A primer on cryo-EM data processing using cryoSPARC on BerzeLiUs
April 15, 2024 @ 08:00 – April 16, 2024 @ 17:00 CEST
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 and information
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: Tim Schulte , Piotr Draczkowski
Course fee
The course is free of charge.
Course content
What is this 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
Who should apply?
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.
Learning outcomes
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
Entry requirements
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 (supr.naiss.se)
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.
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