SIB Community Days meeting at ECCB2026 - 2026, September 4th (Friday)
You can register to the event through this Google Form. Registration is free, costs will be covered by ELIXIR (morning break, lunch, afternoon break for ELIXIR session) and by scFAIR (afternoon break for scFAIR session).
In recent years, single-cell and spatial transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems.
This workshop aims to bring together the ELIXIR Single-Cell Omics Community and the scFAIR international consortium led by SIB resources, to align ongoing efforts, advance FAIR standards, and strengthen international collaboration around best practices and trainings in single-cell and spatial omics.
In the morning will take place a shared session between the ELIXIR Single-Cell Omics Community and scFAIR, focusing on efforts from the ELIXIR community, and from the individual resources part of scFAIR, in order to discuss synergies and coordination. Two parallel sessions will take place in the afternoon: for the ELIXIR community, a session about training, European biohackathon, spatial technologies and perturbation modelling; for scFAIR, a session about the data standards and portal proposed by the consortium, analysis and tool reproducibility.
The event will provide updates on ongoing activities and collaborative projects, share progress from ELIXIR Nodes and initiatives, and discuss future priorities in single-cell and spatial omics. It will also include presentations, open discussions, and networking opportunities aimed at strengthening collaborations, welcoming new members, and fostering engagement with researchers and trainers interested in advancing single-cell and spatial omics within and beyond ELIXIR. More information about the community: https://elixir-europe.org/communities/single-cell-omics; https://www.singlecellomics.org/
The Deplancke and Robinson-Rechavi/Bastian SIB groups have together launched in 2023 the scFAIR consortium, for FAIRification of single-cell metadata, data exchange formats and platforms, reproducible worflows for single-cell analyses. The consortium includes members from other important international resources, such as CELLxGENE (funded by the Chan Zuckerber Initiative), the EBI Single Cell Expression Atlas, or the Alliance of Genome Resources. The consortium meets once a month remotely to discuss, e.g., metadata schema, ontologies to use, shared annotation efforts of major datasets. This event is a perfect opportunity to gather participants face-to-face, to improve the consortium recommendations, underlying tools, and collaboration between international single-cell resources.
2026.09.04 from 09:00 AM to 04:00 PM (Swiss time, CEST / GMT+2).
CICG congress venue in Geneva. Virtual attendance accepted.
- 09:30 – 09:40: Introduction - General info
- 09:40 – 09:50: Presentation of the ELIXIR Single-Cell Omics community and connection to data standardization
- 09:50 – 10:00: Presentation of scFAIR and connection to data standardization
- 10:00 – 10:30: Single-cell data and metadata standard for dataset deposition over multiple international resources session 1
- ☕10:30 – 11:00: Coffee break
- 11:00 – 11:25: Single-cell data and metadata standard for dataset deposition over multiple international resources session 2
- 11:25 – 11:40: Open discussion on metadata and data standardization
- 11:40 – 12:10: ELIXIR Interoperability Platform FAIRification Framework
- 12:10 – 12:30: Data and metadata curation best practices and coordination
- 🍽️12:30 – 13:30: Lunch break
- 13:30 – 13:35: welcome
- 13:35 - 14:20: ELIXIR SCO Training, EU Biohackathons, Inter-community collaborations
- 14:20 – 15:10: Spatial2Galaxy: Leveraging ELIXIR ecosystem for spatial transcriptomics
- ☕15:10 – 15:30: Coffee break
- 15:30 – 16:20: Unveiling causality in single-cell omics: Trajectories and in silico perturbations in non-model organisms
- 16:20 – 16:30: Wrap-up and next steps
- 13:30 – 14:00: presentation of scFAIR outputs
- scFAIR portal connecting individual resources
- how to connect your resource to scFAIR
- 14:00 – 14:30: Open discussion about analysis reproducibility issues and presentation of conclusions from previous scFAIR workshops
- 14:30 – 15:00: ASAP tool for reproducible analyses, and compatibility with scFAIR
- ☕15:00 – 15:30: Coffee break
- 15:30 – 16:00: Bioconductor packages for single-cell analyses
- 16:00 – 16:30: Open discussion about single-cell analysis workflows across tool ecosystems
- Frédéric Bastian, Associate Director Evolutionary Bioinformatics, SIB Swiss Institute of Bioinformatics, University of Lausanne, scFAIR, Bgee, Lausanne, 🇨🇭 Switzerland
- Wen Chen, highthroughput data curation team lead, California Institute of Technology, Alliance of Genome Resources, Pasadena, 🇺🇸 USA
- Christina Ernst, Functional Genomics Team Leader, EMBL-EBI, EBI Single Cell Expression Atlas, Cambridge, 🇬🇧 United Kingdom
- Vincent Gardeux, Senior Scientist, EPFL, scFAIR, ASAP, Lausanne, 🇨🇭 Switzerland
- Georgios Gavriilidis, Senior Postdoctoral Fellow, Berlin Institute of Health, ELIXIR Germany, SCO community lead, Berlin, 🇩🇪 Germany
- Jason Hilton, Senior Research Engineer, Standford University, CELLxGENE, Stanford, 🇺🇸 USA
- Garth Ilsley, Ensembl Regulation Project Leader, EMBL-EBI, FAANG, Cambridge, 🇬🇧 United Kingdom
- Sabrina Jagot, Post-doctoral fellow, Institut NeuroMyoGene - MéLiS, CNRS UMR5284 UCBL, 🇫🇷 IFB/ELIXIR-France.
- Eija Korpelainen, Training Coordinator, CSC - IT Center for Science, ELIXIR Finland, SCO community, Espoo, 🇫🇮 Finland
- Kevin Rue-Albrecht, Software Sustainability Institute Fellow, University of Oxford, Oxford, 🇬🇧 United Kingdom