National Coordination

Anne-Françoise Adam-Blondon

► To cite this version:

Anne-Françoise Adam-Blondon. National Coordination. 10 Years of ELIXIR: Enabling excellence and impact, ELIXIR, Dec 2023, Bruxelles (BE), Belgium. hal-04503439

HAL Id: hal-04503439

https://hal.inrae.fr/hal-04503439

Submitted on 13 Mar 2024

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\#DecadeofData
\#ELIXIRis10

National Coordination

Anne-Françoise Adam-Blondon

Head of Node, ELIXIR France
# The French Institute of Bioinformatics (IFB) is ELIXIR-FR, the French Node of ELIXIR

## IFB is a distributed French National Research Infrastructure

- 36 platforms and research teams spread all over France

## Coordination: IFB-core

- Multi-research organizations : CNRS, Inserm, INRAE, CEA

## Common resources

- Supported by the French Ministry of Higher Education and Research since 2012

## A large set of expertise in bioinformatics

- >400 experts (~200 FTE)

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# IFB/ELIXIR-FR has a large set of domain of applications

IFB's domains of application encompass the three scientific priorities of the 2024-2028 programme of ELIXIR

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Enabling and responding to
advances in cellular and molecular
research will drive life science

Connect the latest developments and
established data resources to realise
the potential of cellular and molecular
biology

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Biodiversity, food security and
pathogens are interrelated
societal challenges

Mobilise and integrate molecular data
to support transnational research
programmes in biodiversity, food
security and pathogens

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The promise of genomics
research to improve health
and disease outcomes

Provide the infrastructure to support
the discovery, access, sharing and
analysis of human genomics data and
linked data on a massive scale
<figure><img src="image_10.png" /></figure>

* Contribution to transversal activities addressing common challenges

* Multi-research organizations governance

* FAIR data management and data interoperability

* Partnership in large national projects

* Enhance partnerships in ELIXIR activities and in European projects

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# IFB-ELIXIR-FR is contributing to ELIXIR's activities

* Liaising and networking with all platforms and most of the communities and contributing to their activities

* Co-coordinating and contributing to the strategic planning of some of them => **France**

* Contributing to European projects: 9 since 2020

## Communities

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Science

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Technology,

## Platforms

ELIXIR Platforms bring together experts from Nodes to develop ELIXIR's technical vision and coordinate activities in defined technical areas. There are five Platforms: Data, Tools, Interoperability, Compute and Training.

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### Data Platform

Aims to identify key data resources across Europe and support the linkages between data and literature.

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### Tools Platform

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Helps researchers find the best software tools to analyse their data.

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### Compute Platform

Develops services to make it easier to store, share and analyse large datasets.

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### Interoperability Platform

Develops and encourages the adoption of standards to describe life science data.

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### Training Platform

Helps scientists and developers find the training they need, and also provides that training.

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### 3D-Bioinfo

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### Biodiversity

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### Food and nutrition

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### Galaxy

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### Intrinsically Disordered Proteins

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### Marine Metagenomics

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### Metabolomics

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### Microbial Biotechnology

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### Plant Sciences

litate
crop and

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### Proteomics

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### Single-Cell Omics

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### Systems Biology

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### Toxicology

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R

## Human Data Communities

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### Federated Human Data

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### Human Copy Number Variation

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### Rare diseases

### Cancer Data (focus group)

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# IFB-ELIXIR-FR's 2022-2025 road map and organisation in transversal Task Forces

Develop with the task forces a strategy that integrates national and ELIXIR's activities for node's benefice

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## National activities

* Software development task force

* Sharing good practices for development

* Sharing recipes for deployment

* Deployment of environments for analysis

* E.g. [Usegalaxy.fr](https://usegalaxy.fr) (metabolomics, proteomics, covid19, ...)

<table><thead><tr><td>Tools development and deployment</td><td>2021</td><td>2022</td></tr></thead><tbody><tr><td>New tools</td><td>19</td><td>16</td></tr><tr><td>Number of unique users of the platforms web tools</td><td>573 244</td><td>352 644</td></tr><tr><td>Number of uploads of the tools developed by the platforms</td><td>16 912</td><td>24 307</td></tr></tbody></table>

<figure><img src="image_43.png" /><figcaption>Vincent Lefort</figcaption></figure>

<figure><img src="image_44.png" /><figcaption>Hervé Ménager
ELIXIR Tools PF coord
EDAM steering committee</figcaption></figure>

<figure><img src="image_45.png" /><figcaption>Anthony Bretaudieu
Elixir Galaxy community</figcaption></figure>

<figure><img src="image_46.png" /><figcaption>Olivier Sallou
Elixir Tech Coord</figcaption></figure>

## International/ELIXIR activities

* Service Delivery Plan ELIXIR-FR: labelling of French services

* Involvement in the coordination of the ELIXIR Tools Platform (Hervé Ménager): contribution to the strategic planning, coordination of activities, outreach, good practices

* Involvement in strategic projects for the ELIXIR Tools platform: BioContainers (Olivier Sallou) Dynamic deployment of virtual environments

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* Involvement in the ELIXIR Galaxy community (Anthony Bretaudieu): contribution to [usegalaxy.eu](https://usegalaxy.eu)
# Data management in the Plant Science community: another example of synergy

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anr

agence nationale
de la recherche

IFB

agence nationale
de la recherche

anr

agence nationale
de la recherche

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MUDIS4LS

FRANCE

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BReIF

- DM interoperable
between national
RIs

- on boarding
domestic animals

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-Independent
standards: MIAPPE,
BrAPI

-POC: portal for a
wheat data federation

-Interoperable and well
specified standards: MIAPPE,
BrAPI, ISA

-On boarding forest trees

-Tested training resources

-FAIDARE: plant data portal

- DM guidelines in
RDMkit validated by a
project

-FAIR Cookbook recipes

-Learning path
# IFB/ELIXIR-FR in the national « ecosystem » supporting Open Science

* 2022: the French Ministry of Research and Higher Education launches Recherche Data Gouv

* IFB/ELIXIR-FR is mandated to organize a « thematic reference center » for Life Science data :

* Development and dissemination of data standards

* Support to data management and data curation

* Data brokering

* Harvesting data for the national data catalog

## Recherche Data Gouv at a glance

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**Modules to support research teams on all issues linked to data:**

* Data management clusters

* Thematic reference centres

* Resources centres

* Institutional reference centers

**Modules to deposit, publish and disseminate data:**

* A repository to deposit and disseminate data

* A registry to search for data published in the repository itself or other external repositories

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RÉPUBLIQUE
FRANÇAISE

Liberté
Égalité
Fraternité

recherche.data.gouv.fr