SIB Community Days @ ECCB2026

Single-cell and spatial data FAIRification, community standards and training

SIB Community Days meeting at ECCB2026 - 2026, September 4th (Friday)

Registration

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).

Summary

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.

ELIXIR Single-Cell Omics Community

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/

scFAIR: FAIRification of single-cell data

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.

Date

2026.09.04 from 09:00 AM to 04:00 PM (Swiss time, CEST / GMT+2).

Location

CICG congress venue in Geneva. Virtual attendance accepted.

Programme

Morning session

• 09:00 – 09:10: Introduction - General info

• 09:10 – 09:20: Presentation of the ELIXIR Single-Cell Omics community and connection to data standardization

• 09:20 – 09:30: Presentation of scFAIR and connection to data standardization

• 09:30 – 10:20: Single-cell data and metadata standard for dataset deposition over multiple international resources, including:

  • CELLxGENE
  • The EBI Single Cell Expression Atlas
  • The Alliance of Genome Resources
  • FAANG
  • Bgee

• 10:20 – 10:40: Open discussion on metadata and data standardization

• ☕10:40 – 11:00: Coffee break

• 11:00 – 11:30: ELIXIR Interoperability Platform FAIRification Framework

• 11:30 – 12:00: Data and metadata curation best practices and coordination

• 🍽️12:00 – 13:00: Lunch break

ELIXIR Single Cell Omics (SCO) Community afternoon session

• 13:00 – 13:05: welcome
• 13:05 – 13:15: SPODAverse: Spatial transcriptomic training
• 13:15 – 14:00: ELIXIR SCO in European Biohackathons
• 14:00 – 14:10: short break
• 14:10 – 15:00: Single-cell and spatial technologies in Biodiversity samples
• 15:00 – 15:10: short break
• 15:10 – 15:55: Perturbation modelling and community considerations

scFAIR afternoon session

• 13:00 – 13:30: presentation of some of scFAIR outputs:
  • metadata schema
  • scFAIR portal connecting individual resources
  • how to connect your resource to scFAIR
• 13:30 – 14:00: Open discussion about analysis reproducibility issues and presentation of conclusions from previous scFAIR workshops
• 14:00 – 14:20: ASAP tool for reproducible analyses, and compatibility with scFAIR
• ☕14:20 – 14:40: break
• 14:40 – 15:10: Bioconductor packages for single-cell analyses
• 15:10 – 15:55: Open discussion about single-cell analysis workflows across tool ecosystems

Staff

Lecturers:

• 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
• 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