the physical, technical and human resources developed within the Mudis4LS project to extend its use to sensitive data
- Implement services to manage, process (large-scale workflows), compare, host and share health data
- Provide guidelines, templates and tools for biomedical DMPs to apply the FAIR principles – adapting the researchers’ digital environment (WP1) to sensitive data.
IS4 – FAIR Integration and Sharing of the New Data Deluge in Microbiome Research
Co-coordinators : Claudine Médigue (IFB, CNRS), Nicolas Pons (INRAE-MGP)
Goals :
- Contribute to the development of a shared data space for the storage and integration of genomic and metagenomic data from massive sequencing and other types of data.
- Provide guidelines and templates for DMP implementation, including FAIR principles and covering minimum standards for microbiome data acquisition, processing, deposition, and interoperability, with specific recommendations for multi-omics data integration.
- Establishing minimum requirements for metagenome annotation strategies
- Define recommendations and considerations in structuring large datasets with respect to the application of the microbiome for AI and HPC implementation.
Use cases: Diffusion of antimicrobial resistance; link between microbiome signatures and susceptibility to viral infections; implementation of AI on the Jean-Zay calculator.
IS5 – FAIR Integration and Sharing of Genetic and Multi-OMICs Data for Agriculture
Co-coordinators : Anne-Françoise Adam-Blondon (RARe, PlantBioinfoPF), M. Boichard (RARe), V. Loux (Migale)
Goals :
- Supporting FAIR management of data on biological resources managed by the AgroBRC-RARe infrastructure (https://www.agrobrc-rare.org)
- Launch the development of services that help connect biological resources with highly heterogeneous data types, including various types of “omics” data, phenotypic measurements, including images, and environmental data.
- Pay particular attention to holobiontic studies on animals and plants as well as their commensal, symbiotic and pathogenic microorganisms.
Method : Use existing projects as guinea pigs, such as:
- Plants: ANR DeepImpact
- Animals: CYATHOMICS, H2020 Sapphire
August 1st, 2021 – Project launch
April 2022 – MUDIS4LS Kickathon
January 2025 – MUDIS4LS SAB Meeting
July 2025 – Mid-term evaluation report
31 juillet 2027 – End of the equipment installation phase
July 31, 2029 – End o project
All publications affiliated with the MUDIS4LS project can be found in HAL.