User workshop for cryo-EM data processing on Berzelius.
Title: User workshop for cryo-EM data processing on Berzelius.
DNr: Berzelius-2024-20
Project Type: LiU Berzelius
Principal Investigator: Tim Schulte <>
Affiliation: Stockholms universitet
Duration: 2024-02-27 – 2024-09-01
Classification: 10601


The Cryo-EM National Facility, the Bioinformatics Platform (NBIS) and the PReSTO Team herein apply for resources to organize a user workshop. The main aims of the proposed workshop are to train structural biologists to perform cryo-EM data processing using primarily the cryoSPARC software on Berzelius, taking advantage of the Presto installation. The workshop will be offered initially to a group of 15 users. In a one-day introduction we the organizer demonstrate: - how to access Berzelius - how to use Presto, and in particular cryoSPARC - how to transfer data between the local and remote machines After the one-day workshop, the users will have the opportunity to run tests and familiarize themselves for a period of one week. During that time the users can ask for support to the course organizers. At the end of the week, there will be a feedback round. We provide a dataset ( comprising 1338 micrographs with a total size of 320 GB. This is the standard dataset that has been used as Tutorial dataset for Relion. We have already processed this dataset on Berzelius using cryoSPARC. We apply for 6 months so that we can offer the course to additional users in a second round if the demand is higher. We will also create a workshop-related webpage providing additional information for the users shortly.