Date: 15 - 16 April 2024

Timezone: Stockholm

National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of cryo-EM data processing using national supercomputing resources.

Important Dates

Application opens: 2024-03-18
Application closes: 2024-04-07
Confirmation to accepted students: 2024-04-08

Course Leader and teachers:

Tim Schulte , Piotr Draczkowski

In case you miss information on any of the above dates, please contact one of the course leaders.

Course fee

The course is free of charge.

What is this course about?

How to use Berzelius compute cluster for cryo-EM data processing. We will process the beta- galactosidase dataset, known from the Relion tutorials, but applying cryoSPARC on BerzeLiUs, as implemented by the PReSTO team.

The main purpose of this training is to learn how to:

● access and use BerzeLiUs
● apply Presto, especially cryoSPARC on BerzeLiUs to process cryo-EM data

Contact: In case you miss information on any of the above dates, please contact: Tim Schulte ( or Piotr Draczkowski

Keywords: CryoEM, BerzeLiUs, data processing

Country: Sweden


Anyone interested in processing cryo-EM data using national supercomputing resources, especially BerzeLiUs cluster. This is a primer for data processing on Berzelius, not an introduction to cryo-EM. We expect applicants to be familiar with the general concepts of cryo-EM and data processing. Participants need to have a computer to access Berzelius remotely.

The following is a list of skills required for being able to follow the course and complete the exercises:

● Basic knowledge of Linux
● Ability to bring your own laptop
● Set up an account in NAISS SUPR (

Desirable, but not essential, skills increasing the output of the course, include:

● Experience in processing cryo-EM data using any of the available software packages

Due to limited space the course can accommodate a maximum of 15 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.

Learning objectives:

Upon completion of this course, you will be able to:’

● apply for the allocation of computational resources on BerzeLiUs cluster
● set up and start your cryoSPARC instance on BerzeLiUs
● submit jobs to the cluster using the predefined submission lines
● manage the jobs
● process cryo-EM data on BezleLIUs using a standard data processing pipeline in CryoSPARC

Organizer: National Bioinformatics Infrastructure Sweden, NBIS

Event types:

  • Workshops and courses

Activity log