SUPR
Establishing Relion/cryolo installation on Dardel to support Swedish cryo-EM community
Dnr:

NAISS 2024/23-730

Type:

NAISS Small Storage

Principal Investigator:

Tim Schulte

Affiliation:

Stockholms universitet

Start Date:

2024-12-30

End Date:

2026-01-01

Primary Classification:

10601: Structural Biology

Allocation

Abstract

As part of the National Bioinformatics Infrastructure Sweden (NBIS), the national cryo-EM facility (https://www.scilifelab.se/units/cryo-em/) and the Presto enablers team (https://www.nsc.liu.se/support/presto/) we provide support to the Swedish cryo-EM research community. This support is enabled by funding from the Knut and Alice Wallenberg Foundation, and is part of the SciLifeLab & Wallenberg National Program for Data-Driven Life Science. Many users do not have their own or access to GPU workstations or clusters. Previously, we used the AI-focused BerzeLiUs cluster, but unfortunately user projects have recently been denied due to changes in prioritization. To provide a basic cryo-EM processing solution to the Swedish cryo-EM community, we herein apply for a small compute project to implement and test a Relion/cryolo pipeline on Dardel. In contrast to most other software solutions for cryo-EM data processing, Relion can be compiled on AMD GPUs (https://relion.readthedocs.io/en/latest/Installation.html). To provide an advanced solution for particle picking, we also aim to install the particle-picker Cryolo that can be compiled in CPU-only mode. Alternatively, we could attempt to port Cryolo for execution on AMD GPUs. Both Relion and cryolo may be implemented within the existing Presto software stack, that has already been successfully installed on Cosmos, Tetralith and BerzeLiUs. After successful installation and testing, we would invite users to process their data under our supervision. Depending on the community requirements we could expand our solution to a medium compute resource. Furthermore we could prepare a workshop and tutorial as we have done previously for the cryoSPARC workflow on BerzeLiUs (https://www.nsc.liu.se/support/presto/BerzeLiUs_CryoSparc_workshop-20240415_latest.pdf).