Workshop for Single-Cell Omics data analysis trainers

21-22 March 2023, Geneva, Switzerland

Registration: 20 Jan - 12 March 2023


GOBLET1 and ELIXIR2 co-organized a workshop in 2021 to bring together single-cell RNA-seq data analysis trainers to share experiences, challenges and best practices. The newly established ELIXIR Single-Cell Omics (SCO) Community together with GOBLET would like to pursue this effort and equip SCO trainers with the best FAIR and open research tools, materials and practices to be able to teach and upskill scientists in SCO data analysis and standards.

The aim of this workshop is to get SCO data analysis trainers, members of the community and beyond together, for exchanging ideas about best practices, methods and datasets. A survey will be run before the workshop to serve as a basis for discussion. The workshop will be divided into sessions, each representing a topic of interest. Participants will have the opportunity to discuss the training aspects of the management of different types of SCO data, the diversity of analysis tools and methods, as well as computational environments, datasets and standards currently used. The workshop discussions will also aim to address what works well and what is challenging when teaching, what is actually missing in SCO training, and how it could be expanded and improved in the near future. This workshop will also be the occasion to bring on board any ELIXIR Node members interested in developing and offering SCO training. Following this workshop, on 22-26 May 2023, a pedagogical training will also be offered in the form of the ELIXIR Train-the-Trainer (TtT) course online.

This workshop abides by the ELIXIR Code of Conduct. Attendees are required to abide by the same code. The ELIXIR Implementation Study SCONE will cover coffee breaks and lunches. GOBLET will fund the dinner. Each participant will take care of his/her own travel expenses with his/her own SCONE budget, if any.


Tue, 21 Mar 2023

12:00 - 13:30 Arrival and lunch
13:20 Zoom opens for virtual attendees
13:30 - 13:45 Introduction, aims and objectives
13:45 - 15:15 Session #1: Single cell Omics
15:15 - 15:45 Coffee break
15:45 - 17:15 Session #2: Spatial Omics
17:15 - 17:45 Wrap up 1st day
19:00 - 19:00 Joint dinner

Wed, 22 Mar 2023

09:00 - 10:30 Session #3: Multi-omics
10:30 - 11:00 Coffee break
11:00 - 12:30 Session #4: Teaching Practices3
12:30 Wrap up and closing remarks
13:00 - 14:00 Lunch and departure


The workshop will take place in Geneva, in the Centre Médical Universitaire (CMU), room B04.1522a, in the B building, 4th floor. More details and maps on how to access the CMU and the B building are in this link.

For those joining online, please use the following zoom link.

Travel information

The Geneva airport (GVA) has many direct flights from European cities. How to reach the CMU building:

  • From the airport, take bus #5 and get down at Genève Hôpital (35’ ride). Otherwise, take the train to the Geneva central station Cornavin (6’, any train from the Airport stops in the Geneva central train station).
  • From the Geneva Central Train Station Cornavin, take bus #5 or bus #1 and get down at Genève Hôpital.


Here is a non exhaustive list of hotels where to stay in Geneva that are close to the CMU:

  • Hotel Adriatica (The closest from CMU (2’ walk))
  • Hotel le Prince (env. 10’ walking from CMU)
  • Hotel Comédie (10’ walking from CMU )
  • Starling Hotel Residence (env. 15’ walking from CMU)

Contributing Institutions


  1. GOBLET is the Global Organization for Bioinformatics Learning Education and Training 

  2. ELIXIR is an intergovernmental organization that brings together life science resources from across Europe. 

  3. Teaching styles, format, pedagogical techniques and use of environment and containers