# IFB/ELIXIR-FR, the french node of ELIXIR

Anne-Françoise Adam-Blondon, Jacques van Helden, Gildas Le Corguillé, Christophe Blanchet, Hélène Chiapello, Christine Gaspin, David Salgado, Julien Seiler, Morgane Thomas-Chollier, Yves Vandenbrouck, et al.

► To cite this version:

Anne-Françoise Adam-Blondon, Jacques van Helden, Gildas Le Corguillé, Christophe Blanchet, Hélène Chiapello, et al. IFB/ELIXIR-FR, the french node of ELIXIR. ISMB ECCB 2023, International Society for Computational Biology, Jul 2023, Lyon, France. hal-04503051

HAL Id: hal-04503051

https://hal.inrae.fr/hal-04503051

Submitted on 13 Mar 2024

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# IFB/ELIXIR-FR, the french node of ELIXIR

A-F Adam-Blondon, J van Helden, G Le Corguillé, C Blanchet, H Chiapello, C Gaspin, D Salgado, J Seiler, M. Thomas-Chollier, Y Vandenbrouck, G Perrière
## ELIXIR and the French Institute of
Bioinformatics (IFB)

Two collaborative networks of people building
resources and services for research in Life
Sciences

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26 nodes: 25 national nodes + EMBL-EBI collaborate in order to:

Develop people and
capacity to benefit science
and society

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People

Enable scientists to access and
analyse life science data

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Science

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Nodes

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Technology

Equip national Nodes for
successful long-term
operations

Deliver services to support
distributed data
management and
analytics
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<figure><img src="image_10.png" /></figure>

INSTITUT FRANÇAIS DE BIOINFORMATIQUE

## 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)

<figure><img src="image_11.png" /></figure>

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IFB

elixir
FRANCE

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INRAE

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Inserm

cea

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INSTITUT FRANÇAIS DE BIOINFORMATIQUE
<figure><img src="image_16.png" /></figure>

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

<figure><img src="image_17.png" /></figure>

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

<figure><img src="image_18.png" /></figure>

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

<figure><img src="image_19.png" /></figure>

<figure><img src="image_20.png" /></figure>

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

Better deliver the data, services and expertise necessary to address important societal challenges
<figure><img src="image_21.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

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INRAO

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Inserm

ce2

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* 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 FR

* Contributing to European projects: 9 since 2020

<figure><img src="image_29.png" /></figure>

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.

<figure><img src="image_30.png" /></figure>

### Data Platform

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

<figure><img src="image_31.png" /></figure>

### Tools Platform

FR

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

<figure><img src="image_32.png" /></figure>

### 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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Science

## Communities

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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 FR

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Metabolomics

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Microbial Biotechnology

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Plant Sciences

Plant and

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Proteomics

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Single-Cell Omics

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Systems Biology

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Toxicology

FR

### Human Data Communities

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Federated Human Data

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Human Copy Number Variation FR

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Rare diseases

Cancer Data (focus group) FR
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<figure><img src="image_53.png" /><figcaption>Guy Perrière
ELIXIR-FR Head of Node</figcaption></figure>

<figure><img src="image_54.png" /><figcaption>Anne-Françoise Adam-Blondon
ELIXIR-FR Head of Node</figcaption></figure>

<figure><img src="image_55.png" /><figcaption>Angela Sáenz
ELIXIR-FR Node coordinator</figcaption></figure>
Development of the 2022-2025 roadmap

<figure><img src="image_56.png" /></figure>
## ...and brainstorming on the next roadmap

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<figure><img src="image_58.png" /><figcaption>**Claudine Médigue**
Director of IFB
Head of Node ELIXIR-FR
2017-2022</figcaption></figure>

<figure><img src="image_59.png" /><figcaption>**Gildas Le Corguillé**
Interim director of IFB
2022-2023</figcaption></figure>

<figure><img src="image_60.png" /><figcaption>**Jacques van Helden**
IFB's scientific coordinator
Head of Node ELIXIR-FR</figcaption></figure>

<figure><img src="image_61.png" /><figcaption>**Anne-Françoise Adam-Blondon**
Deputy Head of Node ELIXIR-FR
2018-2023</figcaption></figure>
<figure><img src="image_62.png" /></figure>

## Infrastructure

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* National Network of Computing Resources (NNCR)

* Two modalities: **cluster + cloud**

* Compliance to law (GDPR)

## Support to users

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* One stop portal and contact address

* Co-development of the bioinformatic/statistical part of the project

* DMP

* Development of **workflows**

* Data Science

## Prospective and innovation

<figure><img src="image_65.png" /></figure>

* Identification of emerging needs in bioinformatics

* Funding of Pilot-projects

## Tools

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* Development of dedicated tools

* Packaging (conda)

* Virtualisation (appliances, containers)

* Software development practices

* Collaborative development, open code

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## Task Forces

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## Knowledge bases

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* Development of data and knowledge bases

* Quality and data standards

* Technical support to developers

* Deployment of databases developed up in France

## Training

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* **Thematic schools** (NGS, multi-omics, phylogeny, biostat, programming, workflows...)

* **Bring Your Own Data** (BYOD) trainings

* Webinars, MOOC

* **FAIR-data et FAIR-bioinfo** training and capacity building

## Open Science & Interoperability

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* Data Management

* Data Standards, Ontologies, semantics

* Data brokering

* Machine actionable DMP

* Contribution to the network of RIs
A flavour of IFB/ELIXIR-FR in operations
in 2023 - Synergies with ELIXIR

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## Distributed infrastructure leveraging IFB's platforms forces

- www.france-bioinformatique.fr/en/compute-and-storage

- 9 platforms involved

- 27,000+ HT-cores, 135 To RAM, 14 Po storage

## Operation using complementary technologies

- 7 clusters (SLURM)

- 8 clouds (Openstack)

## Managed by a distributed team of experts from IFB's platforms (+ 17 persons)

- Sharing of experience, best practices, development

## Collaborations with other regional and national computing centers

<figure><img src="image_74.png" /><figcaption>Julien Seiler</figcaption></figure>

<figure><img src="image_75.png" /><figcaption>Gildas Le Corguillé</figcaption></figure>

<figure><img src="image_76.png" /><figcaption>Christophe Blanchet</figcaption></figure>

<figure><img src="image_77.png" /><figcaption>Olivier Collin
ELIXIR Tech Coordinator</figcaption></figure>

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<table><thead><tr><td>A few indicators</td><td>2021</td><td>2022</td></tr></thead><tbody><tr><td>Total number of active accounts</td><td>10 900</td><td>10 329</td></tr><tr><td>New accounts</td><td>2 884</td><td>4 272</td></tr></tbody></table>
## National activities

- Software development

- Sharing good practices for development

- Sharing recipes for deployment

- Deployment of environments for analysis

- E.g. [Usegalaxy.fr](http://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_79.png" /><figcaption>Vincent Lefort</figcaption></figure>

<figure><img src="image_80.png" /><figcaption>Hervé Ménager
ELIXIR Tools PF coord</figcaption></figure>

<figure><img src="image_81.png" /><figcaption>Anthony Bretaudieu
Elixir Galaxy community</figcaption></figure>

<figure><img src="image_82.png" /><figcaption>Olivier Sallou
Elixir Tech Coord</figcaption></figure>

## International/ELIXIR activities

- Service Delivery Plan (SDP) d'ELIXIR: 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

<figure><img src="image_83.png" /></figure>

- Involvement in the ELIXIR Galaxy community (Anthony Bretaudieu): contribution to
<figure><img src="image_84.png" /></figure>

<figure><img src="image_85.png" /></figure>

## National activities

- IFB web portal: www.france-bioinformatique.fr

- Catalogue of the French resources (in progress)

- Computing and storage resources, tools, knowledge bases

- Training material and events

- Expertises

- IFB platforms

- Support of user's projects by IFB's platforms: data analysis and data valorisation

<figure><img src="image_86.png" /><figcaption>Sylvain Milanesi</figcaption></figure>

<figure><img src="image_87.png" /><figcaption>Valérie Cognat</figcaption></figure>

<figure><img src="image_88.png" /><figcaption>Christine Gaspin</figcaption></figure>

<table><thead><tr><td>Project Support</td><td>2021</td><td>2022</td></tr></thead><tbody><tr><td>Total number</td><td>255</td><td>309</td></tr><tr><td>International</td><td>19</td><td>37</td></tr><tr><td>Private companies</td><td>13</td><td>13</td></tr></tbody></table>

## International activities (carried out by the Tools + the training Task Forces)

- Automatic synchronisation IFB's catalogue with ELIXIR's registries:

- Bio.tools: softwares

- TeSS: training material and events

- Improvement of searches by users, thematic collections of resources, cross referencing: EDAM, bioinformatic ontology co-supported by ELIXIR-FR and ELIXIR-Norway

<figure><img src="image_89.png" /></figure>
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<figure><img src="image_91.png" /></figure>

* ELIXIR coordination towards the development of a European Health Data space based on access to a federation of databases

* Beyond One Million Genomes (B1MG)

* Genome Data Infrastructure (GDI)

* EOSC4Cancer

## GDI main objectives :

- Support the EU 1+Million Genomes (1+MG) initiative (Digital Europe policy) ambition

- Establishing a federated, sustainable, interoperable and secure infrastructure based on open community standards.

- Each 20 1+MG signatory countries in GDI

* Will provide a node or Data Hub

* Each country manages their own data (e.g. regional hubs):

* Data hubs provide cross-border data analysis

## France:

- **October 2022**: signature by the French Ministry of Research of the 1+MG consortium agreement

- **By 2027**: set-up of an operational national node giving access to genomic and clinical data

* Leader: the French genomic medicine infrastructure (CAD)

* IFB/ELIXIR-FR leverage its services benefiting to the data node

<figure><img src="image_92.png" /></figure>

<figure><img src="image_93.png" /></figure>

European
Genomic Data
Infrastructure

<figure><img src="image_94.png" /></figure>
<figure><img src="image_95.png" /></figure>

## National activities

- Trainings provided under different formats to best address the diversity of training needs

- Schools for researchers in collaboration with research institutes: EBAII, ETBii 2023

- University Diploma in collaboration with Université Paris Diderot (2019-2021): DUBii

- Trainings for capacity building on FAIR DM and Reproducible analysis: FAIR data and FAIR bioinfo

- E-trainings (in progress)

- Common training resources

- IFB's training catalog synchronized with TeSS

- Management of the trainings and training materials: Moodle, IFB's GITlab

<table><thead><tr><td>Trainings</td><td>2021</td><td>2022</td></tr></thead><tbody><tr><td>Total number of training events</td><td>132</td><td>160</td></tr><tr><td>Total number of trainees</td><td>4 458</td><td>4 936</td></tr><tr><td>Satisfaction rate</td><td>95%</td><td>92%</td></tr></tbody></table>

## International activities

- Contribution to ELIXIR Training Platform and FAIR Training Focus Group transversal activities

- Training Coordinators Group

- Best practices, FAIRification of the training material: Manuel FAIR Training

- Improvement of the discoverability and interoperability of training resources registered in TeSS

- Train-the-Trainer

- "Integrative bioinformatics summer school" organized in collaboration with ELIXIR-CH (CAES d'Aussois, FR, sept 2023)

<figure><img src="image_96.png" /><figcaption>Hélène Chiapello
ELIXIR Training Coord.</figcaption></figure>

<figure><img src="image_97.png" /><figcaption>Olivier Sand
ELIXIR Training Coord.</figcaption></figure>
<figure><img src="image_98.png" /></figure>

<figure><img src="image_99.png" /></figure>

## National activities: development of tool supporting FAIR data management

* **FAIRchecker:** evaluation of the FAIRness of web resources

* Planning (in progress)

* Machine actionable transfert of information between DMPs and compute infrastructures

* Improvement of **DMP knowledge models** for projects and for the national infrastructures

* Interoperability between DMP softwares

* Data brokering (in progress)

<figure><img src="image_100.png" /><figcaption>Frédéric de Lamotte</figcaption></figure>

<figure><img src="image_101.png" /><figcaption>Marie-Dominique Devignes</figcaption></figure>

<figure><img src="image_102.png" /><figcaption>Alban Gaignard
Bioschemas steering committee</figcaption></figure>

<figure><img src="image_103.png" /><figcaption>Jean-François Dufayard</figcaption></figure>

<figure><img src="image_104.png" /><figcaption>Christophe Bruley</figcaption></figure>

## International activities: development of guidelines, standards and ontologies

* Participation to the emergence of the **ELIXIR Data Management community**: definition of its missions, contribution to the network of data stewards

* Contribution to some **Research Data Alliance** activities

* Standards: **Bioschemas**

<figure><img src="image_105.png" /></figure>

Liaison with the network of French Research Infrastructures for Life Sciences
<figure><img src="image_106.png" /></figure>

* 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

<figure><img src="image_107.png" /></figure>

RÉPUBLIQUE
FRANÇAISE

Liberté
Égalité
Fraternité

recherche.data.gouv.fr

## Recherche Data Gouv at a glance

<figure><img src="image_108.png" /></figure>

**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
<figure><img src="image_109.png" /></figure>

With a board of 3 deputy directors

<figure><img src="image_110.png" /><figcaption>Director</figcaption></figure>

Guy Perrière
ELIXIR-FR Head of Node

<figure><img src="image_111.png" /><figcaption>International
coordination</figcaption></figure>

Anne-Françoise Adam-Blondon
ELIXIR-FR Head of Node

<figure><img src="image_112.png" /><figcaption>Platform/service
coordination</figcaption></figure>

Morgane Thomas-Chollier

<figure><img src="image_113.png" /><figcaption>Scientific
coordination</figcaption></figure>

Jacques van Helden
Thank you for your attention!

<figure><img src="image_114.png" /></figure>

https://www.france-bioinformatique.fr/en/elixir-fr/

Contact us: angela.saenz@france-bioinformatique.fr

Follow us:

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@IFB_Bioinfo @ELIXIREurope

<figure><img src="image_116.png" /></figure>

institut-français-de-bioinformatique/
# ELIXIR director recruitment open for applications

Deadline for applications is 9:00 BST on Monday 7 August 2023

https://elixir-europe.org/news/director-recruitment-open

<figure><img src="image_117.png" /></figure>