News | ShareFAIR

ShareFAIR and Neurovasc Days

Wed, 14 Oct 2026 09:00:00 +0000

Overview

As ShareFAIR, Neurovasc is a project funded by the French National Research Agency (ANR) as part of the PEPR Santé Numérique program, within the France 2030 investment plan.

The ShareFAIR and Neurovasc days constitute a two-day scientific gathering bringing together the project partners and the broader research community around a shared objective: advancing the reproducibility of neuro-vascular research.

See ShareFAIR. and Neurovasc DAYS

Journal Club (JC#13)

Wed, 09 Sep 2026 13:00:00 +0000

Overview

Speaker : Jaffar GURA (LAMSADE)

Talk : “From Execution Traces to Queryable Provenance in Nextflow Workflows”

Journal Club (JC#12)

Wed, 11 Mar 2026 13:00:00 +0000

Overview

Speaker : Marie SCHMIT (Institut Pasteur)

Goal : Give some feedbacks and results about Young Researchers Days organized in Nantes to bring together the work of ShareFAIR’s young researchers.

Journal Club (JC#11)

Wed, 28 Jan 2026 13:00:00 +0000

Overview

Speaker : Alberto Marifoglia (University of Bologna)

Article : “Clinical Data Goes MEDS? Let’s OWL make sense of it](https://arxiv.org/abs/2601.04164)", Alberto Marfoglia, Jong Ho Jhee, Adrien Coulet. SWAT4HCLS 2026 conference.

Journal Club (JC#10)

Wed, 03 Dec 2025 13:00:00 +0000

Overview

Speaker : Camille Maumet(IRISA)

Article : “CODE beyond FAIR: a roadmap for reusable research software”, Roberto Di Cosmo, Sabrina Granger, Konrad Hinsen, Nicolas Jullien, Daniel Le Berre, Violaine Louvet, Camille Maumet, Clémentine Maurice, Raphaël Monat, Nicolas P. Rougier. Scientific Data volume 13.

shareFAIR at the Annual PEPR SantéNum Days

Wed, 15 Oct 2025 09:00:00 +0000

Overview

ShareFAIR was at the Annual PEPR Days organized at Lille.

Journal Club (JC#9)

Wed, 10 Sep 2025 13:00:00 +0000

Overview

Speaker : Romain Michelucci (INRIA)

Article : Predicting clinical pathways of traumatic brain injuries (TBIs). Eili, M.Y., Rezaeenour, J. & Roozbahani, M.H. Process mining. npj Digit. Med. 8, 112 (2025).

Journal Club (JC#8)

Thu, 10 Jul 2025 13:00:00 +0000

Overview

Speaker : Clémence Sebe (Université Paris-Saclay)

Article : Extracting Information in a Low-Resource Setting - Case Study on Bioinformatics Workflows](https://arxiv.org/abs/2411.19295]). Clémence Sebe, Sarah Cohen-Boulakia, Olivier Ferret, Aurélie Névéol. IDA (Advances in Intelligent Data Analysis). 2025.

shareFAIR at JOBIM 25

Tue, 08 Jul 2025 09:30:00 +0000

Overview

Session about Workflows, Reproducibility, and Open Science.
- Assessing bioinformatics software annotations : bio.tools case-study by Ulysse Le Clanche, Sarah Cohen Boulakia, Yann Le Cunff, Alban Gaignard and Olivier Dameron
Session about Statistics, Machine Learning, and AI for Biology and Health
- Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives Hervé Ménager, Damien Mornico, Pascal Campagne, Elodie Chapeaublanc, Claudia Chica, Julien Guglielmini, Gaël Millot, Bertrand Néron, Natalia Pietrosemoli, Marie-Agnès Dillies and Laurent Essioux
Poster session.
- Bioinformatics Workflows - Representation and Query" by Mouna El Garb.

Working meeting - WP1 and WP2

Thu, 12 Jun 2025 09:00:00 +0000

Overview

Working meeting for WP1 and WP2 members.

Poster au 7e Symposium du GdR MaDICS (Toulouse)

Tue, 27 May 2025 17:30:00 +0000

Overview

Présentation du Poster “Bioinformatics Workflows - Representation and Query” par Mouna El Garb.

Journal Club (JC#7)

Wed, 07 May 2025 13:00:00 +0000

Overview

Speaker : Mouna El Garb (UCBL 1)

Article : “SPARQL Rewritingù - Towards Desired Results” (Xun Jian et al.)

Journal Club (JC#6)

Wed, 12 Mar 2025 13:00:00 +0000

Overview

Speaker : Ulysse Le Clanche (IRISA)

Articles :

Annual full meeting

Thu, 28 Nov 2024 09:00:00 +0000

Overview

2-days Annual full meeting.

Journal Club (JC#5)

Wed, 20 Nov 2024 13:00:00 +0000

Overview

Speaker : Marie Schmit (Institut Pasteur)

Article : Recording provenance of workflow runs with RO-Crate" (Simone Leo et al.)

Journal Club (JC#4)

Wed, 11 Sep 2024 13:00:00 +0000

Overview

Speaker : Noémie Bossut (LAMSADE)

Article : Chapman A. et al.: Supporting Better Insights of Data Science Pipelines with Fine-grained Provenance.

Link : https://arxiv.org/pdf/2310.18079

Paper accepted at eScience 2024

Tue, 27 Aug 2024 17:30:00 +0000

Overview

Paper accepted at eScience 2024. Our paper on Reproducibility in Named Entity Recognition: A Case Study Analysis got accepted at eScience 2024 (Carlos Cuevas Villarmin, Sarah Cohen-Boulakia, Nona Naderi – U. Paris-Saclay ).

Paper accepted at NAR Genomics and Bioinformatics

Tue, 27 Aug 2024 17:30:00 +0000

Overview

Paper accepted at NAR Genomics and Bioinformatics Our paper on BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization got accepted at NAR Genomics and Bioinformatics (George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen-Boulakia - U. Paris-Saclay & Institut Pasteur). It has been selected as part of the Editor’s choice articles.

Poster at JEP TALN RECITAL 2024 (Toulouse)

Fri, 12 Jul 2024 17:30:00 +0000

Overview

Poster “Extraction d’entités nommées décrivant des chaînes de traitement bioinformatiques dans des articles scientiﬁques en anglais” by Clémence Sebe at JEP TALN RECITAL 2024 (Toulouse).

JEP : Journées d’Études sur la Parole (35e édition),
TALM : Conférence sur le Traitement Automatique des Langues Naturelles (31e édition)
RECITAL : Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (26e édition).

Journal Club (JC#3)

Thu, 04 Jul 2024 13:00:00 +0000

Overview

Speaker : Melvin Atay (INRIA Rennes)

Article : Botvinik-Nezer R, Holzmeister F, Camerer CF, Dreber A, Huber J, Johannesson M, Kirchler M, Iwanir R, Mumford JA, Adcock RA, Avesani P. Variability in the analysis of a single neuroimaging dataset by many teams. Nature. 2020 Jun 4;582(7810):84-8.

Link : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771346/pdf/nihms-1649206.pdf

Poster at ACM Conference on Reproducibility and Replicability REP 2024 (Rennes)

Wed, 19 Jun 2024 17:30:00 +0000

Overview

Poster “BioFlow-Insight: Leveraging Graph representations to Facilitate the Reuse of Bioinformatics Workflows” presented by George Marchment at ACM Conference on Reproducibility and Replicability REP 2024 (Rennes)

Poster au 6e Symposium du GdR MaDICS (Blois)

Wed, 29 May 2024 17:30:00 +0000

Overview

Présentation du Poster “From Headache to Hight-Five! We are trying to make reproductibility in Bioinformatics easier” par Noémie Bossut.

Journal Club (JC#2)

Wed, 22 May 2024 13:00:00 +0000

Overview

Speaker : Clémence Sebe (Université Paris-Saclay)

Article : Ahmed Halioui, Petko Valtchev, Abdoulaye Banire Diallo: Bioinformatic Workflow Extraction from Scientific Texts based on Word Sense Disambiguation IEEE/ACM Trans Comput Biol Bioinform. 2018 Jun 14. doi: 10.1109/TCBB.2018.2847336.

Link : https://partage.liris.cnrs.fr/index.php/s/8DfNaAHHTNz9cNA

Journal Club (JC#1)

Wed, 03 Apr 2024 13:00:00 +0000

Overview

Speaker : George Marchment

Article : Patrick D. Schloss, Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research in mBio 9:10.1128/mbio.00525-18.

Link : https://partage.liris.cnrs.fr/index.php/s/odgk3oiPjo2CpM7

Repro-Hakathon

Sun, 18 Feb 2024 09:00:00 +0000

Overview

Le repro-hackathon a eu lieu le 18/03/2024 à l’Institut Pasteur, de 9h 30 à 17h.

Les détails sur les objectifs est ici : https://partage.liris.cnrs.fr/index.php/f/203062758 (Accès restreint)

Le compte rendu final est ici : https://partage.liris.cnrs.fr/index.php/f/203058381 (Accès restreint)

Kick-off meeting

Mon, 16 Oct 2023 00:00:00 +0000

Overview

Meeting planning (coming soon)

First remote meeting

Mon, 18 Sep 2023 00:00:00 +0000

Overview

Au programme de cette réunion :

Tour de table des partenaires
Point sur les recrutements année 1 (Pasteur, PSL, Rennes-irisa, Lyon) - stratégie en cas de non recrutement (stages…)
Organisation du kickoff en présentiel sur Paris
Modalités d’organisation des échanges
Hackathon - journées doctorants
Point sur le site web - facon de communiquer
Point admin - ANR
Questions diverses

Project Web Site

Wed, 21 Jun 2023 00:00:00 +0000

Overview

Our Web site is on line.