CryoSPARC

CryoSPARC combines powerful innovations in 3D reconstruction algorithms with specially designed software to provide a streamlined end-to-end single particle cryo-EM workflow. Rapidly solve high-resolution structures of biologically important targets, with advanced tools for membrane proteins, heterogeneous samples, and flexible molecules. Process 3D refinements in minutes on GPU.

CryoSPARC is not installed directly on the FRCE cluster but each instance, which is dedicated to a specific lab, is hosted on a Linux VM. The instance is fully self-contained and has privileges to submit jobs to the FRCE cluster. Jobs will be submitted using a service account and file access allowed by group membership and permissions. The process to have a CryoSPARC instance created includes:

  • Request an AD service account with POSIX attributes enabled. The normal pattern for the account name is ncif-lab-cryosparc or ncif-lab-srv.
  • Either in the same request or as a separate request, have an AD group created with POSIX attributes enabled. The members of the group should be any users who own files to be processed as well as the service account. If an AD group already exists with the right users, just have the service account added to the existing group.
  • Determine the file share(s) where the data resides. The permissions on this share and all files under it will need to be changed so that they are owned by the group and the group has read/write permissions. The FRCE admins can make this change.
  • Open a Service Now ticket requesting a Linux VM. Request a custom Virtual Server size:
    • 8 CPUs
    • 24GB memory
    • requirements are justified by the CryoSPARC application needs
    • request a local disk, sized 80GB and mounted as /var/lib/mongo
    • storage requirements
      • fssrgd-qmlo05p:/shared-home mounted as /home
      • fssrgd-qmlo05p:/oel-apps mounted as /mnt/nasapps
      • the share(s) holding the data to be processed should also be mounted
    • no requirements for user access or firewall rules are needed
  • The AppHosting team will install and configure CryoSPARC and will create an Administrator account for one of the lab members.